EricChu:LabNotesMDA/2015-1-7
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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 | ||||||||||||