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 | |||||||