BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068170.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 = 1,922,882 number of mapped reads = 1,653,972 (86.02%) number of supplementary alignments = 10,002 (0.52%) number of secondary alignments = 0 number of mapped bases = 111,167,433 bp number of sequenced bases = 111,114,529 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 323,584 duplication rate = 12.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5898 >>>>>>> ACTG content number of A's = 31,148,961 bp (28.03%) number of C's = 19,774,656 bp (17.8%) number of T's = 36,104,299 bp (32.49%) number of G's = 23,959,235 bp (21.56%) number of N's = 127,378 bp (0.11%) GC percentage = 39.36% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 982,771 number of insertions = 8,050 mapped reads with insertion percentage = 0.48% number of deletions = 30,173 mapped reads with deletion percentage = 1.8% homopolymer indels = 49.08% >>>>>>> Coverage mean coverageData = 0.0359X std coverageData = 0.5201X There is a 1.26% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.22% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 10566148 0.04239166168416487 0.726060318511662 chr2 243199373 10839557 0.04457066178373741 0.5515582814422894 chr3 198022430 7176365 0.036240162288686185 0.451350593782151 chr4 191154276 8120339 0.04248055115439845 0.49296394462290144 chr5 180915260 5495651 0.030376934483028133 0.4123930816529143 chr6 171115067 6097142 0.03563182428581815 0.4594703257019099 chr7 159138663 6932540 0.04356288955374722 0.5878097556692682 chr8 146364022 5133629 0.03507439143753511 0.54104803007793 chr9 141213431 3889288 0.027541912780236887 0.5022057290293968 chr10 135534747 5175332 0.038184540234542215 0.5614717033670396 chr11 135006516 4841780 0.03586330603479909 0.4995115221941697 chr12 133851895 5581257 0.04169725800295917 0.49232157284573147 chr13 115169878 2823717 0.024517843111720585 0.3750966870375181 chr14 107349540 3163606 0.0294701402539778 0.4191349692458525 chr15 102531392 2735136 0.026676083750038233 0.3789482976481084 chr16 90354753 2910468 0.0322115650075431 0.4331608703493017 chr17 81195210 2381334 0.02932850349177002 0.397592401460389 chr18 78077248 2739395 0.035085701278815565 0.8829633495655659 chr19 59128983 1756527 0.0297067006885608 0.5260617663727145 chr20 63025520 1906854 0.030255268024762035 0.4072994176592287 chr21 48129895 1796644 0.03732906543843489 0.45150549380061294 chr22 51304566 1194246 0.02327757728230271 0.3332736849776509 chrMT 16571 230550 13.912859815340052 12.249496400497273 chrX 155270560 7432181 0.047866002415396715 0.5460949540659616 chrY 59373566 247747 0.004172681829486206 0.1367594191480799