BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004061.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,936,427 number of mapped reads = 2,457,044 (83.67%) number of supplementary alignments = 18,239 (0.62%) number of secondary alignments = 0 number of mapped bases = 159,813,188 bp number of sequenced bases = 159,745,826 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 145,302 duplication rate = 4.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1672 >>>>>>> ACTG content number of A's = 43,401,164 bp (27.17%) number of C's = 30,685,141 bp (19.21%) number of T's = 48,901,199 bp (30.61%) number of G's = 36,726,010 bp (22.99%) number of N's = 32,312 bp (0.02%) GC percentage = 42.2% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,300,595 number of insertions = 11,690 mapped reads with insertion percentage = 0.47% number of deletions = 40,441 mapped reads with deletion percentage = 1.63% homopolymer indels = 46.33% >>>>>>> Coverage mean coverageData = 0.0516X std coverageData = 0.4498X There is a 3.76% of reference with a coverageData >= 1X There is a 0.91% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 20534141 0.08238350988902853 0.9130661061510481 chr2 243199373 12541765 0.05156989035493936 0.5130348743114412 chr3 198022430 12068611 0.06094567670945155 0.31768241954948134 chr4 191154276 6779191 0.03546450093535967 0.26366786051769203 chr5 180915260 10627832 0.058744806822818595 0.3139261680139472 chr6 171115067 10927728 0.06386186904277692 0.397379397206616 chr7 159138663 8544758 0.05369379030160634 0.3486202047976857 chr8 146364022 13032234 0.08903987347382405 0.5052950563682055 chr9 141213431 6799203 0.04814841585429647 0.41486676288359603 chr10 135534747 7732487 0.057051694647720114 0.4546558395810665 chr11 135006516 7751623 0.05741665831892143 0.36062798239909644 chr12 133851895 1426635 0.010658310067257546 0.15400193234602216 chr13 115169878 6348724 0.055124865201298556 0.30890070501539935 chr14 107349540 6665354 0.062090196194599434 0.37431295881102306 chr15 102531392 1003206 0.009784379012429676 0.14761126439034944 chr16 90354753 3009730 0.03331014584257676 0.28985104665006794 chr17 81195210 7994370 0.09845864060207493 0.46706710790782846 chr18 78077248 3390999 0.04343133354290356 0.7508844155219572 chr19 59128983 2449610 0.041428245095979414 0.646930865965414 chr20 63025520 1299578 0.02061986953856152 0.21327149399214945 chr21 48129895 2771300 0.05757959787778469 0.3419615419840587 chr22 51304566 501584 0.009776595712748063 0.12062779950488017 chrMT 16571 46208 2.7884859091183394 2.546017318596127 chrX 155270560 5234469 0.033711921950948076 0.2793270291059397 chrY 59373566 331848 0.005589153934260914 0.14632162685599404