BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237316.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 = 3,213,934 number of mapped reads = 2,877,382 (89.53%) number of supplementary alignments = 18,994 (0.59%) number of secondary alignments = 0 number of mapped bases = 194,348,927 bp number of sequenced bases = 194,267,953 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 181,245 duplication rate = 4.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3488 >>>>>>> ACTG content number of A's = 54,571,040 bp (28.09%) number of C's = 35,264,877 bp (18.15%) number of T's = 62,190,417 bp (32.01%) number of G's = 42,238,290 bp (21.74%) number of N's = 3,329 bp (0%) GC percentage = 39.89% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,524,521 number of insertions = 14,780 mapped reads with insertion percentage = 0.51% number of deletions = 49,838 mapped reads with deletion percentage = 1.71% homopolymer indels = 47.39% >>>>>>> Coverage mean coverageData = 0.0628X std coverageData = 0.6259X There is a 4.61% of reference with a coverageData >= 1X There is a 1.09% of reference with a coverageData >= 2X There is a 0.29% 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 14391145 0.05773764952826336 1.045871030545322 chr2 243199373 10557913 0.04341258314017117 0.6246199932095802 chr3 198022430 9767340 0.04932441239106095 0.2828602205661982 chr4 191154276 14428754 0.07548224555541724 0.36670572324242123 chr5 180915260 10007006 0.05531322233403639 0.3090635790860122 chr6 171115067 11516406 0.06730211548232629 0.7430239599139103 chr7 159138663 8805619 0.05533299597973875 0.9454094393419712 chr8 146364022 13084961 0.08940011910850605 0.8020368252637614 chr9 141213431 9229280 0.06535695602495488 0.45710669170832896 chr10 135534747 4904824 0.03618868303933898 0.3724364034151723 chr11 135006516 23588620 0.1747220852658697 1.2110809822997706 chr12 133851895 11650208 0.08703805052591897 0.379380179338796 chr13 115169878 2608185 0.02264641627908992 0.19247598938235155 chr14 107349540 4132173 0.03849269405346311 0.26019518364444355 chr15 102531392 816521 0.007963619571262624 0.14468154324892055 chr16 90354753 8002612 0.08856879947422357 0.3933373435242916 chr17 81195210 5810545 0.07156265745233001 0.669051265748067 chr18 78077248 5306918 0.06797009546238104 0.583417304607926 chr19 59128983 3122971 0.05281624749067644 0.8608836527874899 chr20 63025520 2851107 0.0452373419529105 0.2806717295409564 chr21 48129895 3566531 0.07410219781281467 0.37046321885154654 chr22 51304566 1893936 0.03691554470999716 0.2369554164564901 chrMT 16571 103874 6.268420735019009 4.766391240071895 chrX 155270560 13820829 0.08901126523920568 0.48094626855359246 chrY 59373566 380649 0.0064110853641501 0.12641334626796463