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.
  1. GM Dev9 Oct10 (Index 9-16). Asked for 10 million reads. Sequenced in Lane 1.
  2. PGP1 Dev8 Oct6 (Index 17-24). Asked for 10 million reads. Sequenced in Lane 1.
  3. 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.
  4. GM Dev9.2 Nov4 (Index9-32). Asked for 40 million reads. Sequenced in Lane3.
  5. GM Dev9 Nov14 (Index9-32). Asked for 40 million reads. Sequenced in Lane4.
  6. GM Dev9 Nov18 (Index9-32). Asked for 40 million reads. Sequenced in Lane5.
  7. GM Dev9 Dec2 (Index9-32). Asked for 40 million reads. Sequenced in Lane6.
  8. GM Dev9 Dec3 (Index9-32). Asked for 40 million reads. Sequenced in Lane7.
  9. 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