BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004011.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 = 1,682,667 number of mapped reads = 1,542,701 (91.68%) number of supplementary alignments = 12,477 (0.74%) number of secondary alignments = 0 number of mapped bases = 102,038,753 bp number of sequenced bases = 101,994,590 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,566 duplication rate = 2.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7588 >>>>>>> ACTG content number of A's = 28,371,468 bp (27.82%) number of C's = 19,233,485 bp (18.86%) number of T's = 31,008,848 bp (30.4%) number of G's = 23,359,256 bp (22.9%) number of N's = 21,533 bp (0.02%) GC percentage = 41.76% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 805,479 number of insertions = 8,313 mapped reads with insertion percentage = 0.53% number of deletions = 25,336 mapped reads with deletion percentage = 1.62% homopolymer indels = 45.6% >>>>>>> Coverage mean coverageData = 0.033X std coverageData = 0.3503X There is a 2.92% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8167040 0.03276637774154232 0.5487465730184162 chr2 243199373 8523228 0.0350462581167921 0.3861072606073526 chr3 198022430 6815837 0.034419520051339636 0.20579860985799356 chr4 191154276 6644996 0.03476247635705518 0.22923217441999016 chr5 180915260 5820335 0.03217160896211851 0.20051624909937404 chr6 171115067 5906405 0.03451715330246167 0.22134319615250597 chr7 159138663 6343857 0.03986370678506957 0.5081713874934092 chr8 146364022 6268216 0.042826207659147277 0.48637198729813125 chr9 141213431 3894361 0.027577837125138612 0.27785192652919294 chr10 135534747 4842903 0.03573181864573813 0.2952531684299313 chr11 135006516 4587445 0.03397943400005967 0.350930826976778 chr12 133851895 4584417 0.03424992227416728 0.2073984476622649 chr13 115169878 3141883 0.027280423098129877 0.18416865922544634 chr14 107349540 2725688 0.025390774846357052 0.19742612949214253 chr15 102531392 2885598 0.028143556268113476 0.190447177031598 chr16 90354753 2693718 0.02981268733034996 0.21643483035150946 chr17 81195210 2595577 0.03196711973526517 0.22591892317915865 chr18 78077248 2608390 0.033407811709756985 0.5773093172707567 chr19 59128983 1900231 0.03213704859425707 0.4057067832442277 chr20 63025520 2128871 0.03377792043603924 0.21808357779120563 chr21 48129895 1115246 0.02317158597582646 0.1861214069172959 chr22 51304566 1034589 0.020165632041405437 0.15385420460425697 chrMT 16571 678818 40.964214591756686 29.601075073494094 chrX 155270560 5849181 0.03767089524247224 0.23722725568693118 chrY 59373566 281923 0.004748291520842794 0.11537036812730636