BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716539.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,763,574 number of mapped reads = 1,684,174 (95.5%) number of supplementary alignments = 34,964 (1.98%) number of secondary alignments = 0 number of mapped bases = 133,182,456 bp number of sequenced bases = 133,130,646 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,595 duplication rate = 4.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2738 >>>>>>> ACTG content number of A's = 32,788,539 bp (24.63%) number of C's = 27,194,189 bp (20.43%) number of T's = 38,524,101 bp (28.94%) number of G's = 34,618,669 bp (26%) number of N's = 5,148 bp (0%) GC percentage = 46.43% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 870,552 number of insertions = 10,490 mapped reads with insertion percentage = 0.61% number of deletions = 24,648 mapped reads with deletion percentage = 1.43% homopolymer indels = 40.3% >>>>>>> Coverage mean coverageData = 0.043X std coverageData = 0.3769X There is a 3.52% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% 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 14534524 0.058312889820242415 0.7590726157409157 chr2 243199373 12183407 0.0500963750428748 0.37867034089669244 chr3 198022430 8257635 0.041700503321770166 0.24155858952887835 chr4 191154276 6470311 0.033848633341584264 0.32763738365157946 chr5 180915260 8036316 0.044420332480521546 0.2539272275851882 chr6 171115067 8039678 0.04698404495262828 0.26930883059799227 chr7 159138663 8307732 0.05220435966588459 0.4753008128706865 chr8 146364022 8124557 0.05550924939736898 0.3899557749350354 chr9 141213431 4024211 0.028497367222810415 0.2646932635191011 chr10 135534747 7042136 0.05195815948215848 0.4666296000973432 chr11 135006516 5668017 0.04198328471790206 0.33560988719318724 chr12 133851895 4611682 0.03445361755991576 0.21858282031902365 chr13 115169878 2479774 0.02153144592199707 0.17136748905459132 chr14 107349540 2571044 0.023950209754042728 0.20061332067928447 chr15 102531392 2753851 0.026858613213795048 0.19055501749365739 chr16 90354753 3996723 0.044233677446940727 0.2665584394403656 chr17 81195210 2514018 0.030962639298549754 0.2329881211822597 chr18 78077248 3878106 0.04967011644672722 0.4363904189466929 chr19 59128983 3277197 0.055424545353671986 0.5317413835584296 chr20 63025520 3561763 0.05651302837326848 0.2979807689227138 chr21 48129895 2081945 0.043256794971192024 0.2991573481490475 chr22 51304566 2067520 0.040298947271086946 0.24674586076645538 chrMT 16571 29501 1.7802788003138013 1.9327258568720598 chrX 155270560 8162514 0.05256961783354166 0.2855980372184604 chrY 59373566 508294 0.008560947813038549 0.31491843563220373