BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514769.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 4,683,915 number of mapped reads = 2,443,564 (52.17%) number of supplementary alignments = 393,760 (8.41%) number of secondary alignments = 0 number of mapped bases = 229,874,230 bp number of sequenced bases = 229,727,006 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 923,245 duplication rate = 21.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0552 >>>>>>> ACTG content number of A's = 71,971,625 bp (31.33%) number of C's = 42,404,346 bp (18.46%) number of T's = 70,984,617 bp (30.9%) number of G's = 44,351,413 bp (19.31%) number of N's = 15,005 bp (0.01%) GC percentage = 37.76% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,232,248 number of insertions = 110,915 mapped reads with insertion percentage = 4.36% number of deletions = 52,047 mapped reads with deletion percentage = 2% homopolymer indels = 50.06% >>>>>>> Coverage mean coverageData = 0.0743X std coverageData = 3.3351X There is a 1.32% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.31% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 14774922 0.05927737287362666 1.401694147894206 chr2 243199373 16674495 0.06856306738915811 2.173890795955772 chr3 198022430 19847957 0.10023085263623924 2.0013146277688922 chr4 191154276 15940217 0.08338927767433253 1.5278272694096957 chr5 180915260 16396414 0.09063035368050214 2.2662278132084404 chr6 171115067 13048941 0.07625828180285257 1.6890620352331924 chr7 159138663 12359026 0.07766199468447212 1.7507793274387111 chr8 146364022 8163082 0.05577246298957267 1.6253426344271305 chr9 141213431 15071034 0.10672521652703135 2.745691952342466 chr10 135534747 15850813 0.11695017957277037 2.7245333542288206 chr11 135006516 9239555 0.06843784488150187 1.8357064116628288 chr12 133851895 12750210 0.09525610377051442 2.7042942416038596 chr13 115169878 9816866 0.08523813839587466 12.10333365936999 chr14 107349540 5129196 0.04778032584024114 1.3333904047640794 chr15 102531392 7159882 0.0698311205996306 5.51329941189998 chr16 90354753 3478870 0.038502346412257915 1.0863084362122157 chr17 81195210 5529787 0.06810484263788467 1.7442842938622498 chr18 78077248 7043752 0.09021516741983529 4.2410548566908 chr19 59128983 2782385 0.04705619577458317 1.6416311313131255 chr20 63025520 2078850 0.03298425780540962 1.106524706669352 chr21 48129895 2685907 0.055805378341257546 1.6583538343564759 chr22 51304566 629477 0.01226941477294633 0.4182276501377799 chrMT 16571 4623264 278.9972844125279 328.6036197241413 chrX 155270560 7424168 0.047814395723181524 1.3657964306281603 chrY 59373566 1375160 0.02316114885199922 1.1155943137394477