BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237793.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 = 3,660,934 number of mapped reads = 125,829 (3.44%) number of supplementary alignments = 958 (0.03%) number of secondary alignments = 0 number of mapped bases = 7,477,729 bp number of sequenced bases = 7,473,691 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,121 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3102 >>>>>>> ACTG content number of A's = 2,191,523 bp (29.32%) number of C's = 1,347,673 bp (18.03%) number of T's = 2,253,152 bp (30.15%) number of G's = 1,675,545 bp (22.42%) number of N's = 5,798 bp (0.08%) GC percentage = 40.45% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 78,727 number of insertions = 605 mapped reads with insertion percentage = 0.48% number of deletions = 2,708 mapped reads with deletion percentage = 2.13% homopolymer indels = 49.11% >>>>>>> Coverage mean coverageData = 0.0024X std coverageData = 0.0532X There is a 0.23% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 647332 0.0025971128874338893 0.05804112322856019 chr2 243199373 660873 0.002717412433460509 0.05770399302265754 chr3 198022430 572679 0.0028919905689471642 0.05653039500067726 chr4 191154276 442648 0.0023156583742861185 0.050817449312324535 chr5 180915260 426444 0.0023571477607803788 0.051009004810636895 chr6 171115067 474908 0.0027753722002750347 0.05814106539680055 chr7 159138663 408362 0.002566076604526959 0.056323257508163665 chr8 146364022 517110 0.003533040380647643 0.0669030059728127 chr9 141213431 274301 0.0019424568757910854 0.04724826660628575 chr10 135534747 360378 0.0026589343911934257 0.05454883134069338 chr11 135006516 318709 0.0023606934646028493 0.05193406492804131 chr12 133851895 340456 0.002543527680351481 0.0529638879066191 chr13 115169878 235504 0.0020448402315751345 0.04762313502848804 chr14 107349540 235924 0.002197717847696413 0.04966194861885522 chr15 102531392 192574 0.0018781955091373382 0.04539829359141576 chr16 90354753 188401 0.002085125505240438 0.048337650577909216 chr17 81195210 172147 0.002120162014483367 0.048242589683137264 chr18 78077248 151420 0.0019393613873275861 0.05172313355807508 chr19 59128983 120222 0.002033216096410791 0.04890606669856696 chr20 63025520 147563 0.0023413214202754693 0.05054097385638997 chr21 48129895 88958 0.0018482899245884496 0.04462694733657509 chr22 51304566 80846 0.0015758051632285516 0.04117428301272068 chrMT 16571 5766 0.3479572747571058 0.7208654414403138 chrX 155270560 394202 0.0025388070990405394 0.053629260903135655 chrY 59373566 20002 3.368839257524131E-4 0.019417543186086756