BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238078.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 = 1,178,783 number of mapped reads = 1,046,549 (88.78%) number of supplementary alignments = 6,343 (0.54%) number of secondary alignments = 0 number of mapped bases = 68,132,280 bp number of sequenced bases = 68,099,753 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,413 duplication rate = 2.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3292 >>>>>>> ACTG content number of A's = 18,238,766 bp (26.78%) number of C's = 12,541,613 bp (18.42%) number of T's = 20,882,228 bp (30.66%) number of G's = 16,315,497 bp (23.96%) number of N's = 121,649 bp (0.18%) GC percentage = 42.37% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 638,971 number of insertions = 6,578 mapped reads with insertion percentage = 0.62% number of deletions = 19,365 mapped reads with deletion percentage = 1.83% homopolymer indels = 46.19% >>>>>>> Coverage mean coverageData = 0.022X std coverageData = 0.3142X There is a 2% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 6046065 0.02425697065765786 0.5947305037070469 chr2 243199373 5462762 0.022462072712662793 0.4012079137367889 chr3 198022430 4253101 0.021477875006381854 0.16462938462401971 chr4 191154276 4339632 0.022702249150837725 0.18148639746459724 chr5 180915260 4075976 0.022529752327139236 0.1611876889277174 chr6 171115067 4056144 0.02370418964917917 0.21062836901754586 chr7 159138663 3606639 0.022663499441364542 0.38249193634896567 chr8 146364022 3159836 0.021588884732888797 0.287042062286525 chr9 141213431 2859224 0.020247535802738196 0.3409091258234055 chr10 135534747 4174354 0.03079914259920373 0.40133519284250746 chr11 135006516 3258014 0.024132272252696308 0.2809670569827336 chr12 133851895 2967281 0.02216838992081509 0.16306338276691731 chr13 115169878 2016130 0.017505705788800088 0.13755165641938377 chr14 107349540 1994809 0.0185823711960014 0.18371956021521726 chr15 102531392 1785446 0.017413652201269246 0.14000846146309098 chr16 90354753 2106775 0.02331670366029333 0.2092333966812426 chr17 81195210 1842069 0.022686917122327784 0.19842848852610423 chr18 78077248 1895815 0.02428127333586348 0.6115726411688752 chr19 59128983 1560598 0.02639311418564395 0.4292151658624446 chr20 63025520 1260371 0.019997788197542835 0.16534007263264788 chr21 48129895 879435 0.01827211549079839 0.16641625837323112 chr22 51304566 750233 0.014623123407768423 0.12653384013892258 chrMT 16571 38863 2.345241687285016 2.0823101038829672 chrX 155270560 3517538 0.022654249459781686 0.20549911587546585 chrY 59373566 225170 0.003792428435240019 0.11470633388676824