BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008744.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 = 1,805,521 number of mapped reads = 1,235,516 (68.43%) number of supplementary alignments = 5,082 (0.28%) number of secondary alignments = 0 number of mapped bases = 78,773,797 bp number of sequenced bases = 78,727,523 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,153 duplication rate = 2.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4388 >>>>>>> ACTG content number of A's = 22,705,348 bp (28.84%) number of C's = 13,507,271 bp (17.16%) number of T's = 23,769,283 bp (30.19%) number of G's = 18,741,807 bp (23.81%) number of N's = 3,814 bp (0%) GC percentage = 40.96% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 754,374 number of insertions = 6,548 mapped reads with insertion percentage = 0.53% number of deletions = 29,217 mapped reads with deletion percentage = 2.33% homopolymer indels = 47.05% >>>>>>> Coverage mean coverageData = 0.0254X std coverageData = 0.2257X There is a 2.3% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.03% 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 7255907 0.02911088835361417 0.30208912600707766 chr2 243199373 6096323 0.025067182225013383 0.31721717036118013 chr3 198022430 4879025 0.02463874925683924 0.17756896977470507 chr4 191154276 5017404 0.0262479297088808 0.17896742474499225 chr5 180915260 4607634 0.025468465180880816 0.1744470989962848 chr6 171115067 4578913 0.02675926252595863 0.19568683773671378 chr7 159138663 4634431 0.029121967676704687 0.3083140761523372 chr8 146364022 5238108 0.03578822123376741 0.27550417631200963 chr9 141213431 2491401 0.017642804812241973 0.19673251860286078 chr10 135534747 4034349 0.02976616025999591 0.25516125520977695 chr11 135006516 3059861 0.022664543095090313 0.20433886700991513 chr12 133851895 3775275 0.028204867775685954 0.18892880934767223 chr13 115169878 2079469 0.01805566729870114 0.15225269018598747 chr14 107349540 3130157 0.029158550656109006 0.19292233995085523 chr15 102531392 2165030 0.02111577691249915 0.16186831849843808 chr16 90354753 2291421 0.02536027075410189 0.1839530528496122 chr17 81195210 2027855 0.024975057026147232 0.186599180187951 chr18 78077248 1459597 0.018694268015184142 0.2704219636253612 chr19 59128983 1256207 0.021245198822377853 0.20840815034489482 chr20 63025520 1951695 0.030966741726208686 0.19369120742024007 chr21 48129895 766422 0.015924032246486305 0.14238538484140537 chr22 51304566 826849 0.016116479769071625 0.14003295095639995 chrMT 16571 26753 1.6144469253515177 1.6551386827617598 chrX 155270560 4927020 0.031731836350690046 0.20780985569017973 chrY 59373566 196691 0.003312770534954899 0.07221650723279711