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) ==


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|-
|-
| ||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]

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