EricChu:LabNotesMDA/2014-8-25: Difference between revisions

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(Created page with "==PGP1 21 Combined CoRE and Tag Reads (mapped by BWA) == {| {{table}} | align="center" style="background:#f0f0f0;"|'''sample''' | align="center" style="background:#f0f0f0;"|'...")
 
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| ||73,874,844||81.50%||60,213,831||27.76%||43,697,428||||||||||||37537
| ||73,874,844||81.50%||60,213,831||27.76%||43,697,428||||||||||||37537
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==PGP1 22 Combined Simplified and Tag Reads (mapped by BWA) ==
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''sample'''
| align="center" style="background:#f0f0f0;"|'''Raw_reads'''
| align="center" style="background:#f0f0f0;"|'''Mapping_rate'''
| align="center" style="background:#f0f0f0;"|'''Mappable_reads'''
| align="center" style="background:#f0f0f0;"|'''Clonal_rate'''
| 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'''
|-
| 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
|-
|-
|  
|  
|}
|}

Revision as of 19:39, 28 August 2014

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