BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231797.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 = 5,730,592 number of mapped reads = 4,647,570 (81.1%) number of supplementary alignments = 43,932 (0.77%) number of secondary alignments = 0 number of mapped bases = 285,780,753 bp number of sequenced bases = 285,681,566 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 550,278 duplication rate = 7.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9171 >>>>>>> ACTG content number of A's = 83,334,387 bp (29.17%) number of C's = 55,408,294 bp (19.4%) number of T's = 80,581,245 bp (28.21%) number of G's = 66,336,625 bp (23.22%) number of N's = 21,015 bp (0.01%) GC percentage = 42.62% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,759,854 number of insertions = 22,036 mapped reads with insertion percentage = 0.47% number of deletions = 58,575 mapped reads with deletion percentage = 1.25% homopolymer indels = 44.74% >>>>>>> Coverage mean coverageData = 0.0923X std coverageData = 15.0337X There is a 5.65% of reference with a coverageData >= 1X There is a 1.94% of reference with a coverageData >= 2X There is a 0.71% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 22533828 0.09040630634978437 1.3927675886899866 chr2 243199373 30345251 0.12477520244264774 53.565854919040454 chr3 198022430 20076484 0.1013848986703173 0.46813838116433615 chr4 191154276 18652339 0.09757740914987431 0.5839945896867316 chr5 180915260 13435750 0.07426543233555864 0.4066131266621278 chr6 171115067 17703577 0.10346007111109626 0.5705318009275044 chr7 159138663 16737593 0.10517615697198612 1.2519205381368894 chr8 146364022 19384386 0.1324395553983888 1.4705435653936603 chr9 141213431 10526111 0.07454043801258536 0.6513417137123111 chr10 135534747 15625200 0.11528556584829129 0.8604461889009579 chr11 135006516 11471805 0.08497223200693513 0.6029413298408675 chr12 133851895 10712484 0.08003236711740241 0.42585584087625084 chr13 115169878 7667336 0.06657414363154922 0.38234632516288763 chr14 107349540 9750535 0.09082977905634249 0.6123261677622795 chr15 102531392 7891029 0.07696207811164799 0.4154041532874747 chr16 90354753 7527558 0.08331114578997299 0.47680151680831756 chr17 81195210 6575873 0.08098843515522652 0.4743948470135345 chr18 78077248 6804207 0.08714711614835605 1.2199256566852095 chr19 59128983 6923770 0.11709604408382941 1.032065915635004 chr20 63025520 5214759 0.08274043593769635 0.45225374697829773 chr21 48129895 3296968 0.06850145839711473 0.4732083353946987 chr22 51304566 2701765 0.05266129724204274 0.3238056435642243 chrMT 16571 340513 20.548729708526945 13.590270128459485 chrX 155270560 12815710 0.08253792605629812 0.47333693155550927 chrY 59373566 1065922 0.017952804114881697 0.4369341407925654