BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234084.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 = 954,563 number of mapped reads = 706,809 (74.05%) number of supplementary alignments = 4,186 (0.44%) number of secondary alignments = 0 number of mapped bases = 46,041,202 bp number of sequenced bases = 46,014,921 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,490 duplication rate = 2.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3735 >>>>>>> ACTG content number of A's = 12,923,858 bp (28.09%) number of C's = 7,841,052 bp (17.04%) number of T's = 15,147,939 bp (32.92%) number of G's = 10,094,936 bp (21.94%) number of N's = 7,136 bp (0.02%) GC percentage = 38.98% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 397,440 number of insertions = 3,600 mapped reads with insertion percentage = 0.5% number of deletions = 15,148 mapped reads with deletion percentage = 2.11% homopolymer indels = 45.3% >>>>>>> Coverage mean coverageData = 0.0149X std coverageData = 0.1815X There is a 1.35% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 3880975 0.015570573041822031 0.23938357531155613 chr2 243199373 2829231 0.01163338114362655 0.1641562884432059 chr3 198022430 3640482 0.0183841901142209 0.1475938436918008 chr4 191154276 1658953 0.008678607848667743 0.10292303437482102 chr5 180915260 2998805 0.016575743804032893 0.13869302371439346 chr6 171115067 2843091 0.016615082761823656 0.14592029380489835 chr7 159138663 2916567 0.018327205626956913 0.20238533671509268 chr8 146364022 3155110 0.021556595376970442 0.43513905055026103 chr9 141213431 1581849 0.011201831077951785 0.13067248270743814 chr10 135534747 2361773 0.01742559050189543 0.15552714194359696 chr11 135006516 1699551 0.012588659054056324 0.1807662290670148 chr12 133851895 1687753 0.012609107999554283 0.12128263704970879 chr13 115169878 2247489 0.019514555707005263 0.15107331022589418 chr14 107349540 2361824 0.02200124937656929 0.16253812872706036 chr15 102531392 935842 0.009127370474010535 0.10362081099484882 chr16 90354753 1085748 0.012016501223792843 0.12348760707288987 chr17 81195210 1116221 0.013747374999091694 0.12866404100970202 chr18 78077248 1106770 0.01417532031866697 0.22521485358773616 chr19 59128983 1123457 0.019000106935713742 0.17790014593276476 chr20 63025520 996452 0.01581029398884769 0.14170032604337263 chr21 48129895 1053796 0.021894832722988488 0.16210845240915575 chr22 51304566 439719 0.008570757620286662 0.09840323087074285 chrMT 16571 37605 2.269325930843039 2.3042519442981595 chrX 155270560 2169342 0.013971367141330591 0.13475798748859819 chrY 59373566 112797 0.00189978483017173 0.052509102481821494