BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716905.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 = 618,823 number of mapped reads = 519,224 (83.91%) number of supplementary alignments = 1,530 (0.25%) number of secondary alignments = 0 number of mapped bases = 28,783,825 bp number of sequenced bases = 28,775,575 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,463 duplication rate = 1.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.2941 >>>>>>> ACTG content number of A's = 7,006,526 bp (24.35%) number of C's = 5,770,022 bp (20.05%) number of T's = 8,477,692 bp (29.46%) number of G's = 7,520,444 bp (26.13%) number of N's = 891 bp (0%) GC percentage = 46.19% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 155,518 number of insertions = 2,506 mapped reads with insertion percentage = 0.48% number of deletions = 4,989 mapped reads with deletion percentage = 0.95% homopolymer indels = 37.24% >>>>>>> Coverage mean coverageData = 0.0093X std coverageData = 0.1117X There is a 0.88% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.01% 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 2832029 0.011362174299256811 0.1291549834002757 chr2 243199373 2480078 0.01019771543572195 0.14152437325165196 chr3 198022430 1934289 0.009768029813592328 0.10629530027676488 chr4 191154276 1792532 0.009377409899007438 0.10810588305222314 chr5 180915260 1867676 0.010323485149898356 0.1065270482369628 chr6 171115067 1232775 0.007204362664335105 0.09196657597020699 chr7 159138663 1632712 0.010259681520637132 0.12105316263037795 chr8 146364022 1769087 0.012086897967316039 0.12002509388198411 chr9 141213431 1252567 0.008870027384293213 0.10309101683644137 chr10 135534747 1482866 0.010940854893837667 0.1415760725692719 chr11 135006516 1182784 0.008760940101587393 0.10998974685695935 chr12 133851895 1392820 0.010405680098888401 0.10684785868818651 chr13 115169878 521505 0.004528137122798723 0.07126148658373706 chr14 107349540 933632 0.008697121571270823 0.09935288668112367 chr15 102531392 573795 0.005596286062321284 0.07855475711650786 chr16 90354753 784619 0.008683760111656771 0.10218994269464994 chr17 81195210 1126890 0.01387877437597612 0.12810468128832908 chr18 78077248 780987 0.010002747535363952 0.12060633380589196 chr19 59128983 781945 0.013224394540998616 0.13628214402612782 chr20 63025520 716186 0.011363428655566825 0.11452457089795978 chr21 48129895 395851 0.008224638761418449 0.09962009612870255 chr22 51304566 315518 0.006149900965929621 0.08288902108905108 chrMT 16571 4192 0.2529720596222316 0.5186487323005462 chrX 155270560 906018 0.005835091983953687 0.0860386733725317 chrY 59373566 90472 0.0015237757489587201 0.05381205358522027