BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238071.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 = 1,276,302 number of mapped reads = 647,438 (50.73%) number of supplementary alignments = 5,107 (0.4%) number of secondary alignments = 0 number of mapped bases = 37,829,852 bp number of sequenced bases = 37,805,381 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,804 duplication rate = 5.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5471 >>>>>>> ACTG content number of A's = 9,702,007 bp (25.66%) number of C's = 6,281,973 bp (16.62%) number of T's = 12,540,749 bp (33.17%) number of G's = 9,279,223 bp (24.54%) number of N's = 1,429 bp (0%) GC percentage = 41.16% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 321,352 number of insertions = 2,868 mapped reads with insertion percentage = 0.44% number of deletions = 15,163 mapped reads with deletion percentage = 2.31% homopolymer indels = 44.11% >>>>>>> Coverage mean coverageData = 0.0122X std coverageData = 0.1494X There is a 1.05% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% 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 2853015 0.011446370679252992 0.1817237153685685 chr2 243199373 2900545 0.01192661380751175 0.20461275706788012 chr3 198022430 2797708 0.014128237897090749 0.13564025839323943 chr4 191154276 2196054 0.01148838543376346 0.1278400290756099 chr5 180915260 2329237 0.012874740361868866 0.1296892083847378 chr6 171115067 2503236 0.01462896309417335 0.1498799287562482 chr7 159138663 2086658 0.013112200144599682 0.1791417865458597 chr8 146364022 1892343 0.012929017487644606 0.16211405970865128 chr9 141213431 1595190 0.011296305094378735 0.13511279119716554 chr10 135534747 2067245 0.015252509380491188 0.16273326899396895 chr11 135006516 1304172 0.00966006707409589 0.11781436692963501 chr12 133851895 1943701 0.014521281151828295 0.14387732735972894 chr13 115169878 1242175 0.010785589266665715 0.12017980717861393 chr14 107349540 1017796 0.009481139835345358 0.11364356982241806 chr15 102531392 1079916 0.010532540121956015 0.11836701126496817 chr16 90354753 1047610 0.011594409427470849 0.1266380736578912 chr17 81195210 1089299 0.013415803715514745 0.13357075655171363 chr18 78077248 973287 0.012465692950653178 0.18323697350084148 chr19 59128983 705818 0.011936921018918929 0.15671830869401904 chr20 63025520 733640 0.011640364093782963 0.12380096111626537 chr21 48129895 401805 0.008348345659179185 0.10729245548478454 chr22 51304566 377896 0.007365738168411755 0.09730827421764024 chrMT 16571 19479 1.1754872970852694 1.3304682812722934 chrX 155270560 2545359 0.01639305609511552 0.15074933121478895 chrY 59373566 126668 0.00213340731462887 0.059934607255664483