EricChu:LabNotesMDA/2014-8-25: Difference between revisions
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==Mapping with BWA == | |||
*New BWA read mapping using the script: [[Media:batch_bwa_fastq2bam.txt|batch_bwa_fastq2bam.pl]] | |||
*Bowtie2 read mapping using the script: [[Media:batch_fastq2bam.txt|batch_fastq2bam.pl]] | |||
*Mapping in Eric_15T/HL163/BWA folder | |||
nohup batch_bwa_fastq2bam.pl hg19 > EC_PGP1_21_BWA_batch_fastq2bam.log & | |||
*Gather coverage statistics | |||
get_covstats.pl > EC_PGP1_21_BWA_covStat.txt & | |||
grep rmdupse EC_PGP1_BWA_batch_fastq2bam.log | |||
wc -l *targetcut.out | |||
grep -B1 'Version' EC_PGP1_BWA_batch_fastq2bam.log|grep -v 'Version' | |||
*copy and paste to excel sheet1 and then text separate | |||
=OFFSET(Sheet1!$B$1,(ROW()-1)*4,0) | |||
==PGP1 21 Combined CoRE and Tag Reads (mapped by BWA) == | ==PGP1 21 Combined CoRE and Tag Reads (mapped by BWA) == | ||
Line 206: | Line 219: | ||
|- | |- | ||
| ||45,512,165||87.42%||39,786,329||0.350808152||||||||||||||17440 | | ||45,512,165||87.42%||39,786,329||0.350808152||||||||||||||17440 | ||
|- | |||
| | |||
|} | |||
==PGP1 24 Device V8 Random 8-mer Simplified Tag (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''' | |||
|- | |||
| 1||1640076||95.86%||1572110||23.70%||1,199,520||21981168||10833773||3586672||1983134||5566369||804 | |||
|- | |||
| 2||1340818||95.77%||1284162||13.60%||1,109,516||26878170||14846041||4999405||2504898||4511311||1206 | |||
|- | |||
| 3||1714130||96.38%||1652070||18.07%||1,353,541||29351675||16037131||5006442||2542811||5748756||1383 | |||
|- | |||
| 4||1675286||96.03%||1608742||19.46%||1,295,681||25392163||12842259||4284882||2329807||5918879||1187 | |||
|- | |||
| 5||2011370||95.69%||1924708||21.85%||1,504,159||28380830||14133749||4720764||2587161||6922616||1327 | |||
|- | |||
| 6||1632231||91.70%||1496836||21.74%||1,171,424||22255355||11267675||3718429||2003514||5250643||1082 | |||
|- | |||
| 7||2010717||95.96%||1929506||27.10%||1,406,610||22903223||10893768||3379772||1936197||6677816||1058 | |||
|- | |||
| 8||2216786||96.19%||2132279||15.90%||1,793,247||40572299||21744432||7303293||3772678||7735989||1806 | |||
|- | |||
| 9||1094654||96.98%||1061620||19.77%||851,738||21817547||14231060||3456982||1427346||2686762||741 | |||
|- | |||
| 10||1096361||96.44%||1057340||19.88%||847,141||21156073||13555741||3336781||1415793||2831203||756 | |||
|- | |||
| 11||1075544||96.86%||1041760||23.30%||799,030||18986625||11799379||3099265||1338004||2733617||709 | |||
|- | |||
| 12||1316826||96.86%||1275469||31.36%||875,482||19801901||12226333||3289857||1438165||2831979||806 | |||
|- | |||
| 13||1343854||96.37%||1295056||24.23%||981,264||22602977||13944466||3678119||1609733||3354090||901 | |||
|- | |||
| 14||1288277||96.57%||1244036||30.19%||868,462||19602494||12368556||3022251||1301830||2893879||771 | |||
|- | |||
| 15||1572440||95.57%||1502812||32.18%||1,019,207||22486162||13952547||3544203||1527498||3445845||889 | |||
|- | |||
| 16||1477916||96.97%||1433068||28.98%||1,017,765||23493259||14912324||3707302||1564398||3292831||858 | |||
|- | |||
| 17||1612105||96.27%||1551932||13.14%||1,348,008||35924685||22001492||6346556||2850192||4709919||1593 | |||
|- | |||
| 18||1114338||95.41%||1063188||9.17%||965,694||29830442||20323479||4902495||1982092||2605856||1134 | |||
|- | |||
| 19||1739110||96.24%||1673768||13.44%||1,448,814||37374913||22359095||6627724||3068474||5303082||1856 | |||
|- | |||
| 20||1937720||95.90%||1858214||13.76%||1,602,524||42209334||26860849||6734502||2999877||5597561||1777 | |||
|- | |||
| 21||3138051||96.40%||3025212||12.04%||2,660,976||75671146||50186704||12176283||5048131||8243493||2999 | |||
|- | |||
| 22||2220512||95.72%||2125468||13.38%||1,841,080||48501173||29550492||8619506||3857800||6456863||2362 | |||
|- | |||
| 23||2698960||95.70%||2582802||19.60%||2,076,573||42819488||22664347||7286868||3795462||9056286||2501 | |||
|- | |||
| 24||63146||96.23%||60766||2.52%||59,235||2806948||2610635||164089||20234||6945||1 | |||
|- | |||
| ||39031228||96.00%||37452924||0.196386061||30,096,689||||||||||||30507 | |||
|- | |||
| | |||
|} | |||
==PGP1 25 Device V8 Random 9-mer 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''' | |||
|- | |||
| 1||2,184,291||97.10%||2,120,990||22.11%||1,652,039||31,986,378||18,232,069||4,734,194||2,355,190||6,658,943||788 | |||
|- | |||
| 2||2,499,709||96.74%||2,418,339||26.33%||1,781,590||35,636,576||22,425,584||4,707,619||2,140,726||6,353,419||782 | |||
|- | |||
| 3||2,493,052||96.91%||2,416,100||25.47%||1,800,719||39,636,619||26,273,842||5,178,322||2,199,214||5,972,929||799 | |||
|- | |||
| 4||2,282,055||96.54%||2,203,111||27.41%||1,599,238||30,211,006||18,461,426||3,979,706||1,852,751||5,905,061||741 | |||
|- | |||
| 5||1,741,480||96.36%||1,678,023||23.41%||1,285,198||30,550,974||20,731,298||4,141,377||1,707,914||3,959,700||675 | |||
|- | |||
| 6||1,513,290||96.45%||1,459,504||23.85%||1,111,412||22,320,418||13,654,657||3,107,903||1,456,327||4,097,034||561 | |||
|- | |||
| 7||4,195,597||97.25%||4,080,055||29.98%||2,856,855||54,798,794||32,503,456||7,964,290||3,658,513||10,659,124||1363 | |||
|- | |||
| 8||1,147,030||96.04%||1,101,583||23.61%||841,499||15,193,645||8,583,803||2,159,621||1,117,557||3,327,824||440 | |||
|- | |||
| 9||1,995,481||96.63%||1,928,196||30.95%||1,331,419||22,749,515||13,207,834||3,098,844||1,511,914||4,923,075||543 | |||
|- | |||
| 10||2,317,908||97.01%||2,248,522||43.25%||1,276,036||16,413,864||8,881,713||2,033,889||1,048,444||4,441,895||435 | |||
|- | |||
| 11||2,070,348||95.40%||1,975,128||20.00%||1,580,102||34,827,621||21,483,010||5,197,168||2,369,989||5,774,483||906 | |||
|- | |||
| 12||1,481,367||95.63%||1,416,639||31.16%||975,214||15,051,833||8,138,743||2,063,584||1,071,142||3,774,004||440 | |||
|- | |||
| 13||1,092,801||96.79%||1,057,744||24.52%||798,385||14,797,509||8,274,996||2,315,300||1,191,540||3,014,347||433 | |||
|- | |||
| 14||912,307||96.49%||880,282||21.06%||694,895||12,543,654||6,997,807||1,762,223||934,775||2,844,234||392 | |||
|- | |||
| 15||2,433,854||96.21%||2,341,514||35.46%||1,511,213||22,980,808||12,453,974||3,019,964||1,558,760||5,933,848||610 | |||
|- | |||
| 16||1,022,561||96.52%||986,983||12.00%||868,545||21,251,937||13,076,239||3,467,264||1,606,037||3,101,750||619 | |||
|- | |||
| 17||1,121,374||96.81%||1,085,658||36.95%||684,507||11,128,413||6,543,958||1,449,179||723,509||2,408,399||322 | |||
|- | |||
| 18||1,986,108||97.05%||1,927,481||30.35%||1,342,491||27,438,155||18,259,396||3,473,613||1,439,458||4,261,360||590 | |||
|- | |||
| 19||2,302,925||97.19%||2,238,241||40.34%||1,335,335||20,079,043||11,386,392||2,563,472||1,296,522||4,816,482||493 | |||
|- | |||
| 20||2,302,136||96.67%||2,225,362||22.40%||1,726,881||39,063,557||26,082,919||5,242,624||2,174,525||5,553,666||818 | |||
|- | |||
| 21||1,300,810||96.35%||1,253,315||27.20%||912,413||19,754,539||13,720,482||2,265,691||924,804||2,836,642||352 | |||
|- | |||
| 22||1,320,415||96.93%||1,279,878||24.26%||969,380||22,530,006||15,532,204||2,742,149||1,161,541||3,086,644||432 | |||
|- | |||
| 23||4,038,941||97.18%||3,925,079||38.16%||2,427,269||50,797,424||33,453,499||7,069,956||2,871,948||7,391,188||1109 | |||
|- | |||
| 24||1,359,113||96.09%||1,305,981||24.20%||989,934||18,056,452||10,532,393||2,488,816||1,225,086||3,798,095||431 | |||
|- | |||
| ||47,114,953||96.69%||45,553,708||0.289644616||32,352,570||||||||||||15074 | |||
|- | |||
| | |||
|} | |||
==PGP1 26 Device V8 Random 10-mer Simplified Tag (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;"|'''contig''' | |||
| 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''' | |||
|- | |||
| 1||690,277||96.70%||667,502||44.81%||368,394||162||5,636,948||3,220,301||681,567||355,998||1,371,366||162 | |||
|- | |||
| 2||573,767||96.32%||552,669||31.63%||377,860||217||6,165,818||3,264,608||816,265||450,841||1,625,894||217 | |||
|- | |||
| 3||764,141||96.41%||736,674||41.70%||429,481||215||6,452,790||3,395,150||831,767||458,764||1,752,274||215 | |||
|- | |||
| 4||572,351||95.85%||548,627||32.58%||369,884||203||6,030,417||3,250,837||788,447||429,731||1,545,798||203 | |||
|- | |||
| 5||688,067||95.85%||659,504||41.75%||384,161||161||5,653,088||3,240,852||658,088||335,507||1,409,822||161 | |||
|- | |||
| 6||619,413||96.31%||596,537||40.45%||355,238||174||4,988,329||2,650,568||594,056||328,050||1,402,879||174 | |||
|- | |||
| 7||746,320||96.07%||716,961||41.30%||420,856||214||6,313,822||3,382,543||791,438||434,916||1,690,622||214 | |||
|- | |||
| 8||740,681||96.48%||714,629||46.52%||382,184||175||6,122,312||3,677,066||722,628||356,090||1,353,567||175 | |||
|- | |||
| 9||796,267||96.19%||765,943||51.37%||372,478||181||5,623,958||3,090,982||712,580||380,280||1,430,482||181 | |||
|- | |||
| 10||824,214||96.26%||793,363||39.86%||477,129||174||6,413,486||3,268,950||754,872||423,993||1,953,599||174 | |||
|- | |||
| 11||907,032||96.74%||877,441||46.38%||470,484||187||6,571,047||3,397,058||820,126||446,728||1,903,087||187 | |||
|- | |||
| 12||723,182||96.72%||699,459||44.51%||388,130||185||5,842,914||3,093,034||780,119||427,748||1,532,426||185 | |||
|- | |||
| 13||757,465||96.54%||731,244||37.24%||458,929||227||7,078,124||3,777,507||924,935||498,188||1,863,922||227 | |||
|- | |||
| 14||704,605||96.63%||680,867||32.90%||456,862||232||7,225,566||3,886,003||942,941||506,321||1,882,708||232 | |||
|- | |||
| 15||848,248||96.18%||815,834||38.26%||503,696||236||7,942,109||4,361,859||998,320||540,109||2,036,434||236 | |||
|- | |||
| 16||671,708||96.57%||648,695||35.82%||416,332||206||6,196,604||3,224,629||806,557||443,002||1,710,215||206 | |||
|- | |||
| 17||674,292||94.37%||636,303||24.29%||481,745||272||9,489,870||5,467,445||1,330,773||685,117||1,993,825||272 | |||
|- | |||
| 18||719,253||96.53%||694,276||26.01%||513,695||297||9,343,787||5,254,577||1,259,271||651,657||2,166,764||297 | |||
|- | |||
| 19||710,519||96.55%||685,974||32.20%||465,090||237||7,490,712||4,013,960||963,650||541,520||1,956,549||237 | |||
|- | |||
| 20||616,598||96.21%||593,224||30.58%||411,816||240||6,896,372||3,880,733||869,639||465,347||1,674,485||240 | |||
|- | |||
| 21||537,817||96.28%||517,799||30.32%||360,802||246||6,522,265||3,491,940||969,645||525,126||1,521,163||246 | |||
|- | |||
| 22||555,866||95.99%||533,555||28.61%||380,905||264||6,469,170||3,589,897||844,288||449,894||1,574,465||264 | |||
|- | |||
| 23||757,629||96.13%||728,324||32.25%||493,440||284||8,665,874||5,040,136||1,105,371||568,271||1,937,579||284 | |||
|- | |||
| 24||927,550||96.79%||897,816||38.55%||551,708||280||8,264,275||4,557,481||1,007,562||531,964||2,154,889||280 | |||
|- | |||
| ||17,127,262||96.30%||16,493,220||0.375887603||10,291,298||5269||||||||||||5269 | |||
|- | |||
| | |||
|} | |||
==PGP1 26 Device V8 Random 10-mer Simplified Tag (mapped by Bowtie2) == | |||
{| {{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;"|'''contig''' | |||
| 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''' | |||
| align="center" style="background:#f0f0f0;"|'''%Mito''' | |||
|- | |||
| 1||690,277||99.35%||685,798||39.48%||415,045||162||5,839,447||3,375,697||708,870||360,464||1,386,445||162||0.03% | |||
|- | |||
| 2||573,767||99.42%||570,427||26.51%||419,207||220||6,375,239||3,448,254||827,457||452,689||1,638,490||220||0.07% | |||
|- | |||
| 3||764,141||99.45%||759,906||36.53%||482,312||214||6,713,978||3,607,242||856,516||466,413||1,768,838||214||0.17% | |||
|- | |||
| 4||572,351||99.19%||567,740||27.78%||410,022||203||6,223,838||3,398,581||812,009||432,905||1,564,592||203||0.33% | |||
|- | |||
| 5||688,067||99.32%||683,379||36.27%||435,517||161||5,906,220||3,437,517||686,533||343,575||1,429,864||161||0.05% | |||
|- | |||
| 6||619,413||99.47%||616,108||35.41%||397,944||175||5,189,574||2,822,230||608,976||329,729||1,415,507||175||0.11% | |||
|- | |||
| 7||746,320||99.37%||741,605||35.70%||476,852||216||6,560,499||3,581,318||812,705||439,852||1,712,228||216||0.14% | |||
|- | |||
| 8||740,681||99.45%||736,620||41.65%||429,818||175||6,302,838||3,770,033||774,083||373,843||1,371,564||175||0.13% | |||
|- | |||
| 9||796,267||99.26%||790,371||46.58%||422,216||185||5,912,422||3,315,249||750,314||391,048||1,446,279||185||0.06% | |||
|- | |||
| 10||824,214||99.42%||819,412||34.25%||538,763||173||6,659,016||3,452,549||789,807||429,692||1,974,699||173||0.13% | |||
|- | |||
| 11||907,032||99.49%||902,377||41.43%||528,522||187||6,821,254||3,589,634||848,971||457,821||1,920,495||187||0.01% | |||
|- | |||
| 12||723,182||99.42%||718,992||40.04%||431,108||186||6,007,739||3,189,111||820,376||441,005||1,547,588||186||0.05% | |||
|- | |||
| 13||757,465||99.40%||752,939||32.25%||510,116||226||7,312,418||3,957,401||949,337||506,277||1,885,676||226||0.11% | |||
|- | |||
| 14||704,605||99.47%||700,873||28.40%||501,825||236||7,414,385||4,036,453||962,666||505,719||1,901,834||236||0.04% | |||
|- | |||
| 15||848,248||99.36%||842,826||32.82%||566,211||237||8,209,359||4,558,756||1,039,097||548,348||2,057,758||237||0.02% | |||
|- | |||
| 16||671,708||99.48%||668,214||30.39%||465,144||207||6,411,985||3,394,381||825,615||450,626||1,728,994||207||0.09% | |||
|- | |||
| 17||674,292||99.00%||667,560||20.75%||529,041||271||9,834,370||5,669,224||1,397,474||711,518||2,043,394||271||0.12% | |||
|- | |||
| 18||719,253||99.46%||715,397||21.75%||559,798||293||9,533,510||5,373,414||1,291,891||665,480||2,190,928||293||0.08% | |||
|- | |||
| 19||710,519||99.45%||706,632||27.78%||510,330||238||7,693,018||4,174,384||985,573||543,665||1,974,396||238||0.19% | |||
|- | |||
| 20||616,598||99.41%||612,983||26.13%||452,811||239||7,116,202||4,053,692||887,895||473,315||1,694,875||239||0.04% | |||
|- | |||
| 21||537,817||99.41%||534,664||26.32%||393,940||248||6,713,399||3,640,490||986,162||533,538||1,538,588||248||0.18% | |||
|- | |||
| 22||555,866||99.37%||552,346||24.06%||419,452||267||6,674,472||3,745,222||864,374||456,875||1,597,321||267||0.07% | |||
|- | |||
| 23||757,629||99.41%||753,167||27.27%||547,778||285||8,975,868||5,274,165||1,149,491||580,488||1,957,153||285||0.16% | |||
|- | |||
| 24||927,550||99.47%||922,657||33.11%||617,165||278||8,519,122||4,747,103||1,043,645||541,589||2,174,018||278||0.08% | |||
|- | |||
| ||17,127,262||99.39%||17,022,993||0.326725564||11,460,937||5282|||||||||||||| | |||
|} | |||
==PGP1 27 Device V9 (Single Denaturation Chamber) Random 8-mer Simplified Tag (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''' | |||
|- | |||
| 1||1,480,684||85.07%||1,259,630||11.35%||1,116,662||28,202,462||17,827,314||4,461,358||2,002,027||3,900,784||1172 | |||
|- | |||
| 2||2,476,110||84.84%||2,100,648||10.62%||1,877,559||50,199,659||32,697,547||7,891,411||3,466,986||6,133,949||2052 | |||
|- | |||
| 3||2,076,640||84.70%||1,758,960||13.46%||1,522,204||36,562,106||22,615,204||5,731,936||2,678,237||5,525,374||1569 | |||
|- | |||
| 4||2,585,471||84.95%||2,196,309||18.85%||1,782,305||38,366,483||23,350,637||5,558,526||2,683,868||6,761,756||1575 | |||
|- | |||
| 5||2,509,697||84.99%||2,132,876||16.38%||1,783,511||38,695,018||23,346,934||5,711,895||2,755,220||6,868,105||1557 | |||
|- | |||
| 6||2,507,716||83.81%||2,101,637||11.55%||1,858,898||48,577,207||30,697,865||8,089,904||3,572,249||6,205,117||1864 | |||
|- | |||
| 7||1,588,435||85.30%||1,354,986||11.82%||1,194,827||30,546,845||19,599,233||4,750,889||2,151,443||4,034,198||1213 | |||
|- | |||
| 8||1,830,362||84.94%||1,554,642||13.78%||1,340,412||31,477,052||19,449,511||4,799,064||2,251,458||4,964,223||1295 | |||
|- | |||
| 9||1,538,587||84.87%||1,305,738||11.89%||1,150,486||27,875,370||16,930,165||4,554,439||2,150,968||4,227,130||1176 | |||
|- | |||
| 10||1,803,655||83.93%||1,513,729||17.81%||1,244,134||26,099,118||14,937,914||4,111,228||2,073,787||4,963,100||1178 | |||
|- | |||
| 11||685,896||82.96%||568,994||9.24%||516,419||14,515,013||9,575,229||2,369,611||1,003,588||1,555,774||564 | |||
|- | |||
| 12||1,675,696||84.09%||1,409,135||18.18%||1,152,954||25,261,348||15,210,431||3,886,271||1,852,526||4,299,523||1092 | |||
|- | |||
| 13||801,322||83.09%||665,855||8.66%||608,192||16,626,916||10,639,944||2,770,778||1,225,417||1,981,825||692 | |||
|- | |||
| 14||1,237,749||84.48%||1,045,664||14.18%||897,389||21,610,252||13,211,504||3,549,909||1,643,587||3,193,289||948 | |||
|- | |||
| 15||1,795,853||84.39%||1,515,525||12.90%||1,320,022||31,113,300||18,820,522||4,986,232||2,367,286||4,924,145||1368 | |||
|- | |||
| 16||1,388,962||83.72%||1,162,800||11.81%||1,025,473||24,626,927||14,722,640||4,090,553||1,951,357||3,850,085||1111 | |||
|- | |||
| 17||898,337||83.76%||752,461||8.90%||685,492||19,839,335||13,493,328||3,049,461||1,278,103||2,002,794||714 | |||
|- | |||
| 18||2,183,939||84.70%||1,849,691||12.36%||1,621,069||45,154,767||32,652,070||5,432,330||2,257,855||4,796,727||1321 | |||
|- | |||
| 19||2,926,888||86.70%||2,537,523||21.26%||1,998,046||41,607,868||25,394,175||5,972,928||2,840,457||7,383,998||1736 | |||
|- | |||
| 20||2,816,541||85.39%||2,404,954||15.92%||2,022,085||50,893,687||35,550,833||6,281,460||2,616,744||6,428,559||1540 | |||
|- | |||
| 21||2,564,937||84.85%||2,176,410||20.53%||1,729,593||37,400,147||24,062,720||4,855,664||2,251,674||6,213,763||1393 | |||
|- | |||
| 22||2,287,061||84.89%||1,941,550||24.02%||1,475,190||29,662,766||18,667,830||3,780,716||1,797,528||5,401,079||1122 | |||
|- | |||
| 23||1,717,383||85.58%||1,469,733||18.70%||1,194,893||27,798,882||18,740,085||3,488,855||1,541,205||4,013,052||960 | |||
|- | |||
| 24||973,638||87.05%||847,546||20.08%||677,359||14,139,245||8,532,615||2,085,848||988,931||2,521,439||603 | |||
|- | |||
| ||44,351,559||84.84%||37,626,996||0.154775334||31,795,173||||||||||||29815 | |||
|- | |||
| | |||
|} | |||
==Nucleus 1 Device V8 Simplified Tag (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;"|'''Contigs''' | |||
|- | |||
| 1||1,367,845||94.40%||1,291,213||25.82%||957,822||17,894,592||9,936,378||2,664,537||1,361,344||3,924,192||971 | |||
|- | |||
| 2||1,515,583||93.97%||1,424,260||25.04%||1,067,625||19,506,866||10,412,189||2,975,810||1,559,090||4,553,664||1111 | |||
|- | |||
| 3||1,272,014||93.55%||1,189,928||26.36%||876,263||16,099,815||8,900,555||2,405,438||1,209,395||3,581,648||897 | |||
|- | |||
| 4||1,421,005||96.23%||1,367,436||14.19%||1,173,397||29,025,459||17,225,610||5,028,307||2,359,792||4,395,744||1672 | |||
|- | |||
| 5||1,518,021||93.50%||1,419,328||30.69%||983,736||16,323,724||8,690,515||2,374,148||1,246,613||4,006,208||917 | |||
|- | |||
| 6||1,600,096||93.62%||1,498,045||28.41%||1,072,450||19,064,725||10,488,686||2,819,703||1,426,898||4,327,115||1030 | |||
|- | |||
| 7||996,834||93.08%||927,894||24.40%||701,488||16,003,765||10,379,380||2,192,493||992,354||2,436,996||570 | |||
|- | |||
| 8||2,321,768||94.82%||2,201,485||32.09%||1,495,028||26,180,016||15,020,353||3,592,437||1,779,411||5,775,068||1369 | |||
|- | |||
| 9||1,955,968||97.37%||1,904,532||5.70%||1,795,974||63,663,976||47,571,336||9,582,487||3,224,919||3,271,995||1638 | |||
|- | |||
| 10||1,532,893||94.37%||1,446,520||30.61%||1,003,740||17,394,961||9,269,925||2,689,660||1,362,889||4,064,001||1082 | |||
|- | |||
| 11||1,616,392||95.57%||1,544,742||18.62%||1,257,111||25,215,419||13,187,240||4,267,866||2,226,632||5,526,123||1780 | |||
|- | |||
| 12||2,060,554||94.51%||1,947,448||30.97%||1,344,323||23,226,786||12,427,345||3,600,169||1,807,089||5,381,906||1397 | |||
|- | |||
| 13||2,085,645||95.79%||1,997,839||19.60%||1,606,263||31,586,997||16,391,449||5,315,686||2,791,557||7,082,460||2117 | |||
|- | |||
| 14||1,579,239||95.41%||1,506,754||14.96%||1,281,344||28,605,592||15,795,190||4,987,119||2,498,158||5,308,758||1836 | |||
|- | |||
| 15||2,187,406||95.22%||2,082,874||18.14%||1,705,041||35,552,195||19,339,127||5,847,076||3,010,678||7,344,745||2226 | |||
|- | |||
| 16||1,784,104||95.59%||1,705,507||14.58%||1,456,844||33,420,297||18,696,840||5,801,616||2,903,357||6,004,220||2115 | |||
|- | |||
| 17||2,126,051||95.51%||2,030,567||21.26%||1,598,868||38,795,370||25,517,512||5,600,269||2,349,804||5,319,216||1498 | |||
|- | |||
| 18||1,661,080||95.49%||1,586,198||14.11%||1,362,385||36,596,829||24,282,030||5,527,312||2,347,988||4,429,425||1587 | |||
|- | |||
| 19||812,048||95.79%||777,830||4.60%||742,050||27,813,705||21,776,009||3,728,945||1,194,072||1,107,754||530 | |||
|- | |||
| 20||55,437||94.17%||52,205||1.21%||51,573||2,545,098||2,481,352||59,293||2,268||236||0 | |||
|- | |||
| 21||146,336||95.06%||139,101||1.57%||136,917||6,539,077||6,171,518||325,229||31,862||7,609||2 | |||
|- | |||
| 22||48||75.00%||36||0.00%||36||1,800||1,750||||||||0 | |||
|- | |||
| 23||864,533||95.73%||827,611||2.23%||809,155||35,583,533||31,391,109||3,263,328||599,441||318,752||182 | |||
|- | |||
| 24||253,984||93.52%||237,515||2.00%||232,765||10,830,543||9,928,390||781,324||92,519||20,605||5 | |||
|- | |||
| ||32,734,884||95.03%||31,106,868||0.206239459||24,712,199||||||||||||26532 | |||
|- | |||
| | |||
|} | |||
==Nucleus 1 Device V8 Simplified Tag (mapped by Bowtie2) == | |||
{| {{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;"|'''contag''' | |||
| align="center" style="background:#f0f0f0;"|'''%mito''' | |||
|- | |||
| 1||1367845||0.9953||1361440||0.2327||1044632.912||18478396||10269725||2752942||1401952||4045680||998||0.04164708 | |||
|- | |||
| 2||1515583||0.995||1507980||0.2216||1173811.632||20215597||10816713||3083939||1604768||4703673||1146||0.02274566 | |||
|- | |||
| 3||1272014||0.9937||1263990||0.2333||969101.133||16733796||9285921||2488967||1247161||3709019||924||0.006329164 | |||
|- | |||
| 4||1421005||0.9957||1414862||0.1201||1244937.074||29578942||17549952||5122482||2403131||4487372||1704||0.125383253 | |||
|- | |||
| 5||1518021||0.9937||1508481||0.2654||1108130.143||17009454||9107071||2468074||1283070||4144879||938||0.074313167 | |||
|- | |||
| 6||1600096||0.9939||1590390||0.2412||1206787.932||19820168||10945938||2924753||1470078||4476910||1056||0.00402417 | |||
|- | |||
| 7||996834||0.9938||990695||0.2006||791961.583||16787819||10941408||2285121||1032554||2526016||598||0.007267625 | |||
|- | |||
| 8||2321768||0.9949||2310020||0.2771||1669913.458||27103476||15633565||3710194||1827962||5918760||1404||0.063376075 | |||
|- | |||
| 9||1955968||0.9959||1948025||0.0496||1851402.96||64404637||48059653||9746795||3270488||3314082||1673||0.034599145 | |||
|- | |||
| 10||1532893||0.9952||1525547||0.2717||1111055.88||18014427||9639104||2778493||1405196||4182961||1106||0.029038764 | |||
|- | |||
| 11||1616392||0.9948||1607985||0.1574||1354888.161||25845412||13557984||4359570||2269518||5650734||1819||0.041542676 | |||
|- | |||
| 12||2060554||0.9948||2049835||0.2669||1502734.039||24042624||12931118||3716788||1858723||5525571||1423||0.031612301 | |||
|- | |||
| 13||2085645||0.9955||2076205||0.1642||1735292.139||32305640||16793664||5433622||2841533||7230618||2150||0.013919627 | |||
|- | |||
| 14||1579239||0.9945||1570568||0.1238||1376131.682||29304134||16196441||5104726||2551801||5434768||1894||0.205021368 | |||
|- | |||
| 15||2187406||0.9924||2170785||0.1471||1851462.527||36373988||19801168||5979060||3062538||7520728||2270||0.060208634 | |||
|- | |||
| 16||1784104||0.9944||1774108||0.1198||1561569.862||34184266||19137579||5925294||2959001||6147877||2153||0.066850496 | |||
|- | |||
| 17||2126051||0.9946||2114621||0.1815||1730817.289||39782967||26185672||5746001||2400013||5442381||1535||0.015794793 | |||
|- | |||
| 18||1661080||0.9938||1650735||0.1168||1457929.152||37487080||24893922||5657696||2394067||4530985||1613||0.027866375 | |||
|- | |||
| 19||812048||0.9948||807847||0.0369||778037.4457||28429858||22251003||3817219||1220513||1133954||549||0.024014448 | |||
|- | |||
| 20||55437||0.9935||55074||0.0113||54451.6638||2633540||2566979||61924||2290||293||0||0.081708247 | |||
|- | |||
| 21||146336||0.9939||145437||0.0142||143371.7946||6720035||6338445||337275||33374||7900||2||0.046068057 | |||
|- | |||
| 22||48||0.8542||41||0||41||1980||1930||||||||0||2.43902439 | |||
|- | |||
| 23||864533||0.9947||859916||0.0185||844007.554||36361985||32051042||3352347||617476||330387||192||0.047446495 | |||
|- | |||
| 24||253984||0.9929||252192||0.0178||247702.9824||11250981||10302140||819475||98619||22621||6||0.099527344 | |||
|- | |||
| ||32734884||0.99455298||||||26810172||||||||||||27153||total | |||
|- | |- | ||
| | | | ||
|} | |} |
Latest revision as of 20:20, 28 August 2014
Mapping with BWA[edit]
- New BWA read mapping using the script: batch_bwa_fastq2bam.pl
- Bowtie2 read mapping using the script: batch_fastq2bam.pl
- Mapping in Eric_15T/HL163/BWA folder
nohup batch_bwa_fastq2bam.pl hg19 > EC_PGP1_21_BWA_batch_fastq2bam.log &
- Gather coverage statistics
get_covstats.pl > EC_PGP1_21_BWA_covStat.txt & grep rmdupse EC_PGP1_BWA_batch_fastq2bam.log wc -l *targetcut.out grep -B1 'Version' EC_PGP1_BWA_batch_fastq2bam.log|grep -v 'Version'
- copy and paste to excel sheet1 and then text separate
=OFFSET(Sheet1!$B$1,(ROW()-1)*4,0)
PGP1 21 Combined CoRE and Tag Reads (mapped by BWA)[edit]
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)[edit]
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)[edit]
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 | |||||||
PGP1 24 Device V8 Random 8-mer Simplified Tag (mapped by BWA)[edit]
sample | Raw_reads | Mapping_rate | Mappable_reads | Clonal_rate | unique | 1+ | 1 | 2 | 3 | 4+ | contig |
1 | 1640076 | 95.86% | 1572110 | 23.70% | 1,199,520 | 21981168 | 10833773 | 3586672 | 1983134 | 5566369 | 804 |
2 | 1340818 | 95.77% | 1284162 | 13.60% | 1,109,516 | 26878170 | 14846041 | 4999405 | 2504898 | 4511311 | 1206 |
3 | 1714130 | 96.38% | 1652070 | 18.07% | 1,353,541 | 29351675 | 16037131 | 5006442 | 2542811 | 5748756 | 1383 |
4 | 1675286 | 96.03% | 1608742 | 19.46% | 1,295,681 | 25392163 | 12842259 | 4284882 | 2329807 | 5918879 | 1187 |
5 | 2011370 | 95.69% | 1924708 | 21.85% | 1,504,159 | 28380830 | 14133749 | 4720764 | 2587161 | 6922616 | 1327 |
6 | 1632231 | 91.70% | 1496836 | 21.74% | 1,171,424 | 22255355 | 11267675 | 3718429 | 2003514 | 5250643 | 1082 |
7 | 2010717 | 95.96% | 1929506 | 27.10% | 1,406,610 | 22903223 | 10893768 | 3379772 | 1936197 | 6677816 | 1058 |
8 | 2216786 | 96.19% | 2132279 | 15.90% | 1,793,247 | 40572299 | 21744432 | 7303293 | 3772678 | 7735989 | 1806 |
9 | 1094654 | 96.98% | 1061620 | 19.77% | 851,738 | 21817547 | 14231060 | 3456982 | 1427346 | 2686762 | 741 |
10 | 1096361 | 96.44% | 1057340 | 19.88% | 847,141 | 21156073 | 13555741 | 3336781 | 1415793 | 2831203 | 756 |
11 | 1075544 | 96.86% | 1041760 | 23.30% | 799,030 | 18986625 | 11799379 | 3099265 | 1338004 | 2733617 | 709 |
12 | 1316826 | 96.86% | 1275469 | 31.36% | 875,482 | 19801901 | 12226333 | 3289857 | 1438165 | 2831979 | 806 |
13 | 1343854 | 96.37% | 1295056 | 24.23% | 981,264 | 22602977 | 13944466 | 3678119 | 1609733 | 3354090 | 901 |
14 | 1288277 | 96.57% | 1244036 | 30.19% | 868,462 | 19602494 | 12368556 | 3022251 | 1301830 | 2893879 | 771 |
15 | 1572440 | 95.57% | 1502812 | 32.18% | 1,019,207 | 22486162 | 13952547 | 3544203 | 1527498 | 3445845 | 889 |
16 | 1477916 | 96.97% | 1433068 | 28.98% | 1,017,765 | 23493259 | 14912324 | 3707302 | 1564398 | 3292831 | 858 |
17 | 1612105 | 96.27% | 1551932 | 13.14% | 1,348,008 | 35924685 | 22001492 | 6346556 | 2850192 | 4709919 | 1593 |
18 | 1114338 | 95.41% | 1063188 | 9.17% | 965,694 | 29830442 | 20323479 | 4902495 | 1982092 | 2605856 | 1134 |
19 | 1739110 | 96.24% | 1673768 | 13.44% | 1,448,814 | 37374913 | 22359095 | 6627724 | 3068474 | 5303082 | 1856 |
20 | 1937720 | 95.90% | 1858214 | 13.76% | 1,602,524 | 42209334 | 26860849 | 6734502 | 2999877 | 5597561 | 1777 |
21 | 3138051 | 96.40% | 3025212 | 12.04% | 2,660,976 | 75671146 | 50186704 | 12176283 | 5048131 | 8243493 | 2999 |
22 | 2220512 | 95.72% | 2125468 | 13.38% | 1,841,080 | 48501173 | 29550492 | 8619506 | 3857800 | 6456863 | 2362 |
23 | 2698960 | 95.70% | 2582802 | 19.60% | 2,076,573 | 42819488 | 22664347 | 7286868 | 3795462 | 9056286 | 2501 |
24 | 63146 | 96.23% | 60766 | 2.52% | 59,235 | 2806948 | 2610635 | 164089 | 20234 | 6945 | 1 |
39031228 | 96.00% | 37452924 | 0.196386061 | 30,096,689 | 30507 | ||||||
PGP1 25 Device V8 Random 9-mer Combined Simplified and Tag Reads (mapped by BWA)[edit]
sample | Raw_reads | Mapping_rate | Mappable_reads | Clonal_rate | unique | 1+ | 1 | 2 | 3 | 4+ | contig |
1 | 2,184,291 | 97.10% | 2,120,990 | 22.11% | 1,652,039 | 31,986,378 | 18,232,069 | 4,734,194 | 2,355,190 | 6,658,943 | 788 |
2 | 2,499,709 | 96.74% | 2,418,339 | 26.33% | 1,781,590 | 35,636,576 | 22,425,584 | 4,707,619 | 2,140,726 | 6,353,419 | 782 |
3 | 2,493,052 | 96.91% | 2,416,100 | 25.47% | 1,800,719 | 39,636,619 | 26,273,842 | 5,178,322 | 2,199,214 | 5,972,929 | 799 |
4 | 2,282,055 | 96.54% | 2,203,111 | 27.41% | 1,599,238 | 30,211,006 | 18,461,426 | 3,979,706 | 1,852,751 | 5,905,061 | 741 |
5 | 1,741,480 | 96.36% | 1,678,023 | 23.41% | 1,285,198 | 30,550,974 | 20,731,298 | 4,141,377 | 1,707,914 | 3,959,700 | 675 |
6 | 1,513,290 | 96.45% | 1,459,504 | 23.85% | 1,111,412 | 22,320,418 | 13,654,657 | 3,107,903 | 1,456,327 | 4,097,034 | 561 |
7 | 4,195,597 | 97.25% | 4,080,055 | 29.98% | 2,856,855 | 54,798,794 | 32,503,456 | 7,964,290 | 3,658,513 | 10,659,124 | 1363 |
8 | 1,147,030 | 96.04% | 1,101,583 | 23.61% | 841,499 | 15,193,645 | 8,583,803 | 2,159,621 | 1,117,557 | 3,327,824 | 440 |
9 | 1,995,481 | 96.63% | 1,928,196 | 30.95% | 1,331,419 | 22,749,515 | 13,207,834 | 3,098,844 | 1,511,914 | 4,923,075 | 543 |
10 | 2,317,908 | 97.01% | 2,248,522 | 43.25% | 1,276,036 | 16,413,864 | 8,881,713 | 2,033,889 | 1,048,444 | 4,441,895 | 435 |
11 | 2,070,348 | 95.40% | 1,975,128 | 20.00% | 1,580,102 | 34,827,621 | 21,483,010 | 5,197,168 | 2,369,989 | 5,774,483 | 906 |
12 | 1,481,367 | 95.63% | 1,416,639 | 31.16% | 975,214 | 15,051,833 | 8,138,743 | 2,063,584 | 1,071,142 | 3,774,004 | 440 |
13 | 1,092,801 | 96.79% | 1,057,744 | 24.52% | 798,385 | 14,797,509 | 8,274,996 | 2,315,300 | 1,191,540 | 3,014,347 | 433 |
14 | 912,307 | 96.49% | 880,282 | 21.06% | 694,895 | 12,543,654 | 6,997,807 | 1,762,223 | 934,775 | 2,844,234 | 392 |
15 | 2,433,854 | 96.21% | 2,341,514 | 35.46% | 1,511,213 | 22,980,808 | 12,453,974 | 3,019,964 | 1,558,760 | 5,933,848 | 610 |
16 | 1,022,561 | 96.52% | 986,983 | 12.00% | 868,545 | 21,251,937 | 13,076,239 | 3,467,264 | 1,606,037 | 3,101,750 | 619 |
17 | 1,121,374 | 96.81% | 1,085,658 | 36.95% | 684,507 | 11,128,413 | 6,543,958 | 1,449,179 | 723,509 | 2,408,399 | 322 |
18 | 1,986,108 | 97.05% | 1,927,481 | 30.35% | 1,342,491 | 27,438,155 | 18,259,396 | 3,473,613 | 1,439,458 | 4,261,360 | 590 |
19 | 2,302,925 | 97.19% | 2,238,241 | 40.34% | 1,335,335 | 20,079,043 | 11,386,392 | 2,563,472 | 1,296,522 | 4,816,482 | 493 |
20 | 2,302,136 | 96.67% | 2,225,362 | 22.40% | 1,726,881 | 39,063,557 | 26,082,919 | 5,242,624 | 2,174,525 | 5,553,666 | 818 |
21 | 1,300,810 | 96.35% | 1,253,315 | 27.20% | 912,413 | 19,754,539 | 13,720,482 | 2,265,691 | 924,804 | 2,836,642 | 352 |
22 | 1,320,415 | 96.93% | 1,279,878 | 24.26% | 969,380 | 22,530,006 | 15,532,204 | 2,742,149 | 1,161,541 | 3,086,644 | 432 |
23 | 4,038,941 | 97.18% | 3,925,079 | 38.16% | 2,427,269 | 50,797,424 | 33,453,499 | 7,069,956 | 2,871,948 | 7,391,188 | 1109 |
24 | 1,359,113 | 96.09% | 1,305,981 | 24.20% | 989,934 | 18,056,452 | 10,532,393 | 2,488,816 | 1,225,086 | 3,798,095 | 431 |
47,114,953 | 96.69% | 45,553,708 | 0.289644616 | 32,352,570 | 15074 | ||||||
PGP1 26 Device V8 Random 10-mer Simplified Tag (mapped by BWA)[edit]
sample | Raw_reads | Mapping_rate | Mappable_reads | Clonal_rate | unique | contig | 1+ | 1 | 2 | 3 | 4+ | contig |
1 | 690,277 | 96.70% | 667,502 | 44.81% | 368,394 | 162 | 5,636,948 | 3,220,301 | 681,567 | 355,998 | 1,371,366 | 162 |
2 | 573,767 | 96.32% | 552,669 | 31.63% | 377,860 | 217 | 6,165,818 | 3,264,608 | 816,265 | 450,841 | 1,625,894 | 217 |
3 | 764,141 | 96.41% | 736,674 | 41.70% | 429,481 | 215 | 6,452,790 | 3,395,150 | 831,767 | 458,764 | 1,752,274 | 215 |
4 | 572,351 | 95.85% | 548,627 | 32.58% | 369,884 | 203 | 6,030,417 | 3,250,837 | 788,447 | 429,731 | 1,545,798 | 203 |
5 | 688,067 | 95.85% | 659,504 | 41.75% | 384,161 | 161 | 5,653,088 | 3,240,852 | 658,088 | 335,507 | 1,409,822 | 161 |
6 | 619,413 | 96.31% | 596,537 | 40.45% | 355,238 | 174 | 4,988,329 | 2,650,568 | 594,056 | 328,050 | 1,402,879 | 174 |
7 | 746,320 | 96.07% | 716,961 | 41.30% | 420,856 | 214 | 6,313,822 | 3,382,543 | 791,438 | 434,916 | 1,690,622 | 214 |
8 | 740,681 | 96.48% | 714,629 | 46.52% | 382,184 | 175 | 6,122,312 | 3,677,066 | 722,628 | 356,090 | 1,353,567 | 175 |
9 | 796,267 | 96.19% | 765,943 | 51.37% | 372,478 | 181 | 5,623,958 | 3,090,982 | 712,580 | 380,280 | 1,430,482 | 181 |
10 | 824,214 | 96.26% | 793,363 | 39.86% | 477,129 | 174 | 6,413,486 | 3,268,950 | 754,872 | 423,993 | 1,953,599 | 174 |
11 | 907,032 | 96.74% | 877,441 | 46.38% | 470,484 | 187 | 6,571,047 | 3,397,058 | 820,126 | 446,728 | 1,903,087 | 187 |
12 | 723,182 | 96.72% | 699,459 | 44.51% | 388,130 | 185 | 5,842,914 | 3,093,034 | 780,119 | 427,748 | 1,532,426 | 185 |
13 | 757,465 | 96.54% | 731,244 | 37.24% | 458,929 | 227 | 7,078,124 | 3,777,507 | 924,935 | 498,188 | 1,863,922 | 227 |
14 | 704,605 | 96.63% | 680,867 | 32.90% | 456,862 | 232 | 7,225,566 | 3,886,003 | 942,941 | 506,321 | 1,882,708 | 232 |
15 | 848,248 | 96.18% | 815,834 | 38.26% | 503,696 | 236 | 7,942,109 | 4,361,859 | 998,320 | 540,109 | 2,036,434 | 236 |
16 | 671,708 | 96.57% | 648,695 | 35.82% | 416,332 | 206 | 6,196,604 | 3,224,629 | 806,557 | 443,002 | 1,710,215 | 206 |
17 | 674,292 | 94.37% | 636,303 | 24.29% | 481,745 | 272 | 9,489,870 | 5,467,445 | 1,330,773 | 685,117 | 1,993,825 | 272 |
18 | 719,253 | 96.53% | 694,276 | 26.01% | 513,695 | 297 | 9,343,787 | 5,254,577 | 1,259,271 | 651,657 | 2,166,764 | 297 |
19 | 710,519 | 96.55% | 685,974 | 32.20% | 465,090 | 237 | 7,490,712 | 4,013,960 | 963,650 | 541,520 | 1,956,549 | 237 |
20 | 616,598 | 96.21% | 593,224 | 30.58% | 411,816 | 240 | 6,896,372 | 3,880,733 | 869,639 | 465,347 | 1,674,485 | 240 |
21 | 537,817 | 96.28% | 517,799 | 30.32% | 360,802 | 246 | 6,522,265 | 3,491,940 | 969,645 | 525,126 | 1,521,163 | 246 |
22 | 555,866 | 95.99% | 533,555 | 28.61% | 380,905 | 264 | 6,469,170 | 3,589,897 | 844,288 | 449,894 | 1,574,465 | 264 |
23 | 757,629 | 96.13% | 728,324 | 32.25% | 493,440 | 284 | 8,665,874 | 5,040,136 | 1,105,371 | 568,271 | 1,937,579 | 284 |
24 | 927,550 | 96.79% | 897,816 | 38.55% | 551,708 | 280 | 8,264,275 | 4,557,481 | 1,007,562 | 531,964 | 2,154,889 | 280 |
17,127,262 | 96.30% | 16,493,220 | 0.375887603 | 10,291,298 | 5269 | 5269 | ||||||
PGP1 26 Device V8 Random 10-mer Simplified Tag (mapped by Bowtie2)[edit]
sample | Raw_reads | Mapping_rate | Mappable_reads | Clonal_rate | unique | contig | 1+ | 1 | 2 | 3 | 4+ | contig | %Mito |
1 | 690,277 | 99.35% | 685,798 | 39.48% | 415,045 | 162 | 5,839,447 | 3,375,697 | 708,870 | 360,464 | 1,386,445 | 162 | 0.03% |
2 | 573,767 | 99.42% | 570,427 | 26.51% | 419,207 | 220 | 6,375,239 | 3,448,254 | 827,457 | 452,689 | 1,638,490 | 220 | 0.07% |
3 | 764,141 | 99.45% | 759,906 | 36.53% | 482,312 | 214 | 6,713,978 | 3,607,242 | 856,516 | 466,413 | 1,768,838 | 214 | 0.17% |
4 | 572,351 | 99.19% | 567,740 | 27.78% | 410,022 | 203 | 6,223,838 | 3,398,581 | 812,009 | 432,905 | 1,564,592 | 203 | 0.33% |
5 | 688,067 | 99.32% | 683,379 | 36.27% | 435,517 | 161 | 5,906,220 | 3,437,517 | 686,533 | 343,575 | 1,429,864 | 161 | 0.05% |
6 | 619,413 | 99.47% | 616,108 | 35.41% | 397,944 | 175 | 5,189,574 | 2,822,230 | 608,976 | 329,729 | 1,415,507 | 175 | 0.11% |
7 | 746,320 | 99.37% | 741,605 | 35.70% | 476,852 | 216 | 6,560,499 | 3,581,318 | 812,705 | 439,852 | 1,712,228 | 216 | 0.14% |
8 | 740,681 | 99.45% | 736,620 | 41.65% | 429,818 | 175 | 6,302,838 | 3,770,033 | 774,083 | 373,843 | 1,371,564 | 175 | 0.13% |
9 | 796,267 | 99.26% | 790,371 | 46.58% | 422,216 | 185 | 5,912,422 | 3,315,249 | 750,314 | 391,048 | 1,446,279 | 185 | 0.06% |
10 | 824,214 | 99.42% | 819,412 | 34.25% | 538,763 | 173 | 6,659,016 | 3,452,549 | 789,807 | 429,692 | 1,974,699 | 173 | 0.13% |
11 | 907,032 | 99.49% | 902,377 | 41.43% | 528,522 | 187 | 6,821,254 | 3,589,634 | 848,971 | 457,821 | 1,920,495 | 187 | 0.01% |
12 | 723,182 | 99.42% | 718,992 | 40.04% | 431,108 | 186 | 6,007,739 | 3,189,111 | 820,376 | 441,005 | 1,547,588 | 186 | 0.05% |
13 | 757,465 | 99.40% | 752,939 | 32.25% | 510,116 | 226 | 7,312,418 | 3,957,401 | 949,337 | 506,277 | 1,885,676 | 226 | 0.11% |
14 | 704,605 | 99.47% | 700,873 | 28.40% | 501,825 | 236 | 7,414,385 | 4,036,453 | 962,666 | 505,719 | 1,901,834 | 236 | 0.04% |
15 | 848,248 | 99.36% | 842,826 | 32.82% | 566,211 | 237 | 8,209,359 | 4,558,756 | 1,039,097 | 548,348 | 2,057,758 | 237 | 0.02% |
16 | 671,708 | 99.48% | 668,214 | 30.39% | 465,144 | 207 | 6,411,985 | 3,394,381 | 825,615 | 450,626 | 1,728,994 | 207 | 0.09% |
17 | 674,292 | 99.00% | 667,560 | 20.75% | 529,041 | 271 | 9,834,370 | 5,669,224 | 1,397,474 | 711,518 | 2,043,394 | 271 | 0.12% |
18 | 719,253 | 99.46% | 715,397 | 21.75% | 559,798 | 293 | 9,533,510 | 5,373,414 | 1,291,891 | 665,480 | 2,190,928 | 293 | 0.08% |
19 | 710,519 | 99.45% | 706,632 | 27.78% | 510,330 | 238 | 7,693,018 | 4,174,384 | 985,573 | 543,665 | 1,974,396 | 238 | 0.19% |
20 | 616,598 | 99.41% | 612,983 | 26.13% | 452,811 | 239 | 7,116,202 | 4,053,692 | 887,895 | 473,315 | 1,694,875 | 239 | 0.04% |
21 | 537,817 | 99.41% | 534,664 | 26.32% | 393,940 | 248 | 6,713,399 | 3,640,490 | 986,162 | 533,538 | 1,538,588 | 248 | 0.18% |
22 | 555,866 | 99.37% | 552,346 | 24.06% | 419,452 | 267 | 6,674,472 | 3,745,222 | 864,374 | 456,875 | 1,597,321 | 267 | 0.07% |
23 | 757,629 | 99.41% | 753,167 | 27.27% | 547,778 | 285 | 8,975,868 | 5,274,165 | 1,149,491 | 580,488 | 1,957,153 | 285 | 0.16% |
24 | 927,550 | 99.47% | 922,657 | 33.11% | 617,165 | 278 | 8,519,122 | 4,747,103 | 1,043,645 | 541,589 | 2,174,018 | 278 | 0.08% |
17,127,262 | 99.39% | 17,022,993 | 0.326725564 | 11,460,937 | 5282 |
PGP1 27 Device V9 (Single Denaturation Chamber) Random 8-mer Simplified Tag (mapped by BWA)[edit]
sample | Raw_reads | Mapping_rate | Mappable_reads | Clonal_rate | unique | 1+ | 1 | 2 | 3 | 4+ | contig |
1 | 1,480,684 | 85.07% | 1,259,630 | 11.35% | 1,116,662 | 28,202,462 | 17,827,314 | 4,461,358 | 2,002,027 | 3,900,784 | 1172 |
2 | 2,476,110 | 84.84% | 2,100,648 | 10.62% | 1,877,559 | 50,199,659 | 32,697,547 | 7,891,411 | 3,466,986 | 6,133,949 | 2052 |
3 | 2,076,640 | 84.70% | 1,758,960 | 13.46% | 1,522,204 | 36,562,106 | 22,615,204 | 5,731,936 | 2,678,237 | 5,525,374 | 1569 |
4 | 2,585,471 | 84.95% | 2,196,309 | 18.85% | 1,782,305 | 38,366,483 | 23,350,637 | 5,558,526 | 2,683,868 | 6,761,756 | 1575 |
5 | 2,509,697 | 84.99% | 2,132,876 | 16.38% | 1,783,511 | 38,695,018 | 23,346,934 | 5,711,895 | 2,755,220 | 6,868,105 | 1557 |
6 | 2,507,716 | 83.81% | 2,101,637 | 11.55% | 1,858,898 | 48,577,207 | 30,697,865 | 8,089,904 | 3,572,249 | 6,205,117 | 1864 |
7 | 1,588,435 | 85.30% | 1,354,986 | 11.82% | 1,194,827 | 30,546,845 | 19,599,233 | 4,750,889 | 2,151,443 | 4,034,198 | 1213 |
8 | 1,830,362 | 84.94% | 1,554,642 | 13.78% | 1,340,412 | 31,477,052 | 19,449,511 | 4,799,064 | 2,251,458 | 4,964,223 | 1295 |
9 | 1,538,587 | 84.87% | 1,305,738 | 11.89% | 1,150,486 | 27,875,370 | 16,930,165 | 4,554,439 | 2,150,968 | 4,227,130 | 1176 |
10 | 1,803,655 | 83.93% | 1,513,729 | 17.81% | 1,244,134 | 26,099,118 | 14,937,914 | 4,111,228 | 2,073,787 | 4,963,100 | 1178 |
11 | 685,896 | 82.96% | 568,994 | 9.24% | 516,419 | 14,515,013 | 9,575,229 | 2,369,611 | 1,003,588 | 1,555,774 | 564 |
12 | 1,675,696 | 84.09% | 1,409,135 | 18.18% | 1,152,954 | 25,261,348 | 15,210,431 | 3,886,271 | 1,852,526 | 4,299,523 | 1092 |
13 | 801,322 | 83.09% | 665,855 | 8.66% | 608,192 | 16,626,916 | 10,639,944 | 2,770,778 | 1,225,417 | 1,981,825 | 692 |
14 | 1,237,749 | 84.48% | 1,045,664 | 14.18% | 897,389 | 21,610,252 | 13,211,504 | 3,549,909 | 1,643,587 | 3,193,289 | 948 |
15 | 1,795,853 | 84.39% | 1,515,525 | 12.90% | 1,320,022 | 31,113,300 | 18,820,522 | 4,986,232 | 2,367,286 | 4,924,145 | 1368 |
16 | 1,388,962 | 83.72% | 1,162,800 | 11.81% | 1,025,473 | 24,626,927 | 14,722,640 | 4,090,553 | 1,951,357 | 3,850,085 | 1111 |
17 | 898,337 | 83.76% | 752,461 | 8.90% | 685,492 | 19,839,335 | 13,493,328 | 3,049,461 | 1,278,103 | 2,002,794 | 714 |
18 | 2,183,939 | 84.70% | 1,849,691 | 12.36% | 1,621,069 | 45,154,767 | 32,652,070 | 5,432,330 | 2,257,855 | 4,796,727 | 1321 |
19 | 2,926,888 | 86.70% | 2,537,523 | 21.26% | 1,998,046 | 41,607,868 | 25,394,175 | 5,972,928 | 2,840,457 | 7,383,998 | 1736 |
20 | 2,816,541 | 85.39% | 2,404,954 | 15.92% | 2,022,085 | 50,893,687 | 35,550,833 | 6,281,460 | 2,616,744 | 6,428,559 | 1540 |
21 | 2,564,937 | 84.85% | 2,176,410 | 20.53% | 1,729,593 | 37,400,147 | 24,062,720 | 4,855,664 | 2,251,674 | 6,213,763 | 1393 |
22 | 2,287,061 | 84.89% | 1,941,550 | 24.02% | 1,475,190 | 29,662,766 | 18,667,830 | 3,780,716 | 1,797,528 | 5,401,079 | 1122 |
23 | 1,717,383 | 85.58% | 1,469,733 | 18.70% | 1,194,893 | 27,798,882 | 18,740,085 | 3,488,855 | 1,541,205 | 4,013,052 | 960 |
24 | 973,638 | 87.05% | 847,546 | 20.08% | 677,359 | 14,139,245 | 8,532,615 | 2,085,848 | 988,931 | 2,521,439 | 603 |
44,351,559 | 84.84% | 37,626,996 | 0.154775334 | 31,795,173 | 29815 | ||||||
Nucleus 1 Device V8 Simplified Tag (mapped by BWA)[edit]
sample | Raw_reads | Mapping_rate | Mappable_reads | Clonal_rate | unique | 1+ | 1 | 2 | 3 | 4+ | Contigs |
1 | 1,367,845 | 94.40% | 1,291,213 | 25.82% | 957,822 | 17,894,592 | 9,936,378 | 2,664,537 | 1,361,344 | 3,924,192 | 971 |
2 | 1,515,583 | 93.97% | 1,424,260 | 25.04% | 1,067,625 | 19,506,866 | 10,412,189 | 2,975,810 | 1,559,090 | 4,553,664 | 1111 |
3 | 1,272,014 | 93.55% | 1,189,928 | 26.36% | 876,263 | 16,099,815 | 8,900,555 | 2,405,438 | 1,209,395 | 3,581,648 | 897 |
4 | 1,421,005 | 96.23% | 1,367,436 | 14.19% | 1,173,397 | 29,025,459 | 17,225,610 | 5,028,307 | 2,359,792 | 4,395,744 | 1672 |
5 | 1,518,021 | 93.50% | 1,419,328 | 30.69% | 983,736 | 16,323,724 | 8,690,515 | 2,374,148 | 1,246,613 | 4,006,208 | 917 |
6 | 1,600,096 | 93.62% | 1,498,045 | 28.41% | 1,072,450 | 19,064,725 | 10,488,686 | 2,819,703 | 1,426,898 | 4,327,115 | 1030 |
7 | 996,834 | 93.08% | 927,894 | 24.40% | 701,488 | 16,003,765 | 10,379,380 | 2,192,493 | 992,354 | 2,436,996 | 570 |
8 | 2,321,768 | 94.82% | 2,201,485 | 32.09% | 1,495,028 | 26,180,016 | 15,020,353 | 3,592,437 | 1,779,411 | 5,775,068 | 1369 |
9 | 1,955,968 | 97.37% | 1,904,532 | 5.70% | 1,795,974 | 63,663,976 | 47,571,336 | 9,582,487 | 3,224,919 | 3,271,995 | 1638 |
10 | 1,532,893 | 94.37% | 1,446,520 | 30.61% | 1,003,740 | 17,394,961 | 9,269,925 | 2,689,660 | 1,362,889 | 4,064,001 | 1082 |
11 | 1,616,392 | 95.57% | 1,544,742 | 18.62% | 1,257,111 | 25,215,419 | 13,187,240 | 4,267,866 | 2,226,632 | 5,526,123 | 1780 |
12 | 2,060,554 | 94.51% | 1,947,448 | 30.97% | 1,344,323 | 23,226,786 | 12,427,345 | 3,600,169 | 1,807,089 | 5,381,906 | 1397 |
13 | 2,085,645 | 95.79% | 1,997,839 | 19.60% | 1,606,263 | 31,586,997 | 16,391,449 | 5,315,686 | 2,791,557 | 7,082,460 | 2117 |
14 | 1,579,239 | 95.41% | 1,506,754 | 14.96% | 1,281,344 | 28,605,592 | 15,795,190 | 4,987,119 | 2,498,158 | 5,308,758 | 1836 |
15 | 2,187,406 | 95.22% | 2,082,874 | 18.14% | 1,705,041 | 35,552,195 | 19,339,127 | 5,847,076 | 3,010,678 | 7,344,745 | 2226 |
16 | 1,784,104 | 95.59% | 1,705,507 | 14.58% | 1,456,844 | 33,420,297 | 18,696,840 | 5,801,616 | 2,903,357 | 6,004,220 | 2115 |
17 | 2,126,051 | 95.51% | 2,030,567 | 21.26% | 1,598,868 | 38,795,370 | 25,517,512 | 5,600,269 | 2,349,804 | 5,319,216 | 1498 |
18 | 1,661,080 | 95.49% | 1,586,198 | 14.11% | 1,362,385 | 36,596,829 | 24,282,030 | 5,527,312 | 2,347,988 | 4,429,425 | 1587 |
19 | 812,048 | 95.79% | 777,830 | 4.60% | 742,050 | 27,813,705 | 21,776,009 | 3,728,945 | 1,194,072 | 1,107,754 | 530 |
20 | 55,437 | 94.17% | 52,205 | 1.21% | 51,573 | 2,545,098 | 2,481,352 | 59,293 | 2,268 | 236 | 0 |
21 | 146,336 | 95.06% | 139,101 | 1.57% | 136,917 | 6,539,077 | 6,171,518 | 325,229 | 31,862 | 7,609 | 2 |
22 | 48 | 75.00% | 36 | 0.00% | 36 | 1,800 | 1,750 | 0 | |||
23 | 864,533 | 95.73% | 827,611 | 2.23% | 809,155 | 35,583,533 | 31,391,109 | 3,263,328 | 599,441 | 318,752 | 182 |
24 | 253,984 | 93.52% | 237,515 | 2.00% | 232,765 | 10,830,543 | 9,928,390 | 781,324 | 92,519 | 20,605 | 5 |
32,734,884 | 95.03% | 31,106,868 | 0.206239459 | 24,712,199 | 26532 | ||||||
Nucleus 1 Device V8 Simplified Tag (mapped by Bowtie2)[edit]
sample | Raw_reads | Mapping_rate | Mappable_reads | Clonal_rate | unique | 1+ | 1 | 2 | 3 | 4+ | contag | %mito |
1 | 1367845 | 0.9953 | 1361440 | 0.2327 | 1044632.912 | 18478396 | 10269725 | 2752942 | 1401952 | 4045680 | 998 | 0.04164708 |
2 | 1515583 | 0.995 | 1507980 | 0.2216 | 1173811.632 | 20215597 | 10816713 | 3083939 | 1604768 | 4703673 | 1146 | 0.02274566 |
3 | 1272014 | 0.9937 | 1263990 | 0.2333 | 969101.133 | 16733796 | 9285921 | 2488967 | 1247161 | 3709019 | 924 | 0.006329164 |
4 | 1421005 | 0.9957 | 1414862 | 0.1201 | 1244937.074 | 29578942 | 17549952 | 5122482 | 2403131 | 4487372 | 1704 | 0.125383253 |
5 | 1518021 | 0.9937 | 1508481 | 0.2654 | 1108130.143 | 17009454 | 9107071 | 2468074 | 1283070 | 4144879 | 938 | 0.074313167 |
6 | 1600096 | 0.9939 | 1590390 | 0.2412 | 1206787.932 | 19820168 | 10945938 | 2924753 | 1470078 | 4476910 | 1056 | 0.00402417 |
7 | 996834 | 0.9938 | 990695 | 0.2006 | 791961.583 | 16787819 | 10941408 | 2285121 | 1032554 | 2526016 | 598 | 0.007267625 |
8 | 2321768 | 0.9949 | 2310020 | 0.2771 | 1669913.458 | 27103476 | 15633565 | 3710194 | 1827962 | 5918760 | 1404 | 0.063376075 |
9 | 1955968 | 0.9959 | 1948025 | 0.0496 | 1851402.96 | 64404637 | 48059653 | 9746795 | 3270488 | 3314082 | 1673 | 0.034599145 |
10 | 1532893 | 0.9952 | 1525547 | 0.2717 | 1111055.88 | 18014427 | 9639104 | 2778493 | 1405196 | 4182961 | 1106 | 0.029038764 |
11 | 1616392 | 0.9948 | 1607985 | 0.1574 | 1354888.161 | 25845412 | 13557984 | 4359570 | 2269518 | 5650734 | 1819 | 0.041542676 |
12 | 2060554 | 0.9948 | 2049835 | 0.2669 | 1502734.039 | 24042624 | 12931118 | 3716788 | 1858723 | 5525571 | 1423 | 0.031612301 |
13 | 2085645 | 0.9955 | 2076205 | 0.1642 | 1735292.139 | 32305640 | 16793664 | 5433622 | 2841533 | 7230618 | 2150 | 0.013919627 |
14 | 1579239 | 0.9945 | 1570568 | 0.1238 | 1376131.682 | 29304134 | 16196441 | 5104726 | 2551801 | 5434768 | 1894 | 0.205021368 |
15 | 2187406 | 0.9924 | 2170785 | 0.1471 | 1851462.527 | 36373988 | 19801168 | 5979060 | 3062538 | 7520728 | 2270 | 0.060208634 |
16 | 1784104 | 0.9944 | 1774108 | 0.1198 | 1561569.862 | 34184266 | 19137579 | 5925294 | 2959001 | 6147877 | 2153 | 0.066850496 |
17 | 2126051 | 0.9946 | 2114621 | 0.1815 | 1730817.289 | 39782967 | 26185672 | 5746001 | 2400013 | 5442381 | 1535 | 0.015794793 |
18 | 1661080 | 0.9938 | 1650735 | 0.1168 | 1457929.152 | 37487080 | 24893922 | 5657696 | 2394067 | 4530985 | 1613 | 0.027866375 |
19 | 812048 | 0.9948 | 807847 | 0.0369 | 778037.4457 | 28429858 | 22251003 | 3817219 | 1220513 | 1133954 | 549 | 0.024014448 |
20 | 55437 | 0.9935 | 55074 | 0.0113 | 54451.6638 | 2633540 | 2566979 | 61924 | 2290 | 293 | 0 | 0.081708247 |
21 | 146336 | 0.9939 | 145437 | 0.0142 | 143371.7946 | 6720035 | 6338445 | 337275 | 33374 | 7900 | 2 | 0.046068057 |
22 | 48 | 0.8542 | 41 | 0 | 41 | 1980 | 1930 | 0 | 2.43902439 | |||
23 | 864533 | 0.9947 | 859916 | 0.0185 | 844007.554 | 36361985 | 32051042 | 3352347 | 617476 | 330387 | 192 | 0.047446495 |
24 | 253984 | 0.9929 | 252192 | 0.0178 | 247702.9824 | 11250981 | 10302140 | 819475 | 98619 | 22621 | 6 | 0.099527344 |
32734884 | 0.99455298 | 26810172 | 27153 | total | ||||||||