EricChu:LabNotesMDA/2014-8-25

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PGP1 21 Combined CoRE and Tag Reads (mapped by BWA)

sample Raw_reads Mapping_rate Mappable_reads Clonal_rate unique 1+ 1 2 3 4+ contig
25 8,915 30.67% 2,734 1.13% 2,703 129431 127599 921 66 695 0
1 1,767,726 74.59% 1,318,562 55.73% 583,727 9516093 5692190 1230581 626839 1965634 218
2 2,600,727 82.44% 2,143,913 55.31% 958,115 10846262 6082060 1213949 640543 2900424 321
3 2,166,722 75.21% 1,629,621 50.70% 803,403 9026307 4990213 1012535 533179 2484844 299
4 2,982,718 81.90% 2,442,744 51.83% 1,176,670 13628682 8211575 1393897 676569 3340779 341
5 2,985,776 78.28% 2,337,121 49.13% 1,188,893 12998138 7214372 1415290 747580 3619125 389
6 4,794,307 84.40% 4,046,302 60.66% 1,591,815 16517249 9582723 1686003 842768 4400376 443
7 2,875,956 72.92% 2,097,091 49.00% 1,069,516 12972372 6903851 1650877 879066 3533693 389
8 2,882,183 78.40% 2,259,734 40.67% 1,340,700 17241147 9578019 2195105 1139208 4321040 487
9 2,973,394 84.98% 2,526,707 35.87% 1,620,377 20867654 10813806 2862995 1540997 5640480 775
10 2,167,476 77.03% 1,669,648 30.19% 1,165,581 18640056 9981373 2888407 1482285 4278796 591
11 2,137,080 81.27% 1,736,911 37.14% 1,091,822 20917290 12273611 3154542 1551941 3927547 633
12 4,553,703 87.66% 3,991,612 13.50% 3,452,744 67452229 34571848 12154514 6502810 14206613 3151
13 3,197,307 68.98% 2,205,348 13.50% 1,907,626 53586423 34648595 9749094 4047238 5126604 2131
14 3,931,535 89.05% 3,500,954 11.01% 3,115,499 74902025 43560883 13922451 6635791 10767573 3442
15 3,372,990 70.22% 2,368,534 16.55% 1,976,542 58662869 38491396 10903238 4382136 4871109 2284
16 3,264,362 79.82% 2,605,704 10.80% 2,324,288 74432147 52049786 12877420 4769835 4723437 2293
17 3,496,240 77.57% 2,711,982 15.77% 2,284,302 74071152 52407506 12878522 4583367 4187083 2170
18 3,017,219 81.47% 2,458,031 11.25% 2,181,503 64755388 42915926 11790071 4687801 5346162 2471
19 1,402,425 92.07% 1,291,258 5.86% 1,215,590 43381886 32591056 6837623 2191031 1749037 947
20 3,720,498 83.96% 3,123,552 16.56% 2,606,292 66777895 41039684 12050112 5461023 8211943 2787
21 3,298,736 88.73% 2,926,946 12.84% 2,551,126 67473637 42974264 11765137 5143403 7574981 2694
22 4,405,230 90.49% 3,986,500 12.00% 3,508,120 77232990 43439158 13826921 6860909 13089956 3770
23 1,718,252 78.28% 1,344,992 20.32% 1,071,690 33514168 23733165 5446737 2025667 2296236 994
24 4,153,367 83.96% 3,487,330 16.59% 2,908,782 68349048 39717105 12252959 5937268 10425575 3517
73,874,844 81.50% 60,213,831 27.76% 43,697,428 37537

PGP1 22 Combined Simplified and Tag Reads (mapped by BWA)

sample Raw_reads Mapping_rate Mappable_reads Clonal_rate unique 1+ 1 2 3 4+ contig
25 1,014,446 89.82% 911,158 0.96% 902,411 42,007,823 39,361,716 2,142,641 338,443 160,432 104
1 1,721,573 76.75% 1,321,337 20.42% 1,051,520 26,956,965 19,051,494 3,293,984 1,411,110 3,197,334 512
2 1,393,623 78.75% 1,097,511 24.89% 824,341 19,914,102 13,790,175 2,354,223 1,067,455 2,694,387 538
3 1,214,890 16.75% 203,469 16.10% 170,710 4,795,763 3,374,611 633,185 276,101 510,241 103
4 3,249,097 74.90% 2,433,488 42.20% 1,406,556 21,453,982 12,382,109 2,617,083 1,339,660 5,108,391 813
5 2,452,694 54.75% 1,342,758 43.41% 759,867 15,253,924 9,950,700 1,802,084 868,142 2,625,918 427
6 3,942,205 74.05% 2,919,107 45.80% 1,582,156 23,982,090 14,367,384 2,717,722 1,358,064 5,530,237 863
7 3,487,723 78.87% 2,750,913 39.87% 1,654,124 25,511,841 14,450,825 3,317,927 1,661,491 6,075,289 1031
8 2,404,304 84.55% 2,032,896 15.63% 1,715,154 40,702,300 24,475,918 6,767,943 3,183,182 6,266,812 1577
9 2,401,126 83.10% 1,995,326 15.63% 1,683,457 36,503,127 20,048,241 6,286,353 3,251,678 6,900,584 1422
10 574,906 85.77% 493,106 9.05% 448,480 12,842,508 8,994,652 1,854,628 720,982 1,264,979 293
11 1,431,850 76.01% 1,088,404 17.70% 895,756 22,304,961 14,479,148 3,354,659 1,458,058 2,998,419 584
12 3,739,082 78.86% 2,948,590 29.67% 2,073,743 37,924,722 21,551,076 5,745,717 2,839,631 7,773,491 1367
13 2,149,038 83.52% 1,794,982 11.47% 1,589,098 42,816,684 26,876,392 7,267,967 3,307,014 5,351,301 1444
14 900,164 72.81% 655,410 10.33% 587,706 19,140,058 14,646,725 2,395,761 809,554 1,275,945 291
15 1,792,737 82.55% 1,479,862 23.61% 1,130,467 23,386,851 14,283,418 3,391,849 1,534,792 4,162,573 631
16 1,661,017 82.10% 1,363,654 8.73% 1,244,607 35,717,554 23,412,821 5,965,297 2,562,005 3,761,684 1090
17 3,867,925 81.19% 3,140,423 22.89% 2,421,580 55,923,111 36,224,492 8,385,727 3,587,365 7,709,229 1637
18 2,417,798 77.27% 1,868,138 15.18% 1,584,555 37,211,161 22,222,683 6,118,456 2,927,473 5,926,351 1267
19 1,750,911 76.70% 1,342,934 20.50% 1,067,633 27,150,915 17,680,402 4,334,702 1,846,382 3,273,962 915
20 5,714,105 77.00% 4,399,962 27.69% 3,181,613 70,042,421 45,315,865 9,478,137 4,323,910 10,907,983 1905
21 1,969,271 79.82% 1,571,794 12.67% 1,372,648 34,767,438 20,991,038 5,950,750 2,856,329 4,953,514 1308
22 1,800,697 82.96% 1,493,816 16.43% 1,248,382 33,614,515 22,084,346 5,146,470 2,329,712 4,037,882 1156
23 888,208 69.63% 618,445 8.60% 565,259 17,936,086 12,900,500 2,542,565 1,052,910 1,425,040 501
24 1,589,080 86.10% 1,368,126 7.45% 1,266,201 37,663,022 25,615,733 6,062,029 2,545,006 3,425,221 1241
55,528,470 76.78% 42,635,609 0.243894032 23026

PGP1 23 Device V8 5min Incubation + 5min Pump (instead of 10min pump) with Simplified Tag (mapped by BWA)

sample Raw_reads Mapping_rate Mappable_reads Clonal_rate unique 1+ 1 2 3 4+ contig
25 390,006 76.46% 298,208 19.78% 239,222 7,489,203 4,894,180 1,385,612 490,980 713,755 108
1 2,659,539 83.08% 2,209,639 68.80% 689,407 10,215,316 6,323,889 1,192,133 508,564 2,189,316 237
2 727,413 84.81% 616,910 50.99% 302,348 6,944,381 4,641,825 1,081,690 292,160 926,611 103
3 521,423 88.41% 461,015 24.38% 348,620 10,988,404 7,439,409 1,948,035 616,985 975,599 196
4 525,708 87.83% 461,722 26.72% 338,350 10,973,235 7,122,683 2,186,736 662,365 993,915 185
5 1,700,163 82.25% 1,398,437 25.37% 1,043,654 32,861,572 22,484,596 5,805,589 1,679,607 2,878,622 579
6 1,107,542 87.84% 972,830 32.98% 651,991 16,436,441 9,150,974 3,251,616 1,268,754 2,752,930 523
7 427,288 87.25% 372,800 19.48% 300,179 11,615,241 8,570,940 2,122,883 434,522 481,619 66
8 2,584,602 88.64% 2,291,090 41.08% 1,349,910 28,798,510 15,619,951 4,994,143 2,123,651 6,046,375 1129
9 8,180,400 85.99% 7,034,677 32.43% 4,753,331 121,509,729 69,122,660 24,492,005 9,368,317 18,510,607 3456
10 404,400 83.99% 339,654 34.66% 221,930 7,760,462 5,112,640 1,666,236 439,459 534,630 71
11 998,664 90.16% 900,378 29.85% 631,615 16,598,420 9,966,845 2,988,858 1,238,997 2,394,799 564
12 668,384 89.85% 600,517 27.41% 435,915 13,216,397 7,977,879 2,754,209 946,845 1,528,978 287
13 941,089 83.01% 781,226 24.63% 588,810 17,251,261 10,357,161 3,493,552 1,277,657 2,115,129 425
14 845,880 87.41% 739,366 25.34% 552,011 15,217,472 9,419,365 2,775,760 1,087,924 1,922,064 389
15 1,076,847 86.73% 933,979 27.65% 675,734 19,058,713 12,003,172 3,363,353 1,295,367 2,388,385 455
16 3,014,868 87.74% 2,645,176 36.71% 1,674,132 34,422,449 19,592,176 5,511,154 2,455,845 6,847,834 1237
17 2,698,774 89.26% 2,408,808 33.73% 1,596,317 34,399,231 19,620,188 5,548,784 2,522,603 6,694,835 1113
18 1,105,299 87.76% 970,032 25.47% 722,965 21,725,473 14,343,768 3,789,616 1,318,271 2,261,808 435
19 1,397,539 87.53% 1,223,256 27.54% 886,371 22,667,350 13,420,963 4,044,354 1,654,389 3,535,910 713
20 2,017,225 89.65% 1,808,414 28.25% 1,297,537 41,916,943 28,711,133 7,523,306 2,213,918 3,453,860 685
21 3,095,545 89.04% 2,756,401 30.84% 1,906,327 45,754,077 27,486,317 7,756,429 3,078,720 7,416,737 1556
22 3,334,210 89.28% 2,976,897 31.61% 2,035,900 59,238,516 37,021,927 12,163,660 3,461,182 6,576,644 1260
23 3,992,688 90.34% 3,607,191 39.49% 2,182,711 46,879,680 28,760,337 7,287,374 2,780,214 8,035,223 1492
24 1,096,669 89.15% 977,706 56.73% 423,053 7,537,136 5,042,783 873,363 360,918 1,258,672 176
45,512,165 87.42% 39,786,329 0.350808152 17440