EricChu:LabNotesMDA/2015-1-7: Difference between revisions
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* These 9 single cell libraries were sequenced in HL175. GM stands for GM20431. | * These 9 single cell libraries were sequenced in HL175. GM stands for GM20431. | ||
# GM Dev9 Oct10 (Index 9-16). Asked for 10 million reads. Sequenced in Lane 1. | # GM Dev9 Oct10 (Index 9-16). Asked for 10 million reads. Sequenced in Lane 1. | ||
# PGP1 | # PGP1 Dev8 Oct6 (Index 17-24). Asked for 10 million reads. Sequenced in Lane 1. | ||
# GM Dev9.2 Oct23 (Index 25-32). Asked for 20 million reads. Sequenced in Lane 1. GM Dev9.2 Oct23 (Index 9-24). Asked for 40 million reads. Sequenced in Lane 2. | # GM Dev9.2 Oct23 (Index 25-32). Asked for 20 million reads. Sequenced in Lane 1. GM Dev9.2 Oct23 (Index 9-24). Asked for 40 million reads. Sequenced in Lane 2. | ||
# GM Dev9.2 Nov4 (Index9-32). Asked for 40 million reads. Sequenced in Lane3. | # GM Dev9.2 Nov4 (Index9-32). Asked for 40 million reads. Sequenced in Lane3. | ||
Line 18: | Line 18: | ||
* For example, in /data_Syn_15T/HL175/GMDev9Oct10 | * For example, in /data_Syn_15T/HL175/GMDev9Oct10 | ||
* command: nohup ../../batch_bwa_fastq2bam.pl hg19 > EC_GMDev9Oct10_BWA_batch_fastq2bam.log & | * command: nohup ../../batch_bwa_fastq2bam.pl hg19 > EC_GMDev9Oct10_BWA_batch_fastq2bam.log & | ||
* ../../get_covstats.pl > EC_GMDev9Oct10_BWA_covstat.txt & | |||
* /home/kunzhang/softwares/samtools-0.1.19/samtools view -o s_1_1_Indx32_unique.sam s_1_1_Indx32_unique.bam | |||
==Summaries of Sequencing Results== | |||
===PGP1 Dev8 Oct6: 400mM ALS 8min pump, NS 0min=== | |||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''bam_file''' | |||
| align="center" style="background:#f0f0f0;"|'''sample''' | |||
| align="center" style="background:#f0f0f0;"|'''Raw_Reads''' | |||
| align="center" style="background:#f0f0f0;"|'''MappingRate''' | |||
| align="center" style="background:#f0f0f0;"|'''MappableReads''' | |||
| align="center" style="background:#f0f0f0;"|'''ClonalRate''' | |||
| align="center" style="background:#f0f0f0;"|'''Unique''' | |||
| align="center" style="background:#f0f0f0;"|''' 1+''' | |||
| align="center" style="background:#f0f0f0;"|''' 1''' | |||
| align="center" style="background:#f0f0f0;"|''' 2''' | |||
| align="center" style="background:#f0f0f0;"|''' 3''' | |||
| align="center" style="background:#f0f0f0;"|''' 4+''' | |||
| align="center" style="background:#f0f0f0;"|'''contig''' | |||
| align="center" style="background:#f0f0f0;"|'''Mito %''' | |||
|- | |||
| s_1_1_Indx17_sorted.bam||9|| 217,653 ||81.27%|| 176,890 ||2.58%|| 172,326 || 7,047,215 || 5,906,698 || 808,250 || 193,693 || 123,844 ||50||0.72% | |||
|- | |||
| s_1_1_Indx18_sorted.bam||10|| 371,006 ||82.14%|| 304,742 ||2.77%|| 296,301 || 11,816,162 || 9,631,704 || 1,525,191 || 390,584 || 254,448 ||113||0.35% | |||
|- | |||
| s_1_1_Indx19_sorted.bam||11|| 230,506 ||82.31%|| 189,741 ||2.49%|| 185,016 || 7,609,472 || 6,384,424 || 869,077 || 208,944 || 133,657 ||41||0.45% | |||
|- | |||
| s_1_1_Indx20_sorted.bam||12|| 220,926 ||82.00%|| 181,160 ||2.89%|| 175,924 || 6,900,560 || 5,585,808 || 889,076 || 239,564 || 171,647 ||77||0.64% | |||
|- | |||
| s_1_1_Indx21_sorted.bam||13|| 241,578 ||82.45%|| 199,187 ||2.67%|| 193,869 || 7,686,007 || 6,217,752 || 1,019,302 || 270,080 || 164,393 ||80||0.64% | |||
|- | |||
| s_1_1_Indx22_sorted.bam||14|| 290,676 ||83.34%|| 242,246 ||3.18%|| 234,543 || 8,994,661 || 7,116,771 || 1,254,370 || 357,017 || 250,797 ||123||0.81% | |||
|- | |||
| s_1_1_Indx23_sorted.bam||15|| 358,363 ||82.65%|| 296,176 ||3.67%|| 285,306 || 10,525,718 || 8,192,296 || 1,461,782 || 457,003 || 398,991 ||172||0.65% | |||
|- | |||
| s_1_1_Indx24_sorted.bam||16|| 423,102 ||84.62%|| 358,023 ||4.23%|| 342,879 || 11,668,130 || 8,449,278 || 1,926,598 || 656,706 || 619,634 ||282||0.65% | |||
|- | |||
| |||| 2,353,810 |||| 1,948,165 |||| 1,886,164 ||||||||||||938|| | |||
|- | |||
| | |||
|} | |||
===GM Dev9 Oct10: 400mM ALS 5min pump, NS 2min=== | |||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''bam_file''' | |||
| align="center" style="background:#f0f0f0;"|'''sample''' | |||
| align="center" style="background:#f0f0f0;"|'''Raw_Reads''' | |||
| align="center" style="background:#f0f0f0;"|'''MappingRate''' | |||
| align="center" style="background:#f0f0f0;"|'''MappableReads''' | |||
| align="center" style="background:#f0f0f0;"|'''ClonalRate''' | |||
| align="center" style="background:#f0f0f0;"|'''Unique''' | |||
| align="center" style="background:#f0f0f0;"|'''1+''' | |||
| align="center" style="background:#f0f0f0;"|'''1''' | |||
| align="center" style="background:#f0f0f0;"|'''2''' | |||
| align="center" style="background:#f0f0f0;"|'''3''' | |||
| align="center" style="background:#f0f0f0;"|'''4+''' | |||
| align="center" style="background:#f0f0f0;"|'''contig''' | |||
| align="center" style="background:#f0f0f0;"|'''mito %''' | |||
|- | |||
| s_1_1_Indx09_sorted.bam||1|| 1,185,461 ||92.15%|| 1,092,352 ||9.88%|| 984,428 ||25566539||16430816||4066655||1834422||3218141||776||0.65% | |||
|- | |||
| s_1_1_Indx10_sorted.bam||2|| 878,051 ||92.41%|| 811,404 ||4.22%|| 777,163 ||28763373||22943333||3614129||1068962||1120592||416||0.35% | |||
|- | |||
| s_1_1_Indx11_sorted.bam||3|| 599,446 ||92.85%|| 556,598 ||3.51%|| 537,061 ||20323989||16273884||2530109||786467||717353||332||0.37% | |||
|- | |||
| s_1_1_Indx12_sorted.bam||4|| 964,470 ||92.25%|| 889,682 ||10.86%|| 793,063 ||20340153||13258220||3172788||1393513||2499128||641||0.87% | |||
|- | |||
| s_1_1_Indx13_sorted.bam||5|| 1,080,380 ||92.43%|| 998,608 ||7.60%|| 922,714 ||28568106||20506465||4219661||1610385||2215033||771||1.21% | |||
|- | |||
| s_1_1_Indx14_sorted.bam||6|| 1,371,077 ||91.62%|| 1,256,193 ||15.20%|| 1,065,252 ||22584672||13334265||3538903||1720474||3974593||821||0.27% | |||
|- | |||
| s_1_1_Indx15_sorted.bam||7|| 588,560 ||91.64%|| 539,373 ||6.66%|| 503,451 ||15656188||11296394||2257865||866065||1219354||420||0.82% | |||
|- | |||
| s_1_1_Indx16_sorted.bam||8|| 1,545,679 ||91.87%|| 1,419,958 ||18.28%|| 1,160,390 ||18788455||8802440||3049596||1746533||5173393||828||0.43% | |||
|- | |||
| |||| 8,213,124 |||| 7,564,168 |||| 6,743,520 ||||||||||||5005|| | |||
|- | |||
| | |||
|} | |||
===GM Dev9.2 Oct23: 400mM ALS 2min pump, NS 2min=== | |||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''bam_file''' | |||
| align="center" style="background:#f0f0f0;"|'''sample''' | |||
| align="center" style="background:#f0f0f0;"|'''Raw_Reads''' | |||
| align="center" style="background:#f0f0f0;"|'''MappingRate''' | |||
| align="center" style="background:#f0f0f0;"|'''MappableReads''' | |||
| align="center" style="background:#f0f0f0;"|'''ClonalRate''' | |||
| align="center" style="background:#f0f0f0;"|'''Unique''' | |||
| align="center" style="background:#f0f0f0;"|'''1+''' | |||
| align="center" style="background:#f0f0f0;"|'''1''' | |||
| align="center" style="background:#f0f0f0;"|'''2''' | |||
| align="center" style="background:#f0f0f0;"|'''3''' | |||
| align="center" style="background:#f0f0f0;"|'''4+''' | |||
| align="center" style="background:#f0f0f0;"|'''contig''' | |||
| align="center" style="background:#f0f0f0;"|'''%Mito''' | |||
|- | |||
| s_1_1_Indx25_sorted.bam||17|| 2,268,771 ||85.63%|| 1,942,637 ||5.80%|| 1,829,964 || 56,939,904 || 38,624,661 || 9,747,120 || 3,911,513 || 4,640,531 || 2,171 ||0.03% | |||
|- | |||
| s_1_1_Indx26_sorted.bam||18|| 2,547,065 ||88.06%|| 2,243,001 ||5.90%|| 2,110,664 || 67,415,216 || 47,385,256 || 10,747,954 || 4,188,949 || 5,076,851 || 2,303 ||0.01% | |||
|- | |||
| s_1_1_Indx27_sorted.bam||19|| 1,995,724 ||88.08%|| 1,757,862 ||5.43%|| 1,662,410 || 55,980,120 || 40,789,431 || 8,550,722 || 3,115,164 || 3,508,685 || 1,703 ||0.03% | |||
|- | |||
| s_1_1_Indx28_sorted.bam||20|| 2,174,302 ||89.91%|| 1,954,885 ||5.73%|| 1,842,870 || 60,416,600 || 43,216,950 || 9,415,231 || 3,580,427 || 4,187,823 || 1,996 ||0.10% | |||
|- | |||
| s_1_1_Indx29_sorted.bam||21|| 2,536,410 ||88.60%|| 2,247,202 ||6.29%|| 2,105,853 || 67,628,869 || 47,608,592 || 10,774,494 || 4,165,587 || 5,063,988 || 2,321 ||0.08% | |||
|- | |||
| s_1_1_Indx30_sorted.bam||22|| 1,313,829 ||87.49%|| 1,149,447 ||4.09%|| 1,102,435 || 43,912,285 || 35,535,421 || 5,699,823 || 1,558,924 || 1,102,301 || 696 ||0.37% | |||
|- | |||
| s_1_1_Indx31_sorted.bam||23|| 1,188,929 ||85.01%|| 1,010,767 ||3.27%|| 977,715 || 42,901,971 || 37,061,123 || 4,595,040 || 884,469 || 347,247 || 264 ||0.43% | |||
|- | |||
| s_1_1_Indx32_sorted.bam||24|| 426,705 ||77.62%|| 331,204 ||2.66%|| 322,394 || 15,476,138 || 14,492,916 || 888,468 || 72,504 || 8,817 || 1 ||1.17% | |||
|- | |||
| s_2_1_Indx09_sorted.bam||1|| 508,645 ||61.59%|| 313,270 ||4.54%|| 299,048 || 14,135,431 || 12,822,540 || 1,136,402 || 135,215 || 29,071 || 10 ||0.31% | |||
|- | |||
| s_2_1_Indx10_sorted.bam||2|| 360,292 ||41.22%|| 148,525 ||4.37%|| 142,034 || 6,934,177 || 6,480,526 || 409,087 || 31,826 || 3,597 || 1 ||0.73% | |||
|- | |||
| s_2_1_Indx11_sorted.bam||3|| 387,809 ||74.52%|| 288,983 ||3.69%|| 278,320 || 13,344,475 || 12,368,345 || 867,342 || 80,836 || 16,025 || 4 ||0.55% | |||
|- | |||
| s_2_1_Indx12_sorted.bam||4|| 1,093,980 ||67.00%|| 732,986 ||18.57%|| 596,870 || 17,190,892 || 13,473,936 || 1,644,869 || 560,491 || 1,497,723 || 142 ||0.13% | |||
|- | |||
| s_2_1_Indx13_sorted.bam||5|| 1,795,103 ||85.27%|| 1,530,763 ||6.60%|| 1,429,733 || 51,709,503 || 39,121,559 || 7,520,564 || 2,484,592 || 2,566,850 || 1,279 ||0.12% | |||
|- | |||
| s_2_1_Indx14_sorted.bam||6|| 3,304,157 ||87.22%|| 2,881,999 ||9.73%|| 2,601,580 || 76,011,471 || 50,543,658 || 12,444,999 || 5,128,658 || 7,877,626 || 2,779 ||0.12% | |||
|- | |||
| s_2_1_Indx15_sorted.bam||7|| 2,897,378 ||87.71%|| 2,541,382 ||7.36%|| 2,354,336 || 69,608,776 || 46,854,101 || 11,277,938 || 4,695,723 || 6,764,564 || 2,626 ||0.06% | |||
|- | |||
| s_2_1_Indx16_sorted.bam||8|| 3,382,065 ||87.18%|| 2,948,364 ||9.04%|| 2,681,832 || 78,729,729 || 52,386,358 || 13,008,853 || 5,347,651 || 7,970,352 || 2,806 ||0.04% | |||
|- | |||
| s_2_1_Indx17_sorted.bam||9|| 885,232 ||86.87%|| 769,024 ||3.87%|| 739,263 || 26,960,544 || 20,271,643 || 4,260,105 || 1,355,620 || 1,057,682 || 680 ||0.27% | |||
|- | |||
| s_2_1_Indx18_sorted.bam||10|| 2,033,809 ||89.00%|| 1,810,131 ||5.09%|| 1,717,995 || 54,860,118 || 37,624,975 || 9,510,274 || 3,695,378 || 4,013,336 || 2,048 ||0.12% | |||
|- | |||
| s_2_1_Indx19_sorted.bam||11|| 1,104,616 ||87.81%|| 969,970 ||4.04%|| 930,783 || 32,901,124 || 24,216,566 || 5,351,552 || 1,778,372 || 1,538,740 || 925 ||0.21% | |||
|- | |||
| s_2_1_Indx20_sorted.bam||12|| 718,629 ||85.01%|| 610,922 ||3.56%|| 589,173 || 21,917,337 || 16,668,103 || 3,432,954 || 1,054,018 || 746,987 || 513 ||0.36% | |||
|- | |||
| s_2_1_Indx21_sorted.bam||13|| 1,226,760 ||86.29%|| 1,058,547 ||4.69%|| 1,008,901 || 33,196,721 || 23,064,173 || 5,843,270 || 2,158,328 || 2,114,817 || 1,184 ||0.25% | |||
|- | |||
| s_2_1_Indx22_sorted.bam||14|| 1,620,467 ||89.25%|| 1,446,193 ||5.80%|| 1,362,314 || 40,539,964 || 26,360,341 || 7,417,732 || 3,044,398 || 3,701,075 || 1,703 ||0.12% | |||
|- | |||
| s_2_1_Indx23_sorted.bam||15|| 1,340,858 ||88.27%|| 1,183,591 ||4.87%|| 1,125,950 || 36,266,426 || 24,846,902 || 6,416,637 || 2,448,570 || 2,538,568 || 1,390 ||0.07% | |||
|- | |||
| s_2_1_Indx24_sorted.bam||16|| 1,192,263 ||88.23%|| 1,051,952 ||4.26%|| 1,007,139 || 35,107,570 || 25,384,683 || 5,916,287 || 2,037,745 || 1,753,258 || 1,077 ||0.06% | |||
|- | |||
| |||| 38,303,798 |||| 32,923,607 ||||||||||||||||30622|| | |||
|- | |||
| | |||
|} | |||
===GM Dev9.2 Nov4: 400mM ALS 8min pump, NS 3min=== | |||
* low CORE PCR amplification | |||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''bam_file''' | |||
| align="center" style="background:#f0f0f0;"|'''sample''' | |||
| align="center" style="background:#f0f0f0;"|'''Raw_Reads''' | |||
| align="center" style="background:#f0f0f0;"|'''MappingRate''' | |||
| align="center" style="background:#f0f0f0;"|'''MappableReads''' | |||
| align="center" style="background:#f0f0f0;"|'''ClonalRate''' | |||
| align="center" style="background:#f0f0f0;"|'''Unique''' | |||
| align="center" style="background:#f0f0f0;"|'''1+''' | |||
| align="center" style="background:#f0f0f0;"|'''1''' | |||
| align="center" style="background:#f0f0f0;"|'''2''' | |||
| align="center" style="background:#f0f0f0;"|'''3''' | |||
| align="center" style="background:#f0f0f0;"|'''4+''' | |||
| align="center" style="background:#f0f0f0;"|'''contig''' | |||
| align="center" style="background:#f0f0f0;"|'''mito %''' | |||
|- | |||
| s_3_1_Indx09_sorted.bam||1|| 110,070 ||4.84%|| 5,330 ||3.32%|| 5,153 ||255953||245877||9123||622||31||0||0.13% | |||
|- | |||
| s_3_1_Indx10_sorted.bam||2|| 332,866 ||55.14%|| 183,556 ||4.20%|| 175,847 ||7453084||6321882||806591||190239||122142||22||0.39% | |||
|- | |||
| s_3_1_Indx11_sorted.bam||3|| 460,758 ||80.39%|| 370,384 ||4.16%|| 354,976 ||14587217||12269866||1573040||399301||331527||169||0.26% | |||
|- | |||
| s_3_1_Indx12_sorted.bam||4|| 965,330 ||54.95%|| 530,424 ||7.28%|| 491,809 ||16263741||11978596||2370093||825767||1077220||450||0.17% | |||
|- | |||
| s_3_1_Indx13_sorted.bam||5|| 1,923,409 ||76.66%|| 1,474,453 ||15.67%|| 1,243,406 ||29453843||19210771||4281355||1855084||4090991||1324||0.28% | |||
|- | |||
| s_3_1_Indx14_sorted.bam||6|| 679,544 ||80.26%|| 545,421 ||5.21%|| 517,005 ||21140487||17480980||2519059||631775||498159||245||0.08% | |||
|- | |||
| s_3_1_Indx15_sorted.bam||7|| 1,159,520 ||85.68%|| 993,493 ||4.64%|| 947,395 ||36032772||29055149||4370547||1292742||1299267||651||0.13% | |||
|- | |||
| s_3_1_Indx16_sorted.bam||8|| 928,796 ||84.75%|| 787,193 ||6.15%|| 738,781 ||26443068||20147608||3803834||1207322||1268579||600||0.25% | |||
|- | |||
| s_3_1_Indx17_sorted.bam||9|| 794,505 ||84.09%|| 668,073 ||5.51%|| 631,262 ||21932814||16561780||3126181||1037045||1194341||556||0.12% | |||
|- | |||
| s_3_1_Indx18_sorted.bam||10|| 1,569,518 ||88.26%|| 1,385,267 ||5.45%|| 1,309,770 ||47917306||37135195||6662422||2040576||2063795||1000||0.11% | |||
|- | |||
| s_3_1_Indx19_sorted.bam||11|| 1,183,076 ||0.32%|| 3,831 ||0.16%|| 3,825 ||191034||190324||332||78||||0||0.16% | |||
|- | |||
| s_3_1_Indx20_sorted.bam||12|| 135,557 ||31.07%|| 42,115 ||2.85%|| 40,915 ||1984818||1873010||97715||8396||1531||1||0.24% | |||
|- | |||
| s_3_1_Indx21_sorted.bam||13|| 95,795 ||0.89%|| 855 ||0.00%|| 855 ||42583||42447||114||22||||0||0.00% | |||
|- | |||
| s_3_1_Indx22_sorted.bam||14|| 556,870 ||80.33%|| 447,328 ||5.60%|| 422,278 ||14746902||11162550||2071520||703187||795206||306||0.41% | |||
|- | |||
| s_3_1_Indx23_sorted.bam||15|| 1,037,726 ||81.74%|| 848,236 ||6.75%|| 790,980 ||27063965||20208722||4001782||1334142||1503184||697||0.46% | |||
|- | |||
| s_3_1_Indx24_sorted.bam||16|| 1,313,949 ||85.33%|| 1,121,140 ||6.45%|| 1,048,826 ||35312566||25996780||5330442||1818630||2151963||957||0.10% | |||
|- | |||
| s_3_1_Indx25_sorted.bam||17|| 1,672,936 ||70.26%|| 1,175,469 ||9.94%|| 1,058,627 ||34310453||24458278||5477130||1930358||2430398||990||0.13% | |||
|- | |||
| s_3_1_Indx26_sorted.bam||18|| 1,419,693 ||73.97%|| 1,050,213 ||9.61%|| 949,288 ||31115473||22185808||4956077||1754889||2202589||894||0.20% | |||
|- | |||
| s_3_1_Indx27_sorted.bam||19|| 1,689,562 ||80.27%|| 1,356,208 ||10.76%|| 1,210,280 ||37695760||26164066||6220501||2263050||3032491||1207||0.21% | |||
|- | |||
| s_3_1_Indx28_sorted.bam||20|| 972,314 ||29.47%|| 286,549 ||6.59%|| 267,665 ||11156416||9165117||1386360||342305||252877||114||0.15% | |||
|- | |||
| s_3_1_Indx29_sorted.bam||21|| 1,686,064 ||45.78%|| 771,923 ||9.90%|| 695,503 ||25013350||19014006||3611709||1123776||1248028||486||0.34% | |||
|- | |||
| s_3_1_Indx30_sorted.bam||22|| 579,133 ||38.71%|| 224,175 ||6.87%|| 208,774 ||9127430||7725766||1041858||215921||129318||54||0.47% | |||
|- | |||
| s_3_1_Indx31_sorted.bam||23|| 801,090 ||18.83%|| 150,859 ||6.08%|| 141,687 ||6637633||5906835||602699||86177||30258||11||0.35% | |||
|- | |||
| s_3_1_Indx32_sorted.bam||24|| 588,577 ||4.28%|| 25,180 ||5.49%|| 23,798 ||1182222||1108671||65151||4352||623||1||0.31% | |||
|- | |||
| |||| 22,656,658 ||||||||||||||||||||10735|| | |||
|- | |||
| | |||
|} | |||
===GM Dev9 Nov14: 8ul ALS 3min, no NS neutralization, chamber 10&11 not collected so index 18&19 should not appear=== | |||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''bam_file''' | |||
| align="center" style="background:#f0f0f0;"|'''sample''' | |||
| align="center" style="background:#f0f0f0;"|''' Raw_Reads''' | |||
| align="center" style="background:#f0f0f0;"|'''MappingRate''' | |||
| align="center" style="background:#f0f0f0;"|''' MappableReads''' | |||
| align="center" style="background:#f0f0f0;"|'''ClonalRate''' | |||
| align="center" style="background:#f0f0f0;"|'''Unique''' | |||
| align="center" style="background:#f0f0f0;"|''' 1+''' | |||
| align="center" style="background:#f0f0f0;"|''' 1''' | |||
| align="center" style="background:#f0f0f0;"|''' 2''' | |||
| align="center" style="background:#f0f0f0;"|''' 3''' | |||
| align="center" style="background:#f0f0f0;"|''' 4+''' | |||
| align="center" style="background:#f0f0f0;"|'''contig''' | |||
| align="center" style="background:#f0f0f0;"|'''mito %''' | |||
|- | |||
| s_4_1_Indx09_sorted.bam||1|| 856,758 ||30.14%|| 258,203 ||3.44%|| 249,321 || 11,176,695 || 9,821,709 || 1,083,615 || 195,008 || 66,237 ||43||0.16% | |||
|- | |||
| s_4_1_Indx10_sorted.bam||2|| 963,484 ||43.45%|| 418,661 ||3.73%|| 403,045 || 17,366,969 || 14,720,689 || 2,014,268 || 439,046 || 179,245 ||134||0.18% | |||
|- | |||
| s_4_1_Indx11_sorted.bam||3|| 694,992 ||60.77%|| 422,353 ||3.24%|| 408,669 || 17,493,599 || 14,844,533 || 2,009,564 || 440,433 || 188,026 ||133||0.10% | |||
|- | |||
| s_4_1_Indx12_sorted.bam||4|| 1,182,379 ||77.06%|| 911,174 ||4.20%|| 872,905 || 34,541,244 || 27,595,022 || 4,654,848 || 1,365,371 || 911,299 ||437||0.11% | |||
|- | |||
| s_4_1_Indx13_sorted.bam||5|| 950,557 ||59.35%|| 564,124 ||3.92%|| 542,010 || 22,882,839 || 19,035,533 || 2,898,452 || 652,726 || 286,774 ||209||0.06% | |||
|- | |||
| s_4_1_Indx14_sorted.bam||6|| 1,275,809 ||64.17%|| 818,642 ||3.84%|| 787,206 || 31,918,636 || 25,692,721 || 4,452,347 || 1,169,802 || 591,266 ||385||0.06% | |||
|- | |||
| s_4_1_Indx15_sorted.bam||7|| 1,054,052 ||58.84%|| 620,245 ||3.16%|| 600,645 || 24,996,063 || 20,674,313 || 3,195,915 || 769,784 || 345,098 ||258||0.07% | |||
|- | |||
| s_4_1_Indx16_sorted.bam||8|| 1,300,089 ||85.04%|| 1,105,629 ||4.55%|| 1,055,323 || 40,530,314 || 31,436,254 || 5,925,358 || 1,865,041 || 1,290,022 ||677||0.07% | |||
|- | |||
| s_4_1_Indx17_sorted.bam||9|| 948,303 ||82.92%|| 786,354 ||5.57%|| 742,554 || 26,237,029 || 18,530,807 || 4,791,007 || 1,668,497 || 1,231,609 ||552||0.14% | |||
|- | |||
| s_4_1_Indx18_sorted.bam||10|| 977,363 ||63.15%|| 617,224 ||1.40%|| 608,583 || 28,601,880 || 26,667,648 || 1,706,679 || 175,246 || 39,592 ||24||0.09% | |||
|- | |||
| s_4_1_Indx19_sorted.bam||11|| 284,548 ||78.28%|| 222,731 ||2.83%|| 216,428 || 9,557,295 || 8,281,352 || 1,039,203 || 178,065 || 47,811 ||42||0.17% | |||
|- | |||
| s_4_1_Indx20_sorted.bam||12|| 249 ||35.34%|| 88 ||0.00%|| 88 || 4,398 || 4,398 ||||||||0||0.00% | |||
|- | |||
| s_4_1_Indx21_sorted.bam||13|| 444,712 ||78.54%|| 349,290 ||3.79%|| 336,052 || 14,037,639 || 11,503,571 || 1,914,841 || 438,080 || 168,595 ||128||0.17% | |||
|- | |||
| s_4_1_Indx22_sorted.bam||14|| 1,682,346 ||50.71%|| 853,080 ||4.10%|| 818,104 || 35,752,237 || 30,537,535 || 4,083,737 || 811,761 || 305,529 ||209||0.10% | |||
|- | |||
| s_4_1_Indx23_sorted.bam||15|| 1,476,044 ||65.32%|| 964,146 ||5.48%|| 911,311 || 35,170,224 || 26,665,568 || 5,792,584 || 1,713,845 || 984,781 ||620||0.07% | |||
|- | |||
| s_4_1_Indx24_sorted.bam||16|| 1,318,194 ||80.74%|| 1,064,298 ||6.03%|| 1,000,121 || 35,208,227 || 24,848,879 || 6,326,891 || 2,242,352 || 1,774,514 ||761||0.13% | |||
|- | |||
| s_4_1_Indx25_sorted.bam||17|| 2,218,236 ||79.03%|| 1,752,966 ||4.55%|| 1,673,206 || 61,942,679 || 46,981,932 || 9,355,110 || 3,137,461 || 2,456,587 ||1032||0.03% | |||
|- | |||
| s_4_1_Indx26_sorted.bam||18|| 1,419,252 ||71.68%|| 1,017,304 ||4.02%|| 976,408 || 38,562,194 || 30,474,813 || 5,595,187 || 1,573,147 || 903,417 ||565||0.14% | |||
|- | |||
| s_4_1_Indx27_sorted.bam||19|| 1,130,690 ||67.03%|| 757,926 ||4.31%|| 725,259 || 27,519,893 || 21,000,452 || 4,314,284 || 1,336,301 || 854,618 ||452||0.12% | |||
|- | |||
| s_4_1_Indx28_sorted.bam||20|| 764,912 ||52.76%|| 403,584 ||3.59%|| 389,095 || 16,528,651 || 13,931,738 || 1,919,996 || 450,700 || 213,709 ||159||0.14% | |||
|- | |||
| s_4_1_Indx29_sorted.bam||21|| 870,457 ||51.26%|| 446,185 ||4.51%|| 426,062 || 16,268,933 || 12,577,192 || 2,414,077 || 757,295 || 503,987 ||302||0.63% | |||
|- | |||
| s_4_1_Indx30_sorted.bam||22|| 711,139 ||33.11%|| 235,467 ||3.73%|| 226,684 || 9,305,283 || 7,653,781 || 1,162,244 || 307,151 || 168,388 ||97||0.33% | |||
|- | |||
| s_4_1_Indx31_sorted.bam||23|| 670,998 ||34.81%|| 233,574 ||3.36%|| 225,726 || 9,681,494 || 8,213,401 || 1,092,940 || 257,746 || 105,485 ||78||0.21% | |||
|- | |||
| s_4_1_Indx32_sorted.bam||24|| 691,808 ||15.33%|| 106,044 ||2.47%|| 103,425 || 4,756,473 || 4,308,516 || 366,651 || 53,947 || 14,630 ||10||0.61% | |||
|- | |||
| |||| 23,887,371 |||||||| 14,298,230 ||||||||||||7307|| | |||
|- | |||
| | |||
|} | |||
===GM Dev9 Nov18: 6ul ALS 4min pump, no NS neutralization=== | |||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''bam_file''' | |||
| align="center" style="background:#f0f0f0;"|'''sample''' | |||
| align="center" style="background:#f0f0f0;"|''' Raw_Reads''' | |||
| align="center" style="background:#f0f0f0;"|'''MappingRate''' | |||
| align="center" style="background:#f0f0f0;"|''' MappableReads''' | |||
| align="center" style="background:#f0f0f0;"|'''ClonalRate''' | |||
| align="center" style="background:#f0f0f0;"|'''Unique''' | |||
| align="center" style="background:#f0f0f0;"|''' 1+''' | |||
| align="center" style="background:#f0f0f0;"|''' 1''' | |||
| align="center" style="background:#f0f0f0;"|''' 2''' | |||
| align="center" style="background:#f0f0f0;"|''' 3''' | |||
| align="center" style="background:#f0f0f0;"|''' 4+''' | |||
| align="center" style="background:#f0f0f0;"|'''contig''' | |||
| align="center" style="background:#f0f0f0;"|'''mito %''' | |||
|- | |||
| s_5_1_Indx09_sorted.bam||1|| 566,131 ||92.05%|| 521,143 ||2.04%|| 510,512 ||22622085||19949789||2144432||377534||142099||125||0.05% | |||
|- | |||
| s_5_1_Indx10_sorted.bam||2|| 582,196 ||91.82%|| 534,577 ||2.07%|| 523,511 ||23388189||20764386||2130723||357486||127007||95||0.05% | |||
|- | |||
| s_5_1_Indx11_sorted.bam||3|| 456,504 ||93.10%|| 424,992 ||1.81%|| 417,300 ||18981401||17142287||1523148||231991||73967||52||0.09% | |||
|- | |||
| s_5_1_Indx12_sorted.bam||4|| 643,392 ||92.53%|| 595,316 ||2.15%|| 582,517 ||25823907||22813732||2400712||424437||175243||117||0.06% | |||
|- | |||
| s_5_1_Indx13_sorted.bam||5|| 629,502 ||92.54%|| 582,530 ||2.05%|| 570,588 ||25666989||22896028||2277686||363154||120015||102||0.06% | |||
|- | |||
| s_5_1_Indx14_sorted.bam||6|| 637,561 ||92.52%|| 589,901 ||2.17%|| 577,100 ||25564795||22555793||2411714||417001||168493||119||0.08% | |||
|- | |||
| s_5_1_Indx15_sorted.bam||7|| 453,520 ||92.75%|| 420,626 ||1.86%|| 412,802 ||18884198||17130188||1472741||207014||65355||38||0.07% | |||
|- | |||
| s_5_1_Indx16_sorted.bam||8|| 650,948 ||92.55%|| 602,431 ||2.16%|| 589,418 ||26032634||22867514||2540425||445133||171134||132||0.05% | |||
|- | |||
| s_5_1_Indx17_sorted.bam||9|| 2,346,039 ||92.67%|| 2,174,001 ||3.56%|| 2,096,607 ||75589163||56259760||12358534||3919313||3037597||2018||0.04% | |||
|- | |||
| s_5_1_Indx18_sorted.bam||10|| 2,817,253 ||92.65%|| 2,610,104 ||4.06%|| 2,504,134 ||85225081||60441703||14963201||5239476||4566042||2716||0.04% | |||
|- | |||
| s_5_1_Indx19_sorted.bam||11|| 2,169,373 ||92.62%|| 2,009,212 ||3.39%|| 1,941,100 ||70876027||52967667||11676292||3631519||2584197||1902||0.11% | |||
|- | |||
| s_5_1_Indx20_sorted.bam||12|| 2,361,125 ||93.05%|| 2,197,121 ||3.88%|| 2,111,873 ||73803630||53592258||12547968||4178710||3469268||2267||0.07% | |||
|- | |||
| s_5_1_Indx21_sorted.bam||13|| 1,611,752 ||93.04%|| 1,499,635 ||3.60%|| 1,445,648 ||52862674||39877632||8402048||2590210||1980382||1310||0.04% | |||
|- | |||
| s_5_1_Indx22_sorted.bam||14|| 2,507,782 ||92.54%|| 2,320,719 ||3.98%|| 2,228,354 ||75797660||53742181||13299752||4641405||4100391||2497||0.04% | |||
|- | |||
| s_5_1_Indx23_sorted.bam||15|| 7,376 ||80.78%|| 5,958 ||0.13%|| 5,950 ||296822||295568||952||||||0||0.12% | |||
|- | |||
| s_5_1_Indx24_sorted.bam||16|| 23,667 ||84.85%|| 20,081 ||0.52%|| 19,977 ||990882||977245||11788||347||114||0||0.14% | |||
|- | |||
| s_5_1_Indx25_sorted.bam||17|| 1,140,848 ||93.13%|| 1,062,426 ||2.84%|| 1,032,253 ||41587790||33882811||5480352||1399794||810090||633||0.09% | |||
|- | |||
| s_5_1_Indx26_sorted.bam||18|| 1,019,979 ||92.82%|| 946,728 ||2.58%|| 922,302 ||37546283||30956173||4738626||1163567||672624||478||0.15% | |||
|- | |||
| s_5_1_Indx27_sorted.bam||19|| 2,086,116 ||92.98%|| 1,939,644 ||3.80%|| 1,865,938 ||66385622||49500299||10418414||3452195||2999253||1863||0.08% | |||
|- | |||
| s_5_1_Indx28_sorted.bam||20|| 1,758,276 ||92.50%|| 1,626,387 ||3.79%|| 1,564,747 ||56174975||42247364||8743766||2803247||2366358||1484||0.05% | |||
|- | |||
| s_5_1_Indx29_sorted.bam||21|| 1,889,043 ||91.69%|| 1,732,053 ||3.99%|| 1,662,944 ||58934208||43860043||9269312||3077560||2712307||1626||0.08% | |||
|- | |||
| s_5_1_Indx30_sorted.bam||22|| 1,891,903 ||92.36%|| 1,747,380 ||4.09%|| 1,675,912 ||58338925||43070298||9201837||3127366||2923698||1758||0.10% | |||
|- | |||
| s_5_1_Indx31_sorted.bam||23|| 1,527,048 ||90.98%|| 1,389,356 ||3.53%|| 1,340,312 ||49437651||38084465||7219354||2259160||1860052||1212||0.08% | |||
|- | |||
| s_5_1_Indx32_sorted.bam||24|| 764,860 ||90.73%|| 693,971 ||2.62%|| 675,789 ||27969607||23575307||3148383||764504||467033||340||0.16% | |||
|- | |||
| |||| 30,542,194 |||||||| 27,277,587 ||||||||||||22884|| | |||
|- | |||
| | |||
|} | |||
===GM Dev9 Dec2: 8ul ALS 4min pump, no NS neutralization, half concentrations of dNTP, random hexamers, and dUTP=== | |||
* highest overlapping fragments | |||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''bam_file''' | |||
| align="center" style="background:#f0f0f0;"|'''sample''' | |||
| align="center" style="background:#f0f0f0;"|''' Raw_Reads''' | |||
| align="center" style="background:#f0f0f0;"|'''MappingRate''' | |||
| align="center" style="background:#f0f0f0;"|''' MappableReads''' | |||
| align="center" style="background:#f0f0f0;"|'''ClonalRate''' | |||
| align="center" style="background:#f0f0f0;"|'''Unique''' | |||
| align="center" style="background:#f0f0f0;"|''' 1+''' | |||
| align="center" style="background:#f0f0f0;"|''' 1''' | |||
| align="center" style="background:#f0f0f0;"|''' 2''' | |||
| align="center" style="background:#f0f0f0;"|''' 3''' | |||
| align="center" style="background:#f0f0f0;"|''' 4+''' | |||
| align="center" style="background:#f0f0f0;"|'''contig''' | |||
| align="center" style="background:#f0f0f0;"|'''mito %''' | |||
|- | |||
| s_6_1_Indx09_sorted.bam||1|| 147,354 ||91.75%|| 135,198 ||2.11%|| 132,345 ||6461119||6178418||267142||13161||1181||1||0.02% | |||
|- | |||
| s_6_1_Indx10_sorted.bam||2|| 261,254 ||91.64%|| 239,421 ||2.36%|| 233,771 ||10895835||9985035||780195||102630||26266||21||0.02% | |||
|- | |||
| s_6_1_Indx11_sorted.bam||3|| 318,449 ||93.12%|| 296,553 ||2.77%|| 288,338 ||12390788||10687966||1253133||289010||156833||130||0.03% | |||
|- | |||
| s_6_1_Indx12_sorted.bam||4|| 703,962 ||92.54%|| 651,464 ||3.25%|| 630,291 ||25352366||20532246||3384627||903397||523122||399||0.04% | |||
|- | |||
| s_6_1_Indx13_sorted.bam||5|| 827,645 ||92.61%|| 766,495 ||3.30%|| 741,201 ||29446260||23557332||4102560||1123707||655998||495||0.02% | |||
|- | |||
| s_6_1_Indx14_sorted.bam||6|| 801,723 ||92.49%|| 741,482 ||3.16%|| 718,051 ||29350482||23996984||3848518||989884||510334||419||0.02% | |||
|- | |||
| s_6_1_Indx15_sorted.bam||7|| 1,082,996 ||92.76%|| 1,004,553 ||2.99%|| 974,517 ||39264350||31607388||5522735||1430204||700437||577||0.01% | |||
|- | |||
| s_6_1_Indx16_sorted.bam||8|| 1,654,085 ||93.32%|| 1,543,581 ||3.21%|| 1,494,032 ||59585243||47316719||8833250||2303076||1125708||911||0.01% | |||
|- | |||
| s_6_1_Indx17_sorted.bam||9|| 367,635 ||92.12%|| 338,649 ||2.36%|| 330,657 ||15073189||13481813||1363334||188433||35871||25||0.02% | |||
|- | |||
| s_6_1_Indx18_sorted.bam||10|| 811,866 ||92.36%|| 749,857 ||2.81%|| 728,786 ||30753727||25774917||3781051||841453||352186||324||0.01% | |||
|- | |||
| s_6_1_Indx19_sorted.bam||11|| 381,391 ||92.43%|| 352,530 ||2.43%|| 343,964 ||15353188||13475727||1562042||249849||62901||59||0.02% | |||
|- | |||
| s_6_1_Indx20_sorted.bam||12|| 1,085,834 ||92.78%|| 1,007,399 ||3.68%|| 970,327 ||35660274||26511538||5985125||1886258||1267358||783||0.04% | |||
|- | |||
| s_6_1_Indx21_sorted.bam||13|| 1,285,766 ||92.96%|| 1,195,184 ||3.78%|| 1,150,006 ||42558543||32486983||6390013||2046628||1626207||817||0.02% | |||
|- | |||
| s_6_1_Indx22_sorted.bam||14|| 1,023,874 ||92.68%|| 948,955 ||4.39%|| 907,296 ||31090070||21933905||5551413||1971246||1626269||829||0.02% | |||
|- | |||
| s_6_1_Indx23_sorted.bam||15|| 1,309,026 ||92.98%|| 1,217,093 ||5.01%|| 1,156,117 ||36506085||24204720||6838820||2703092||2753135||1122||0.01% | |||
|- | |||
| s_6_1_Indx24_sorted.bam||16|| 1,467,281 ||92.75%|| 1,360,870 ||6.31%|| 1,274,999 ||35758012||21928984||6849748||3041761||3923949||1175||0.05% | |||
|- | |||
| s_6_1_Indx25_sorted.bam||17|| 698,050 ||92.52%|| 645,814 ||3.23%|| 624,954 ||25335784||20661100||3310609||876261||479893||382||0.04% | |||
|- | |||
| s_6_1_Indx26_sorted.bam||18|| 1,277,715 ||93.05%|| 1,188,916 ||4.67%|| 1,133,394 ||38411904||27698065||6092392||2300275||2313090||929||0.02% | |||
|- | |||
| s_6_1_Indx27_sorted.bam||19|| 445,570 ||92.65%|| 412,840 ||3.20%|| 399,629 ||16067503||13125725||2005888||565432||360211||260||0.08% | |||
|- | |||
| s_6_1_Indx28_sorted.bam||20|| 442,411 ||92.72%|| 410,188 ||3.66%|| 395,175 ||15067143||11800147||2102448||656830||495772||321||0.12% | |||
|- | |||
| s_6_1_Indx29_sorted.bam||21|| 666,668 ||92.93%|| 619,561 ||4.69%|| 590,504 ||20484626||15068126||3108547||1166225||1132370||556||0.05% | |||
|- | |||
| s_6_1_Indx30_sorted.bam||22|| 620,288 ||92.97%|| 576,707 ||4.14%|| 552,831 ||19696269||14719563||2953765||1064866||948488||536||0.05% | |||
|- | |||
| s_6_1_Indx31_sorted.bam||23|| 420,564 ||92.66%|| 389,687 ||3.47%|| 376,165 ||15017005||12233581||1868184||536051||368516||246||0.10% | |||
|- | |||
| s_6_1_Indx32_sorted.bam||24|| 150,023 ||92.52%|| 138,796 ||2.10%|| 135,881 ||6487605||6092573||345055||37818||8815||5||0.05% | |||
|- | |||
| |||| 18,251,430 ||||||||||||||||||||11322|| | |||
|- | |||
| | |||
|} | |||
===GM Dev9 Dec3: 8ul ALS 4min pump, no NS neutralization=== | |||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''bam_file''' | |||
| align="center" style="background:#f0f0f0;"|'''sample''' | |||
| align="center" style="background:#f0f0f0;"|''' Raw_Reads''' | |||
| align="center" style="background:#f0f0f0;"|'''MappingRate''' | |||
| align="center" style="background:#f0f0f0;"|''' MappableReads''' | |||
| align="center" style="background:#f0f0f0;"|'''ClonalRate''' | |||
| align="center" style="background:#f0f0f0;"|''' Unique''' | |||
| align="center" style="background:#f0f0f0;"|''' 1+''' | |||
| align="center" style="background:#f0f0f0;"|''' 1''' | |||
| align="center" style="background:#f0f0f0;"|''' 2''' | |||
| align="center" style="background:#f0f0f0;"|''' 3''' | |||
| align="center" style="background:#f0f0f0;"|''' 4+''' | |||
| align="center" style="background:#f0f0f0;"|'''contig''' | |||
| align="center" style="background:#f0f0f0;"|'''mito %''' | |||
|- | |||
| s_7_1_Indx09_sorted.bam||1|| 466,433 ||91.61%|| 427,297 ||2.69%|| 415,803 ||18748607||16680272||1704424||265373||82137||67||0.51% | |||
|- | |||
| s_7_1_Indx10_sorted.bam||2|| 1,480,440 ||91.94%|| 1,361,144 ||5.69%|| 1,283,695 ||38297341||24337528||7383041||3089792||3470526||1532||0.23% | |||
|- | |||
| s_7_1_Indx11_sorted.bam||3|| 590,938 ||91.82%|| 542,621 ||4.35%|| 519,017 ||17419400||12099881||3151858||1159602||992266||576||0.27% | |||
|- | |||
| s_7_1_Indx12_sorted.bam||4|| 1,003,355 ||91.82%|| 921,232 ||7.45%|| 852,600 ||21650089||12473391||4088303||1982639||3089327||853||0.38% | |||
|- | |||
| s_7_1_Indx13_sorted.bam||5|| 999,028 ||92.01%|| 919,203 ||7.04%|| 854,491 ||22484410||13379787||4194695||1974126||2919345||866||0.44% | |||
|- | |||
| s_7_1_Indx14_sorted.bam||6|| 1,167,131 ||92.32%|| 1,077,530 ||8.40%|| 987,017 ||24057372||13724938||4398430||2185016||3732471||874||0.54% | |||
|- | |||
| s_7_1_Indx15_sorted.bam||7|| 1,174,380 ||92.64%|| 1,087,999 ||6.12%|| 1,021,413 ||29510071||18575229||5605243||2412798||2900262||1121||0.58% | |||
|- | |||
| s_7_1_Indx16_sorted.bam||8|| 810,580 ||92.05%|| 746,113 ||4.70%|| 711,046 ||23573340||16359858||4143780||1574717||1479208||714||0.22% | |||
|- | |||
| s_7_1_Indx17_sorted.bam||9|| 1,389,135 ||91.63%|| 1,272,889 ||8.73%|| 1,161,766 ||27540134||14995651||5324564||2680854||4522517||1128||0.60% | |||
|- | |||
| s_7_1_Indx18_sorted.bam||10|| 836,387 ||90.35%|| 755,667 ||7.57%|| 698,463 ||17800371||10135876||3441141||1664788||2542009||713||0.70% | |||
|- | |||
| s_7_1_Indx19_sorted.bam||11|| 1,202,752 ||92.26%|| 1,109,682 ||10.37%|| 994,608 ||21935689||11550954||4195042||2152820||4020323||905||0.96% | |||
|- | |||
| s_7_1_Indx20_sorted.bam||12|| 1,472,508 ||92.30%|| 1,359,052 ||9.73%|| 1,226,816 ||26309658||13313935||4978521||2683507||5317179||950||0.31% | |||
|- | |||
| s_7_1_Indx21_sorted.bam||13|| 446,606 ||90.18%|| 402,746 ||5.80%|| 379,387 ||11638201||7580388||2194669||892143||954743||484||0.66% | |||
|- | |||
| s_7_1_Indx22_sorted.bam||14|| 1,001,886 ||91.63%|| 918,023 ||8.52%|| 839,807 ||19877277||10679954||3862575||1966238||3351971||813||0.65% | |||
|- | |||
| s_7_1_Indx23_sorted.bam||15|| 1,240,713 ||91.08%|| 1,130,020 ||10.07%|| 1,016,227 ||23120319||12602995||4193545||2177034||4130194||888||0.61% | |||
|- | |||
| s_7_1_Indx24_sorted.bam||16|| 260,487 ||86.91%|| 226,389 ||4.65%|| 215,862 ||7558618||5409845||1317898||458331||356452||227||0.72% | |||
|- | |||
| s_7_1_Indx25_sorted.bam||17|| 232,615 ||90.11%|| 209,618 ||3.60%|| 202,072 ||7836636||6164401||1108529||333841||214436||159||0.65% | |||
|- | |||
| s_7_1_Indx26_sorted.bam||18|| 347,852 ||92.12%|| 320,444 ||4.43%|| 306,248 ||10581532||7717357||1673693||601822||572533||303||0.66% | |||
|- | |||
| s_7_1_Indx27_sorted.bam||19|| 180,464 ||91.21%|| 164,594 ||3.87%|| 158,224 ||5897663||4513449||878544||285987||203677||154||1.15% | |||
|- | |||
| s_7_1_Indx28_sorted.bam||20|| 211,830 ||92.24%|| 195,399 ||4.23%|| 187,134 ||6599973||4804263||1095359||380608||303970||209||1.10% | |||
|- | |||
| s_7_1_Indx29_sorted.bam||21|| 5,415,501 ||93.35%|| 5,055,161 ||3.31%|| 4,887,835 ||201810935||166445591||26049371||6006115||3293382||2351||0.06% | |||
|- | |||
| s_7_1_Indx30_sorted.bam||22|| 229,824 ||92.02%|| 211,484 ||4.17%|| 202,665 ||7099611||5208051||1123369||405378||346533||216||1.22% | |||
|- | |||
| s_7_1_Indx31_sorted.bam||23|| 138,962 ||90.20%|| 125,350 ||3.98%|| 120,361 ||4749075||3946664||493809||146315||146519||78||1.18% | |||
|- | |||
| s_7_1_Indx32_sorted.bam||24|| 20,719 ||71.15%|| 14,741 ||2.27%|| 14,406 ||696958||658971||27808||3109||1021||2||1.18% | |||
|- | |||
| |||| 22,320,526 |||||||| 19,256,964 ||||||||||||16183|| | |||
|- | |||
| | |||
|} | |||
===GM Dev7 Dec9: 400mM ALS 5min pump, NS 1min=== | |||
* Chamber 1 empty | |||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''bam_file''' | |||
| align="center" style="background:#f0f0f0;"|'''sample''' | |||
| align="center" style="background:#f0f0f0;"|''' Raw_Reads''' | |||
| align="center" style="background:#f0f0f0;"|'''MappingRate''' | |||
| align="center" style="background:#f0f0f0;"|''' MappableReads''' | |||
| align="center" style="background:#f0f0f0;"|'''ClonalRate''' | |||
| align="center" style="background:#f0f0f0;"|'''Unique''' | |||
| align="center" style="background:#f0f0f0;"|''' 1+''' | |||
| align="center" style="background:#f0f0f0;"|''' 1''' | |||
| align="center" style="background:#f0f0f0;"|''' 2''' | |||
| align="center" style="background:#f0f0f0;"|''' 3''' | |||
| align="center" style="background:#f0f0f0;"|''' 4+''' | |||
| align="center" style="background:#f0f0f0;"|'''contig''' | |||
| align="center" style="background:#f0f0f0;"|'''mito %''' | |||
| align="center" style="background:#f0f0f0;"|''' Index Mixed''' | |||
|- | |||
| s_8_1_Indx09_sorted.bam||1|| 55,429 ||85.20%||47227||18.00%|| 38,726 || 1,107,170 || 820,229 || 149,001 || 48,647 || 72,914 ||27||10.55%||low raw reads | |||
|- | |||
| s_8_1_Indx10_sorted.bam||2|| 363,102 ||89.68%||325629||22.60%|| 252,037 || 5,697,031 || 3,865,026 || 681,604 || 310,276 || 823,580 ||186||3.64%||xx | |||
|- | |||
| s_8_1_Indx11_sorted.bam||3|| 616,785 ||89.79%||553785||37.15%|| 348,054 || 5,290,986 || 2,965,348 || 709,072 || 348,472 || 1,251,532 ||236||11.27%||xx | |||
|- | |||
| s_8_1_Indx12_sorted.bam||4|| 639,054 ||79.26%||506522||35.23%|| 328,074 || 5,437,202 || 3,091,442 || 764,967 || 376,217 || 1,188,024 ||181||2.97%||xx | |||
|- | |||
| s_8_1_Indx13_sorted.bam||5|| 793,528 ||90.18%||715603||53.84%|| 330,322 || 4,000,233 || 2,184,998 || 471,816 || 235,297 || 1,091,554 ||140||15.09%||xx | |||
|- | |||
| s_8_1_Indx14_sorted.bam||6|| 842,206 ||84.76%||713860||58.48%|| 296,395 || 3,613,379 || 2,072,545 || 415,794 || 190,341 || 918,152 ||108||7.41%||9-13,15-16,18,24-32 | |||
|- | |||
| s_8_1_Indx15_sorted.bam||7|| 406,229 ||74.15%||301204||41.75%|| 175,451 || 2,751,294 || 1,523,115 || 393,313 || 193,149 || 625,155 ||130||16.65%||9-14,16,25-32 | |||
|- | |||
| s_8_1_Indx16_sorted.bam||8|| 778,443 ||89.42%||696102||51.32%|| 338,862 || 3,808,996 || 2,002,178 || 467,898 || 224,431 || 1,097,925 ||137||13.70%||xx | |||
|- | |||
| s_8_1_Indx17_sorted.bam||9|| 402,019 ||90.57%||364118||41.73%|| 212,172 || 2,532,525 || 1,120,688 || 352,538 || 205,494 || 837,244 ||121||10.73%||xx | |||
|- | |||
| s_8_1_Indx18_sorted.bam||10|| 1,652 ||79.90%||1320||1.29%|| 1,303 || 58,727 || 50,607 || 2,588 || 345 || 605 ||0||8.33%||low raw reads | |||
|- | |||
| s_8_1_Indx19_sorted.bam||11|| 86,304 ||88.27%||76180||37.74%|| 47,430 || 770,363 || 383,218 || 125,281 || 66,202 || 179,137 ||49||19.22%||xx | |||
|- | |||
| s_8_1_Indx20_sorted.bam||12|| 933,639 ||87.19%||814042||48.70%|| 417,604 || 4,309,063 || 1,862,936 || 542,539 || 323,752 || 1,563,274 ||164||4.86%||9-16,24-32 | |||
|- | |||
| s_8_1_Indx21_sorted.bam||13|| 1,029,835 ||89.07%||917324||89.96%|| 92,099 || 784,154 || 447,249 || 60,381 || 29,543 || 230,413 ||36||47.08%||9-16,22,24-32 | |||
|- | |||
| s_8_1_Indx22_sorted.bam||14|| 1,111,235 ||87.17%||968664||66.04%|| 328,958 || 3,183,958 || 1,568,194 || 333,851 || 177,467 || 1,087,878 ||114||10.85%||xx | |||
|- | |||
| s_8_1_Indx23_sorted.bam||15|| 928,597 ||78.47%||728628||70.51%|| 214,872 || 2,006,042 || 935,234 || 228,001 || 124,912 || 701,327 ||118||23.49%||9-16,22,24-32 | |||
|- | |||
| s_8_1_Indx24_sorted.bam||16|| 1,011,523 ||85.73%||867225||75.81%|| 209,782 || 2,042,121 || 1,026,773 || 229,918 || 116,420 || 652,448 ||91||10.97%||>75% clonal | |||
|- | |||
| s_8_1_Indx25_sorted.bam||17|| 590,735 ||87.20%||515128||58.60%|| 213,263 || 2,813,647 || 1,573,750 || 341,258 || 169,360 || 712,711 ||134||24.66%||xx | |||
|- | |||
| s_8_1_Indx26_sorted.bam||18|| 491,923 ||90.38%||444596||50.41%|| 220,475 || 2,487,677 || 1,189,391 || 297,802 || 164,951 || 818,973 ||90||13.74%||9-14,16,25,27-32 | |||
|- | |||
| s_8_1_Indx27_sorted.bam||19|| 279,340 ||88.78%||248006||46.89%|| 131,716 || 1,978,352 || 1,131,928 || 254,584 || 128,622 || 446,677 ||72||9.70%||28 | |||
|- | |||
| s_8_1_Indx28_sorted.bam||20|| 587,246 ||84.86%||498360||56.16%|| 218,481 || 2,832,723 || 1,610,306 || 344,360 || 165,683 || 695,810 ||138||13.83%||>50% clonal | |||
|- | |||
| s_8_1_Indx29_sorted.bam||21|| 994,877 ||62.80%||624806||70.82%|| 182,318 || 2,571,653 || 1,654,575 || 302,756 || 119,277 || 478,482 ||63||18.89%||>70% clonal | |||
|- | |||
| s_8_1_Indx30_sorted.bam||22|| 780,802 ||87.65%||684397||84.12%|| 108,682 || 1,816,796 || 1,302,856 || 188,087 || 69,584 || 239,701 ||39||51.69%||>80% clonal | |||
|- | |||
| s_8_1_Indx31_sorted.bam||23|| 630,217 ||87.60%||552075||45.32%|| 301,875 || 3,879,471 || 1,993,876 || 515,970 || 270,653 || 1,082,431 ||203||8.82%||xx | |||
|- | |||
| s_8_1_Indx32_sorted.bam||24|| 532,173 ||78.52%||417856||65.36%|| 144,745 || 1,844,914 || 987,372 || 228,348 || 114,437 || 498,197 ||82||19.10%||xx | |||
|- | |||
| |||| 14,886,893 |||||||| 5,153,697 ||||||||||||2659|||| | |||
|- | |||
| | |||
|} |
Latest revision as of 00:27, 16 January 2015
Mapping New Sequencing Libraries[edit]
- These 9 single cell libraries were sequenced in HL175. GM stands for GM20431.
- GM Dev9 Oct10 (Index 9-16). Asked for 10 million reads. Sequenced in Lane 1.
- PGP1 Dev8 Oct6 (Index 17-24). Asked for 10 million reads. Sequenced in Lane 1.
- GM Dev9.2 Oct23 (Index 25-32). Asked for 20 million reads. Sequenced in Lane 1. GM Dev9.2 Oct23 (Index 9-24). Asked for 40 million reads. Sequenced in Lane 2.
- GM Dev9.2 Nov4 (Index9-32). Asked for 40 million reads. Sequenced in Lane3.
- GM Dev9 Nov14 (Index9-32). Asked for 40 million reads. Sequenced in Lane4.
- GM Dev9 Nov18 (Index9-32). Asked for 40 million reads. Sequenced in Lane5.
- GM Dev9 Dec2 (Index9-32). Asked for 40 million reads. Sequenced in Lane6.
- GM Dev9 Dec3 (Index9-32). Asked for 40 million reads. Sequenced in Lane7.
- GM Dev7 Dec9 (Index9-32). Asked for 40 million reads. Sequenced in Lane8.
Commands[edit]
- reference: http://genome-tech.ucsd.edu/LabNotes/index.php/EricChu:LabNotesMDA/2014-8-25
- txt files were copied to /data_Syn_15T/HL175/
- Each single cell data have its own folder.
- For example, in /data_Syn_15T/HL175/GMDev9Oct10
- command: nohup ../../batch_bwa_fastq2bam.pl hg19 > EC_GMDev9Oct10_BWA_batch_fastq2bam.log &
- ../../get_covstats.pl > EC_GMDev9Oct10_BWA_covstat.txt &
- /home/kunzhang/softwares/samtools-0.1.19/samtools view -o s_1_1_Indx32_unique.sam s_1_1_Indx32_unique.bam
Summaries of Sequencing Results[edit]
PGP1 Dev8 Oct6: 400mM ALS 8min pump, NS 0min[edit]
bam_file | sample | Raw_Reads | MappingRate | MappableReads | ClonalRate | Unique | 1+ | 1 | 2 | 3 | 4+ | contig | Mito % |
s_1_1_Indx17_sorted.bam | 9 | 217,653 | 81.27% | 176,890 | 2.58% | 172,326 | 7,047,215 | 5,906,698 | 808,250 | 193,693 | 123,844 | 50 | 0.72% |
s_1_1_Indx18_sorted.bam | 10 | 371,006 | 82.14% | 304,742 | 2.77% | 296,301 | 11,816,162 | 9,631,704 | 1,525,191 | 390,584 | 254,448 | 113 | 0.35% |
s_1_1_Indx19_sorted.bam | 11 | 230,506 | 82.31% | 189,741 | 2.49% | 185,016 | 7,609,472 | 6,384,424 | 869,077 | 208,944 | 133,657 | 41 | 0.45% |
s_1_1_Indx20_sorted.bam | 12 | 220,926 | 82.00% | 181,160 | 2.89% | 175,924 | 6,900,560 | 5,585,808 | 889,076 | 239,564 | 171,647 | 77 | 0.64% |
s_1_1_Indx21_sorted.bam | 13 | 241,578 | 82.45% | 199,187 | 2.67% | 193,869 | 7,686,007 | 6,217,752 | 1,019,302 | 270,080 | 164,393 | 80 | 0.64% |
s_1_1_Indx22_sorted.bam | 14 | 290,676 | 83.34% | 242,246 | 3.18% | 234,543 | 8,994,661 | 7,116,771 | 1,254,370 | 357,017 | 250,797 | 123 | 0.81% |
s_1_1_Indx23_sorted.bam | 15 | 358,363 | 82.65% | 296,176 | 3.67% | 285,306 | 10,525,718 | 8,192,296 | 1,461,782 | 457,003 | 398,991 | 172 | 0.65% |
s_1_1_Indx24_sorted.bam | 16 | 423,102 | 84.62% | 358,023 | 4.23% | 342,879 | 11,668,130 | 8,449,278 | 1,926,598 | 656,706 | 619,634 | 282 | 0.65% |
2,353,810 | 1,948,165 | 1,886,164 | 938 | ||||||||||
GM Dev9 Oct10: 400mM ALS 5min pump, NS 2min[edit]
bam_file | sample | Raw_Reads | MappingRate | MappableReads | ClonalRate | Unique | 1+ | 1 | 2 | 3 | 4+ | contig | mito % |
s_1_1_Indx09_sorted.bam | 1 | 1,185,461 | 92.15% | 1,092,352 | 9.88% | 984,428 | 25566539 | 16430816 | 4066655 | 1834422 | 3218141 | 776 | 0.65% |
s_1_1_Indx10_sorted.bam | 2 | 878,051 | 92.41% | 811,404 | 4.22% | 777,163 | 28763373 | 22943333 | 3614129 | 1068962 | 1120592 | 416 | 0.35% |
s_1_1_Indx11_sorted.bam | 3 | 599,446 | 92.85% | 556,598 | 3.51% | 537,061 | 20323989 | 16273884 | 2530109 | 786467 | 717353 | 332 | 0.37% |
s_1_1_Indx12_sorted.bam | 4 | 964,470 | 92.25% | 889,682 | 10.86% | 793,063 | 20340153 | 13258220 | 3172788 | 1393513 | 2499128 | 641 | 0.87% |
s_1_1_Indx13_sorted.bam | 5 | 1,080,380 | 92.43% | 998,608 | 7.60% | 922,714 | 28568106 | 20506465 | 4219661 | 1610385 | 2215033 | 771 | 1.21% |
s_1_1_Indx14_sorted.bam | 6 | 1,371,077 | 91.62% | 1,256,193 | 15.20% | 1,065,252 | 22584672 | 13334265 | 3538903 | 1720474 | 3974593 | 821 | 0.27% |
s_1_1_Indx15_sorted.bam | 7 | 588,560 | 91.64% | 539,373 | 6.66% | 503,451 | 15656188 | 11296394 | 2257865 | 866065 | 1219354 | 420 | 0.82% |
s_1_1_Indx16_sorted.bam | 8 | 1,545,679 | 91.87% | 1,419,958 | 18.28% | 1,160,390 | 18788455 | 8802440 | 3049596 | 1746533 | 5173393 | 828 | 0.43% |
8,213,124 | 7,564,168 | 6,743,520 | 5005 | ||||||||||
GM Dev9.2 Oct23: 400mM ALS 2min pump, NS 2min[edit]
bam_file | sample | Raw_Reads | MappingRate | MappableReads | ClonalRate | Unique | 1+ | 1 | 2 | 3 | 4+ | contig | %Mito |
s_1_1_Indx25_sorted.bam | 17 | 2,268,771 | 85.63% | 1,942,637 | 5.80% | 1,829,964 | 56,939,904 | 38,624,661 | 9,747,120 | 3,911,513 | 4,640,531 | 2,171 | 0.03% |
s_1_1_Indx26_sorted.bam | 18 | 2,547,065 | 88.06% | 2,243,001 | 5.90% | 2,110,664 | 67,415,216 | 47,385,256 | 10,747,954 | 4,188,949 | 5,076,851 | 2,303 | 0.01% |
s_1_1_Indx27_sorted.bam | 19 | 1,995,724 | 88.08% | 1,757,862 | 5.43% | 1,662,410 | 55,980,120 | 40,789,431 | 8,550,722 | 3,115,164 | 3,508,685 | 1,703 | 0.03% |
s_1_1_Indx28_sorted.bam | 20 | 2,174,302 | 89.91% | 1,954,885 | 5.73% | 1,842,870 | 60,416,600 | 43,216,950 | 9,415,231 | 3,580,427 | 4,187,823 | 1,996 | 0.10% |
s_1_1_Indx29_sorted.bam | 21 | 2,536,410 | 88.60% | 2,247,202 | 6.29% | 2,105,853 | 67,628,869 | 47,608,592 | 10,774,494 | 4,165,587 | 5,063,988 | 2,321 | 0.08% |
s_1_1_Indx30_sorted.bam | 22 | 1,313,829 | 87.49% | 1,149,447 | 4.09% | 1,102,435 | 43,912,285 | 35,535,421 | 5,699,823 | 1,558,924 | 1,102,301 | 696 | 0.37% |
s_1_1_Indx31_sorted.bam | 23 | 1,188,929 | 85.01% | 1,010,767 | 3.27% | 977,715 | 42,901,971 | 37,061,123 | 4,595,040 | 884,469 | 347,247 | 264 | 0.43% |
s_1_1_Indx32_sorted.bam | 24 | 426,705 | 77.62% | 331,204 | 2.66% | 322,394 | 15,476,138 | 14,492,916 | 888,468 | 72,504 | 8,817 | 1 | 1.17% |
s_2_1_Indx09_sorted.bam | 1 | 508,645 | 61.59% | 313,270 | 4.54% | 299,048 | 14,135,431 | 12,822,540 | 1,136,402 | 135,215 | 29,071 | 10 | 0.31% |
s_2_1_Indx10_sorted.bam | 2 | 360,292 | 41.22% | 148,525 | 4.37% | 142,034 | 6,934,177 | 6,480,526 | 409,087 | 31,826 | 3,597 | 1 | 0.73% |
s_2_1_Indx11_sorted.bam | 3 | 387,809 | 74.52% | 288,983 | 3.69% | 278,320 | 13,344,475 | 12,368,345 | 867,342 | 80,836 | 16,025 | 4 | 0.55% |
s_2_1_Indx12_sorted.bam | 4 | 1,093,980 | 67.00% | 732,986 | 18.57% | 596,870 | 17,190,892 | 13,473,936 | 1,644,869 | 560,491 | 1,497,723 | 142 | 0.13% |
s_2_1_Indx13_sorted.bam | 5 | 1,795,103 | 85.27% | 1,530,763 | 6.60% | 1,429,733 | 51,709,503 | 39,121,559 | 7,520,564 | 2,484,592 | 2,566,850 | 1,279 | 0.12% |
s_2_1_Indx14_sorted.bam | 6 | 3,304,157 | 87.22% | 2,881,999 | 9.73% | 2,601,580 | 76,011,471 | 50,543,658 | 12,444,999 | 5,128,658 | 7,877,626 | 2,779 | 0.12% |
s_2_1_Indx15_sorted.bam | 7 | 2,897,378 | 87.71% | 2,541,382 | 7.36% | 2,354,336 | 69,608,776 | 46,854,101 | 11,277,938 | 4,695,723 | 6,764,564 | 2,626 | 0.06% |
s_2_1_Indx16_sorted.bam | 8 | 3,382,065 | 87.18% | 2,948,364 | 9.04% | 2,681,832 | 78,729,729 | 52,386,358 | 13,008,853 | 5,347,651 | 7,970,352 | 2,806 | 0.04% |
s_2_1_Indx17_sorted.bam | 9 | 885,232 | 86.87% | 769,024 | 3.87% | 739,263 | 26,960,544 | 20,271,643 | 4,260,105 | 1,355,620 | 1,057,682 | 680 | 0.27% |
s_2_1_Indx18_sorted.bam | 10 | 2,033,809 | 89.00% | 1,810,131 | 5.09% | 1,717,995 | 54,860,118 | 37,624,975 | 9,510,274 | 3,695,378 | 4,013,336 | 2,048 | 0.12% |
s_2_1_Indx19_sorted.bam | 11 | 1,104,616 | 87.81% | 969,970 | 4.04% | 930,783 | 32,901,124 | 24,216,566 | 5,351,552 | 1,778,372 | 1,538,740 | 925 | 0.21% |
s_2_1_Indx20_sorted.bam | 12 | 718,629 | 85.01% | 610,922 | 3.56% | 589,173 | 21,917,337 | 16,668,103 | 3,432,954 | 1,054,018 | 746,987 | 513 | 0.36% |
s_2_1_Indx21_sorted.bam | 13 | 1,226,760 | 86.29% | 1,058,547 | 4.69% | 1,008,901 | 33,196,721 | 23,064,173 | 5,843,270 | 2,158,328 | 2,114,817 | 1,184 | 0.25% |
s_2_1_Indx22_sorted.bam | 14 | 1,620,467 | 89.25% | 1,446,193 | 5.80% | 1,362,314 | 40,539,964 | 26,360,341 | 7,417,732 | 3,044,398 | 3,701,075 | 1,703 | 0.12% |
s_2_1_Indx23_sorted.bam | 15 | 1,340,858 | 88.27% | 1,183,591 | 4.87% | 1,125,950 | 36,266,426 | 24,846,902 | 6,416,637 | 2,448,570 | 2,538,568 | 1,390 | 0.07% |
s_2_1_Indx24_sorted.bam | 16 | 1,192,263 | 88.23% | 1,051,952 | 4.26% | 1,007,139 | 35,107,570 | 25,384,683 | 5,916,287 | 2,037,745 | 1,753,258 | 1,077 | 0.06% |
38,303,798 | 32,923,607 | 30622 | |||||||||||
GM Dev9.2 Nov4: 400mM ALS 8min pump, NS 3min[edit]
- low CORE PCR amplification
bam_file | sample | Raw_Reads | MappingRate | MappableReads | ClonalRate | Unique | 1+ | 1 | 2 | 3 | 4+ | contig | mito % |
s_3_1_Indx09_sorted.bam | 1 | 110,070 | 4.84% | 5,330 | 3.32% | 5,153 | 255953 | 245877 | 9123 | 622 | 31 | 0 | 0.13% |
s_3_1_Indx10_sorted.bam | 2 | 332,866 | 55.14% | 183,556 | 4.20% | 175,847 | 7453084 | 6321882 | 806591 | 190239 | 122142 | 22 | 0.39% |
s_3_1_Indx11_sorted.bam | 3 | 460,758 | 80.39% | 370,384 | 4.16% | 354,976 | 14587217 | 12269866 | 1573040 | 399301 | 331527 | 169 | 0.26% |
s_3_1_Indx12_sorted.bam | 4 | 965,330 | 54.95% | 530,424 | 7.28% | 491,809 | 16263741 | 11978596 | 2370093 | 825767 | 1077220 | 450 | 0.17% |
s_3_1_Indx13_sorted.bam | 5 | 1,923,409 | 76.66% | 1,474,453 | 15.67% | 1,243,406 | 29453843 | 19210771 | 4281355 | 1855084 | 4090991 | 1324 | 0.28% |
s_3_1_Indx14_sorted.bam | 6 | 679,544 | 80.26% | 545,421 | 5.21% | 517,005 | 21140487 | 17480980 | 2519059 | 631775 | 498159 | 245 | 0.08% |
s_3_1_Indx15_sorted.bam | 7 | 1,159,520 | 85.68% | 993,493 | 4.64% | 947,395 | 36032772 | 29055149 | 4370547 | 1292742 | 1299267 | 651 | 0.13% |
s_3_1_Indx16_sorted.bam | 8 | 928,796 | 84.75% | 787,193 | 6.15% | 738,781 | 26443068 | 20147608 | 3803834 | 1207322 | 1268579 | 600 | 0.25% |
s_3_1_Indx17_sorted.bam | 9 | 794,505 | 84.09% | 668,073 | 5.51% | 631,262 | 21932814 | 16561780 | 3126181 | 1037045 | 1194341 | 556 | 0.12% |
s_3_1_Indx18_sorted.bam | 10 | 1,569,518 | 88.26% | 1,385,267 | 5.45% | 1,309,770 | 47917306 | 37135195 | 6662422 | 2040576 | 2063795 | 1000 | 0.11% |
s_3_1_Indx19_sorted.bam | 11 | 1,183,076 | 0.32% | 3,831 | 0.16% | 3,825 | 191034 | 190324 | 332 | 78 | 0 | 0.16% | |
s_3_1_Indx20_sorted.bam | 12 | 135,557 | 31.07% | 42,115 | 2.85% | 40,915 | 1984818 | 1873010 | 97715 | 8396 | 1531 | 1 | 0.24% |
s_3_1_Indx21_sorted.bam | 13 | 95,795 | 0.89% | 855 | 0.00% | 855 | 42583 | 42447 | 114 | 22 | 0 | 0.00% | |
s_3_1_Indx22_sorted.bam | 14 | 556,870 | 80.33% | 447,328 | 5.60% | 422,278 | 14746902 | 11162550 | 2071520 | 703187 | 795206 | 306 | 0.41% |
s_3_1_Indx23_sorted.bam | 15 | 1,037,726 | 81.74% | 848,236 | 6.75% | 790,980 | 27063965 | 20208722 | 4001782 | 1334142 | 1503184 | 697 | 0.46% |
s_3_1_Indx24_sorted.bam | 16 | 1,313,949 | 85.33% | 1,121,140 | 6.45% | 1,048,826 | 35312566 | 25996780 | 5330442 | 1818630 | 2151963 | 957 | 0.10% |
s_3_1_Indx25_sorted.bam | 17 | 1,672,936 | 70.26% | 1,175,469 | 9.94% | 1,058,627 | 34310453 | 24458278 | 5477130 | 1930358 | 2430398 | 990 | 0.13% |
s_3_1_Indx26_sorted.bam | 18 | 1,419,693 | 73.97% | 1,050,213 | 9.61% | 949,288 | 31115473 | 22185808 | 4956077 | 1754889 | 2202589 | 894 | 0.20% |
s_3_1_Indx27_sorted.bam | 19 | 1,689,562 | 80.27% | 1,356,208 | 10.76% | 1,210,280 | 37695760 | 26164066 | 6220501 | 2263050 | 3032491 | 1207 | 0.21% |
s_3_1_Indx28_sorted.bam | 20 | 972,314 | 29.47% | 286,549 | 6.59% | 267,665 | 11156416 | 9165117 | 1386360 | 342305 | 252877 | 114 | 0.15% |
s_3_1_Indx29_sorted.bam | 21 | 1,686,064 | 45.78% | 771,923 | 9.90% | 695,503 | 25013350 | 19014006 | 3611709 | 1123776 | 1248028 | 486 | 0.34% |
s_3_1_Indx30_sorted.bam | 22 | 579,133 | 38.71% | 224,175 | 6.87% | 208,774 | 9127430 | 7725766 | 1041858 | 215921 | 129318 | 54 | 0.47% |
s_3_1_Indx31_sorted.bam | 23 | 801,090 | 18.83% | 150,859 | 6.08% | 141,687 | 6637633 | 5906835 | 602699 | 86177 | 30258 | 11 | 0.35% |
s_3_1_Indx32_sorted.bam | 24 | 588,577 | 4.28% | 25,180 | 5.49% | 23,798 | 1182222 | 1108671 | 65151 | 4352 | 623 | 1 | 0.31% |
22,656,658 | 10735 | ||||||||||||
GM Dev9 Nov14: 8ul ALS 3min, no NS neutralization, chamber 10&11 not collected so index 18&19 should not appear[edit]
bam_file | sample | Raw_Reads | MappingRate | MappableReads | ClonalRate | Unique | 1+ | 1 | 2 | 3 | 4+ | contig | mito % |
s_4_1_Indx09_sorted.bam | 1 | 856,758 | 30.14% | 258,203 | 3.44% | 249,321 | 11,176,695 | 9,821,709 | 1,083,615 | 195,008 | 66,237 | 43 | 0.16% |
s_4_1_Indx10_sorted.bam | 2 | 963,484 | 43.45% | 418,661 | 3.73% | 403,045 | 17,366,969 | 14,720,689 | 2,014,268 | 439,046 | 179,245 | 134 | 0.18% |
s_4_1_Indx11_sorted.bam | 3 | 694,992 | 60.77% | 422,353 | 3.24% | 408,669 | 17,493,599 | 14,844,533 | 2,009,564 | 440,433 | 188,026 | 133 | 0.10% |
s_4_1_Indx12_sorted.bam | 4 | 1,182,379 | 77.06% | 911,174 | 4.20% | 872,905 | 34,541,244 | 27,595,022 | 4,654,848 | 1,365,371 | 911,299 | 437 | 0.11% |
s_4_1_Indx13_sorted.bam | 5 | 950,557 | 59.35% | 564,124 | 3.92% | 542,010 | 22,882,839 | 19,035,533 | 2,898,452 | 652,726 | 286,774 | 209 | 0.06% |
s_4_1_Indx14_sorted.bam | 6 | 1,275,809 | 64.17% | 818,642 | 3.84% | 787,206 | 31,918,636 | 25,692,721 | 4,452,347 | 1,169,802 | 591,266 | 385 | 0.06% |
s_4_1_Indx15_sorted.bam | 7 | 1,054,052 | 58.84% | 620,245 | 3.16% | 600,645 | 24,996,063 | 20,674,313 | 3,195,915 | 769,784 | 345,098 | 258 | 0.07% |
s_4_1_Indx16_sorted.bam | 8 | 1,300,089 | 85.04% | 1,105,629 | 4.55% | 1,055,323 | 40,530,314 | 31,436,254 | 5,925,358 | 1,865,041 | 1,290,022 | 677 | 0.07% |
s_4_1_Indx17_sorted.bam | 9 | 948,303 | 82.92% | 786,354 | 5.57% | 742,554 | 26,237,029 | 18,530,807 | 4,791,007 | 1,668,497 | 1,231,609 | 552 | 0.14% |
s_4_1_Indx18_sorted.bam | 10 | 977,363 | 63.15% | 617,224 | 1.40% | 608,583 | 28,601,880 | 26,667,648 | 1,706,679 | 175,246 | 39,592 | 24 | 0.09% |
s_4_1_Indx19_sorted.bam | 11 | 284,548 | 78.28% | 222,731 | 2.83% | 216,428 | 9,557,295 | 8,281,352 | 1,039,203 | 178,065 | 47,811 | 42 | 0.17% |
s_4_1_Indx20_sorted.bam | 12 | 249 | 35.34% | 88 | 0.00% | 88 | 4,398 | 4,398 | 0 | 0.00% | |||
s_4_1_Indx21_sorted.bam | 13 | 444,712 | 78.54% | 349,290 | 3.79% | 336,052 | 14,037,639 | 11,503,571 | 1,914,841 | 438,080 | 168,595 | 128 | 0.17% |
s_4_1_Indx22_sorted.bam | 14 | 1,682,346 | 50.71% | 853,080 | 4.10% | 818,104 | 35,752,237 | 30,537,535 | 4,083,737 | 811,761 | 305,529 | 209 | 0.10% |
s_4_1_Indx23_sorted.bam | 15 | 1,476,044 | 65.32% | 964,146 | 5.48% | 911,311 | 35,170,224 | 26,665,568 | 5,792,584 | 1,713,845 | 984,781 | 620 | 0.07% |
s_4_1_Indx24_sorted.bam | 16 | 1,318,194 | 80.74% | 1,064,298 | 6.03% | 1,000,121 | 35,208,227 | 24,848,879 | 6,326,891 | 2,242,352 | 1,774,514 | 761 | 0.13% |
s_4_1_Indx25_sorted.bam | 17 | 2,218,236 | 79.03% | 1,752,966 | 4.55% | 1,673,206 | 61,942,679 | 46,981,932 | 9,355,110 | 3,137,461 | 2,456,587 | 1032 | 0.03% |
s_4_1_Indx26_sorted.bam | 18 | 1,419,252 | 71.68% | 1,017,304 | 4.02% | 976,408 | 38,562,194 | 30,474,813 | 5,595,187 | 1,573,147 | 903,417 | 565 | 0.14% |
s_4_1_Indx27_sorted.bam | 19 | 1,130,690 | 67.03% | 757,926 | 4.31% | 725,259 | 27,519,893 | 21,000,452 | 4,314,284 | 1,336,301 | 854,618 | 452 | 0.12% |
s_4_1_Indx28_sorted.bam | 20 | 764,912 | 52.76% | 403,584 | 3.59% | 389,095 | 16,528,651 | 13,931,738 | 1,919,996 | 450,700 | 213,709 | 159 | 0.14% |
s_4_1_Indx29_sorted.bam | 21 | 870,457 | 51.26% | 446,185 | 4.51% | 426,062 | 16,268,933 | 12,577,192 | 2,414,077 | 757,295 | 503,987 | 302 | 0.63% |
s_4_1_Indx30_sorted.bam | 22 | 711,139 | 33.11% | 235,467 | 3.73% | 226,684 | 9,305,283 | 7,653,781 | 1,162,244 | 307,151 | 168,388 | 97 | 0.33% |
s_4_1_Indx31_sorted.bam | 23 | 670,998 | 34.81% | 233,574 | 3.36% | 225,726 | 9,681,494 | 8,213,401 | 1,092,940 | 257,746 | 105,485 | 78 | 0.21% |
s_4_1_Indx32_sorted.bam | 24 | 691,808 | 15.33% | 106,044 | 2.47% | 103,425 | 4,756,473 | 4,308,516 | 366,651 | 53,947 | 14,630 | 10 | 0.61% |
23,887,371 | 14,298,230 | 7307 | |||||||||||
GM Dev9 Nov18: 6ul ALS 4min pump, no NS neutralization[edit]
bam_file | sample | Raw_Reads | MappingRate | MappableReads | ClonalRate | Unique | 1+ | 1 | 2 | 3 | 4+ | contig | mito % |
s_5_1_Indx09_sorted.bam | 1 | 566,131 | 92.05% | 521,143 | 2.04% | 510,512 | 22622085 | 19949789 | 2144432 | 377534 | 142099 | 125 | 0.05% |
s_5_1_Indx10_sorted.bam | 2 | 582,196 | 91.82% | 534,577 | 2.07% | 523,511 | 23388189 | 20764386 | 2130723 | 357486 | 127007 | 95 | 0.05% |
s_5_1_Indx11_sorted.bam | 3 | 456,504 | 93.10% | 424,992 | 1.81% | 417,300 | 18981401 | 17142287 | 1523148 | 231991 | 73967 | 52 | 0.09% |
s_5_1_Indx12_sorted.bam | 4 | 643,392 | 92.53% | 595,316 | 2.15% | 582,517 | 25823907 | 22813732 | 2400712 | 424437 | 175243 | 117 | 0.06% |
s_5_1_Indx13_sorted.bam | 5 | 629,502 | 92.54% | 582,530 | 2.05% | 570,588 | 25666989 | 22896028 | 2277686 | 363154 | 120015 | 102 | 0.06% |
s_5_1_Indx14_sorted.bam | 6 | 637,561 | 92.52% | 589,901 | 2.17% | 577,100 | 25564795 | 22555793 | 2411714 | 417001 | 168493 | 119 | 0.08% |
s_5_1_Indx15_sorted.bam | 7 | 453,520 | 92.75% | 420,626 | 1.86% | 412,802 | 18884198 | 17130188 | 1472741 | 207014 | 65355 | 38 | 0.07% |
s_5_1_Indx16_sorted.bam | 8 | 650,948 | 92.55% | 602,431 | 2.16% | 589,418 | 26032634 | 22867514 | 2540425 | 445133 | 171134 | 132 | 0.05% |
s_5_1_Indx17_sorted.bam | 9 | 2,346,039 | 92.67% | 2,174,001 | 3.56% | 2,096,607 | 75589163 | 56259760 | 12358534 | 3919313 | 3037597 | 2018 | 0.04% |
s_5_1_Indx18_sorted.bam | 10 | 2,817,253 | 92.65% | 2,610,104 | 4.06% | 2,504,134 | 85225081 | 60441703 | 14963201 | 5239476 | 4566042 | 2716 | 0.04% |
s_5_1_Indx19_sorted.bam | 11 | 2,169,373 | 92.62% | 2,009,212 | 3.39% | 1,941,100 | 70876027 | 52967667 | 11676292 | 3631519 | 2584197 | 1902 | 0.11% |
s_5_1_Indx20_sorted.bam | 12 | 2,361,125 | 93.05% | 2,197,121 | 3.88% | 2,111,873 | 73803630 | 53592258 | 12547968 | 4178710 | 3469268 | 2267 | 0.07% |
s_5_1_Indx21_sorted.bam | 13 | 1,611,752 | 93.04% | 1,499,635 | 3.60% | 1,445,648 | 52862674 | 39877632 | 8402048 | 2590210 | 1980382 | 1310 | 0.04% |
s_5_1_Indx22_sorted.bam | 14 | 2,507,782 | 92.54% | 2,320,719 | 3.98% | 2,228,354 | 75797660 | 53742181 | 13299752 | 4641405 | 4100391 | 2497 | 0.04% |
s_5_1_Indx23_sorted.bam | 15 | 7,376 | 80.78% | 5,958 | 0.13% | 5,950 | 296822 | 295568 | 952 | 0 | 0.12% | ||
s_5_1_Indx24_sorted.bam | 16 | 23,667 | 84.85% | 20,081 | 0.52% | 19,977 | 990882 | 977245 | 11788 | 347 | 114 | 0 | 0.14% |
s_5_1_Indx25_sorted.bam | 17 | 1,140,848 | 93.13% | 1,062,426 | 2.84% | 1,032,253 | 41587790 | 33882811 | 5480352 | 1399794 | 810090 | 633 | 0.09% |
s_5_1_Indx26_sorted.bam | 18 | 1,019,979 | 92.82% | 946,728 | 2.58% | 922,302 | 37546283 | 30956173 | 4738626 | 1163567 | 672624 | 478 | 0.15% |
s_5_1_Indx27_sorted.bam | 19 | 2,086,116 | 92.98% | 1,939,644 | 3.80% | 1,865,938 | 66385622 | 49500299 | 10418414 | 3452195 | 2999253 | 1863 | 0.08% |
s_5_1_Indx28_sorted.bam | 20 | 1,758,276 | 92.50% | 1,626,387 | 3.79% | 1,564,747 | 56174975 | 42247364 | 8743766 | 2803247 | 2366358 | 1484 | 0.05% |
s_5_1_Indx29_sorted.bam | 21 | 1,889,043 | 91.69% | 1,732,053 | 3.99% | 1,662,944 | 58934208 | 43860043 | 9269312 | 3077560 | 2712307 | 1626 | 0.08% |
s_5_1_Indx30_sorted.bam | 22 | 1,891,903 | 92.36% | 1,747,380 | 4.09% | 1,675,912 | 58338925 | 43070298 | 9201837 | 3127366 | 2923698 | 1758 | 0.10% |
s_5_1_Indx31_sorted.bam | 23 | 1,527,048 | 90.98% | 1,389,356 | 3.53% | 1,340,312 | 49437651 | 38084465 | 7219354 | 2259160 | 1860052 | 1212 | 0.08% |
s_5_1_Indx32_sorted.bam | 24 | 764,860 | 90.73% | 693,971 | 2.62% | 675,789 | 27969607 | 23575307 | 3148383 | 764504 | 467033 | 340 | 0.16% |
30,542,194 | 27,277,587 | 22884 | |||||||||||
GM Dev9 Dec2: 8ul ALS 4min pump, no NS neutralization, half concentrations of dNTP, random hexamers, and dUTP[edit]
- highest overlapping fragments
bam_file | sample | Raw_Reads | MappingRate | MappableReads | ClonalRate | Unique | 1+ | 1 | 2 | 3 | 4+ | contig | mito % |
s_6_1_Indx09_sorted.bam | 1 | 147,354 | 91.75% | 135,198 | 2.11% | 132,345 | 6461119 | 6178418 | 267142 | 13161 | 1181 | 1 | 0.02% |
s_6_1_Indx10_sorted.bam | 2 | 261,254 | 91.64% | 239,421 | 2.36% | 233,771 | 10895835 | 9985035 | 780195 | 102630 | 26266 | 21 | 0.02% |
s_6_1_Indx11_sorted.bam | 3 | 318,449 | 93.12% | 296,553 | 2.77% | 288,338 | 12390788 | 10687966 | 1253133 | 289010 | 156833 | 130 | 0.03% |
s_6_1_Indx12_sorted.bam | 4 | 703,962 | 92.54% | 651,464 | 3.25% | 630,291 | 25352366 | 20532246 | 3384627 | 903397 | 523122 | 399 | 0.04% |
s_6_1_Indx13_sorted.bam | 5 | 827,645 | 92.61% | 766,495 | 3.30% | 741,201 | 29446260 | 23557332 | 4102560 | 1123707 | 655998 | 495 | 0.02% |
s_6_1_Indx14_sorted.bam | 6 | 801,723 | 92.49% | 741,482 | 3.16% | 718,051 | 29350482 | 23996984 | 3848518 | 989884 | 510334 | 419 | 0.02% |
s_6_1_Indx15_sorted.bam | 7 | 1,082,996 | 92.76% | 1,004,553 | 2.99% | 974,517 | 39264350 | 31607388 | 5522735 | 1430204 | 700437 | 577 | 0.01% |
s_6_1_Indx16_sorted.bam | 8 | 1,654,085 | 93.32% | 1,543,581 | 3.21% | 1,494,032 | 59585243 | 47316719 | 8833250 | 2303076 | 1125708 | 911 | 0.01% |
s_6_1_Indx17_sorted.bam | 9 | 367,635 | 92.12% | 338,649 | 2.36% | 330,657 | 15073189 | 13481813 | 1363334 | 188433 | 35871 | 25 | 0.02% |
s_6_1_Indx18_sorted.bam | 10 | 811,866 | 92.36% | 749,857 | 2.81% | 728,786 | 30753727 | 25774917 | 3781051 | 841453 | 352186 | 324 | 0.01% |
s_6_1_Indx19_sorted.bam | 11 | 381,391 | 92.43% | 352,530 | 2.43% | 343,964 | 15353188 | 13475727 | 1562042 | 249849 | 62901 | 59 | 0.02% |
s_6_1_Indx20_sorted.bam | 12 | 1,085,834 | 92.78% | 1,007,399 | 3.68% | 970,327 | 35660274 | 26511538 | 5985125 | 1886258 | 1267358 | 783 | 0.04% |
s_6_1_Indx21_sorted.bam | 13 | 1,285,766 | 92.96% | 1,195,184 | 3.78% | 1,150,006 | 42558543 | 32486983 | 6390013 | 2046628 | 1626207 | 817 | 0.02% |
s_6_1_Indx22_sorted.bam | 14 | 1,023,874 | 92.68% | 948,955 | 4.39% | 907,296 | 31090070 | 21933905 | 5551413 | 1971246 | 1626269 | 829 | 0.02% |
s_6_1_Indx23_sorted.bam | 15 | 1,309,026 | 92.98% | 1,217,093 | 5.01% | 1,156,117 | 36506085 | 24204720 | 6838820 | 2703092 | 2753135 | 1122 | 0.01% |
s_6_1_Indx24_sorted.bam | 16 | 1,467,281 | 92.75% | 1,360,870 | 6.31% | 1,274,999 | 35758012 | 21928984 | 6849748 | 3041761 | 3923949 | 1175 | 0.05% |
s_6_1_Indx25_sorted.bam | 17 | 698,050 | 92.52% | 645,814 | 3.23% | 624,954 | 25335784 | 20661100 | 3310609 | 876261 | 479893 | 382 | 0.04% |
s_6_1_Indx26_sorted.bam | 18 | 1,277,715 | 93.05% | 1,188,916 | 4.67% | 1,133,394 | 38411904 | 27698065 | 6092392 | 2300275 | 2313090 | 929 | 0.02% |
s_6_1_Indx27_sorted.bam | 19 | 445,570 | 92.65% | 412,840 | 3.20% | 399,629 | 16067503 | 13125725 | 2005888 | 565432 | 360211 | 260 | 0.08% |
s_6_1_Indx28_sorted.bam | 20 | 442,411 | 92.72% | 410,188 | 3.66% | 395,175 | 15067143 | 11800147 | 2102448 | 656830 | 495772 | 321 | 0.12% |
s_6_1_Indx29_sorted.bam | 21 | 666,668 | 92.93% | 619,561 | 4.69% | 590,504 | 20484626 | 15068126 | 3108547 | 1166225 | 1132370 | 556 | 0.05% |
s_6_1_Indx30_sorted.bam | 22 | 620,288 | 92.97% | 576,707 | 4.14% | 552,831 | 19696269 | 14719563 | 2953765 | 1064866 | 948488 | 536 | 0.05% |
s_6_1_Indx31_sorted.bam | 23 | 420,564 | 92.66% | 389,687 | 3.47% | 376,165 | 15017005 | 12233581 | 1868184 | 536051 | 368516 | 246 | 0.10% |
s_6_1_Indx32_sorted.bam | 24 | 150,023 | 92.52% | 138,796 | 2.10% | 135,881 | 6487605 | 6092573 | 345055 | 37818 | 8815 | 5 | 0.05% |
18,251,430 | 11322 | ||||||||||||
GM Dev9 Dec3: 8ul ALS 4min pump, no NS neutralization[edit]
bam_file | sample | Raw_Reads | MappingRate | MappableReads | ClonalRate | Unique | 1+ | 1 | 2 | 3 | 4+ | contig | mito % |
s_7_1_Indx09_sorted.bam | 1 | 466,433 | 91.61% | 427,297 | 2.69% | 415,803 | 18748607 | 16680272 | 1704424 | 265373 | 82137 | 67 | 0.51% |
s_7_1_Indx10_sorted.bam | 2 | 1,480,440 | 91.94% | 1,361,144 | 5.69% | 1,283,695 | 38297341 | 24337528 | 7383041 | 3089792 | 3470526 | 1532 | 0.23% |
s_7_1_Indx11_sorted.bam | 3 | 590,938 | 91.82% | 542,621 | 4.35% | 519,017 | 17419400 | 12099881 | 3151858 | 1159602 | 992266 | 576 | 0.27% |
s_7_1_Indx12_sorted.bam | 4 | 1,003,355 | 91.82% | 921,232 | 7.45% | 852,600 | 21650089 | 12473391 | 4088303 | 1982639 | 3089327 | 853 | 0.38% |
s_7_1_Indx13_sorted.bam | 5 | 999,028 | 92.01% | 919,203 | 7.04% | 854,491 | 22484410 | 13379787 | 4194695 | 1974126 | 2919345 | 866 | 0.44% |
s_7_1_Indx14_sorted.bam | 6 | 1,167,131 | 92.32% | 1,077,530 | 8.40% | 987,017 | 24057372 | 13724938 | 4398430 | 2185016 | 3732471 | 874 | 0.54% |
s_7_1_Indx15_sorted.bam | 7 | 1,174,380 | 92.64% | 1,087,999 | 6.12% | 1,021,413 | 29510071 | 18575229 | 5605243 | 2412798 | 2900262 | 1121 | 0.58% |
s_7_1_Indx16_sorted.bam | 8 | 810,580 | 92.05% | 746,113 | 4.70% | 711,046 | 23573340 | 16359858 | 4143780 | 1574717 | 1479208 | 714 | 0.22% |
s_7_1_Indx17_sorted.bam | 9 | 1,389,135 | 91.63% | 1,272,889 | 8.73% | 1,161,766 | 27540134 | 14995651 | 5324564 | 2680854 | 4522517 | 1128 | 0.60% |
s_7_1_Indx18_sorted.bam | 10 | 836,387 | 90.35% | 755,667 | 7.57% | 698,463 | 17800371 | 10135876 | 3441141 | 1664788 | 2542009 | 713 | 0.70% |
s_7_1_Indx19_sorted.bam | 11 | 1,202,752 | 92.26% | 1,109,682 | 10.37% | 994,608 | 21935689 | 11550954 | 4195042 | 2152820 | 4020323 | 905 | 0.96% |
s_7_1_Indx20_sorted.bam | 12 | 1,472,508 | 92.30% | 1,359,052 | 9.73% | 1,226,816 | 26309658 | 13313935 | 4978521 | 2683507 | 5317179 | 950 | 0.31% |
s_7_1_Indx21_sorted.bam | 13 | 446,606 | 90.18% | 402,746 | 5.80% | 379,387 | 11638201 | 7580388 | 2194669 | 892143 | 954743 | 484 | 0.66% |
s_7_1_Indx22_sorted.bam | 14 | 1,001,886 | 91.63% | 918,023 | 8.52% | 839,807 | 19877277 | 10679954 | 3862575 | 1966238 | 3351971 | 813 | 0.65% |
s_7_1_Indx23_sorted.bam | 15 | 1,240,713 | 91.08% | 1,130,020 | 10.07% | 1,016,227 | 23120319 | 12602995 | 4193545 | 2177034 | 4130194 | 888 | 0.61% |
s_7_1_Indx24_sorted.bam | 16 | 260,487 | 86.91% | 226,389 | 4.65% | 215,862 | 7558618 | 5409845 | 1317898 | 458331 | 356452 | 227 | 0.72% |
s_7_1_Indx25_sorted.bam | 17 | 232,615 | 90.11% | 209,618 | 3.60% | 202,072 | 7836636 | 6164401 | 1108529 | 333841 | 214436 | 159 | 0.65% |
s_7_1_Indx26_sorted.bam | 18 | 347,852 | 92.12% | 320,444 | 4.43% | 306,248 | 10581532 | 7717357 | 1673693 | 601822 | 572533 | 303 | 0.66% |
s_7_1_Indx27_sorted.bam | 19 | 180,464 | 91.21% | 164,594 | 3.87% | 158,224 | 5897663 | 4513449 | 878544 | 285987 | 203677 | 154 | 1.15% |
s_7_1_Indx28_sorted.bam | 20 | 211,830 | 92.24% | 195,399 | 4.23% | 187,134 | 6599973 | 4804263 | 1095359 | 380608 | 303970 | 209 | 1.10% |
s_7_1_Indx29_sorted.bam | 21 | 5,415,501 | 93.35% | 5,055,161 | 3.31% | 4,887,835 | 201810935 | 166445591 | 26049371 | 6006115 | 3293382 | 2351 | 0.06% |
s_7_1_Indx30_sorted.bam | 22 | 229,824 | 92.02% | 211,484 | 4.17% | 202,665 | 7099611 | 5208051 | 1123369 | 405378 | 346533 | 216 | 1.22% |
s_7_1_Indx31_sorted.bam | 23 | 138,962 | 90.20% | 125,350 | 3.98% | 120,361 | 4749075 | 3946664 | 493809 | 146315 | 146519 | 78 | 1.18% |
s_7_1_Indx32_sorted.bam | 24 | 20,719 | 71.15% | 14,741 | 2.27% | 14,406 | 696958 | 658971 | 27808 | 3109 | 1021 | 2 | 1.18% |
22,320,526 | 19,256,964 | 16183 | |||||||||||
GM Dev7 Dec9: 400mM ALS 5min pump, NS 1min[edit]
- Chamber 1 empty
bam_file | sample | Raw_Reads | MappingRate | MappableReads | ClonalRate | Unique | 1+ | 1 | 2 | 3 | 4+ | contig | mito % | Index Mixed |
s_8_1_Indx09_sorted.bam | 1 | 55,429 | 85.20% | 47227 | 18.00% | 38,726 | 1,107,170 | 820,229 | 149,001 | 48,647 | 72,914 | 27 | 10.55% | low raw reads |
s_8_1_Indx10_sorted.bam | 2 | 363,102 | 89.68% | 325629 | 22.60% | 252,037 | 5,697,031 | 3,865,026 | 681,604 | 310,276 | 823,580 | 186 | 3.64% | xx |
s_8_1_Indx11_sorted.bam | 3 | 616,785 | 89.79% | 553785 | 37.15% | 348,054 | 5,290,986 | 2,965,348 | 709,072 | 348,472 | 1,251,532 | 236 | 11.27% | xx |
s_8_1_Indx12_sorted.bam | 4 | 639,054 | 79.26% | 506522 | 35.23% | 328,074 | 5,437,202 | 3,091,442 | 764,967 | 376,217 | 1,188,024 | 181 | 2.97% | xx |
s_8_1_Indx13_sorted.bam | 5 | 793,528 | 90.18% | 715603 | 53.84% | 330,322 | 4,000,233 | 2,184,998 | 471,816 | 235,297 | 1,091,554 | 140 | 15.09% | xx |
s_8_1_Indx14_sorted.bam | 6 | 842,206 | 84.76% | 713860 | 58.48% | 296,395 | 3,613,379 | 2,072,545 | 415,794 | 190,341 | 918,152 | 108 | 7.41% | 9-13,15-16,18,24-32 |
s_8_1_Indx15_sorted.bam | 7 | 406,229 | 74.15% | 301204 | 41.75% | 175,451 | 2,751,294 | 1,523,115 | 393,313 | 193,149 | 625,155 | 130 | 16.65% | 9-14,16,25-32 |
s_8_1_Indx16_sorted.bam | 8 | 778,443 | 89.42% | 696102 | 51.32% | 338,862 | 3,808,996 | 2,002,178 | 467,898 | 224,431 | 1,097,925 | 137 | 13.70% | xx |
s_8_1_Indx17_sorted.bam | 9 | 402,019 | 90.57% | 364118 | 41.73% | 212,172 | 2,532,525 | 1,120,688 | 352,538 | 205,494 | 837,244 | 121 | 10.73% | xx |
s_8_1_Indx18_sorted.bam | 10 | 1,652 | 79.90% | 1320 | 1.29% | 1,303 | 58,727 | 50,607 | 2,588 | 345 | 605 | 0 | 8.33% | low raw reads |
s_8_1_Indx19_sorted.bam | 11 | 86,304 | 88.27% | 76180 | 37.74% | 47,430 | 770,363 | 383,218 | 125,281 | 66,202 | 179,137 | 49 | 19.22% | xx |
s_8_1_Indx20_sorted.bam | 12 | 933,639 | 87.19% | 814042 | 48.70% | 417,604 | 4,309,063 | 1,862,936 | 542,539 | 323,752 | 1,563,274 | 164 | 4.86% | 9-16,24-32 |
s_8_1_Indx21_sorted.bam | 13 | 1,029,835 | 89.07% | 917324 | 89.96% | 92,099 | 784,154 | 447,249 | 60,381 | 29,543 | 230,413 | 36 | 47.08% | 9-16,22,24-32 |
s_8_1_Indx22_sorted.bam | 14 | 1,111,235 | 87.17% | 968664 | 66.04% | 328,958 | 3,183,958 | 1,568,194 | 333,851 | 177,467 | 1,087,878 | 114 | 10.85% | xx |
s_8_1_Indx23_sorted.bam | 15 | 928,597 | 78.47% | 728628 | 70.51% | 214,872 | 2,006,042 | 935,234 | 228,001 | 124,912 | 701,327 | 118 | 23.49% | 9-16,22,24-32 |
s_8_1_Indx24_sorted.bam | 16 | 1,011,523 | 85.73% | 867225 | 75.81% | 209,782 | 2,042,121 | 1,026,773 | 229,918 | 116,420 | 652,448 | 91 | 10.97% | >75% clonal |
s_8_1_Indx25_sorted.bam | 17 | 590,735 | 87.20% | 515128 | 58.60% | 213,263 | 2,813,647 | 1,573,750 | 341,258 | 169,360 | 712,711 | 134 | 24.66% | xx |
s_8_1_Indx26_sorted.bam | 18 | 491,923 | 90.38% | 444596 | 50.41% | 220,475 | 2,487,677 | 1,189,391 | 297,802 | 164,951 | 818,973 | 90 | 13.74% | 9-14,16,25,27-32 |
s_8_1_Indx27_sorted.bam | 19 | 279,340 | 88.78% | 248006 | 46.89% | 131,716 | 1,978,352 | 1,131,928 | 254,584 | 128,622 | 446,677 | 72 | 9.70% | 28 |
s_8_1_Indx28_sorted.bam | 20 | 587,246 | 84.86% | 498360 | 56.16% | 218,481 | 2,832,723 | 1,610,306 | 344,360 | 165,683 | 695,810 | 138 | 13.83% | >50% clonal |
s_8_1_Indx29_sorted.bam | 21 | 994,877 | 62.80% | 624806 | 70.82% | 182,318 | 2,571,653 | 1,654,575 | 302,756 | 119,277 | 478,482 | 63 | 18.89% | >70% clonal |
s_8_1_Indx30_sorted.bam | 22 | 780,802 | 87.65% | 684397 | 84.12% | 108,682 | 1,816,796 | 1,302,856 | 188,087 | 69,584 | 239,701 | 39 | 51.69% | >80% clonal |
s_8_1_Indx31_sorted.bam | 23 | 630,217 | 87.60% | 552075 | 45.32% | 301,875 | 3,879,471 | 1,993,876 | 515,970 | 270,653 | 1,082,431 | 203 | 8.82% | xx |
s_8_1_Indx32_sorted.bam | 24 | 532,173 | 78.52% | 417856 | 65.36% | 144,745 | 1,844,914 | 987,372 | 228,348 | 114,437 | 498,197 | 82 | 19.10% | xx |
14,886,893 | 5,153,697 | 2659 | ||||||||||||