BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231723.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 = 1,502,786 number of mapped reads = 273,419 (18.19%) number of supplementary alignments = 2,605 (0.17%) number of secondary alignments = 0 number of mapped bases = 16,358,194 bp number of sequenced bases = 16,348,874 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,395 duplication rate = 6.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.2801 >>>>>>> ACTG content number of A's = 4,267,776 bp (26.1%) number of C's = 3,171,479 bp (19.4%) number of T's = 5,021,611 bp (30.72%) number of G's = 3,884,479 bp (23.76%) number of N's = 3,529 bp (0.02%) GC percentage = 43.16% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 165,605 number of insertions = 2,444 mapped reads with insertion percentage = 0.87% number of deletions = 5,421 mapped reads with deletion percentage = 1.95% homopolymer indels = 39.5% >>>>>>> Coverage mean coverageData = 0.0053X std coverageData = 0.1124X There is a 0.39% of reference with a coverageData >= 1X There is a 0.08% 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% 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 1389094 0.005573081400667804 0.12056020950099379 chr2 243199373 1396110 0.0057405986815599235 0.12515396053611458 chr3 198022430 1167617 0.005896387596092018 0.10995235009673907 chr4 191154276 959197 0.0050179207081927895 0.10330624263662734 chr5 180915260 952815 0.005266636987946733 0.1081635698935137 chr6 171115067 976837 0.005708655684890682 0.10979658450309861 chr7 159138663 931346 0.005852418151835296 0.11833193225566516 chr8 146364022 866717 0.0059216533418301395 0.11787469498971573 chr9 141213431 664602 0.004706365359821899 0.09988766712992483 chr10 135534747 742227 0.005476285723247043 0.10791315637230765 chr11 135006516 741180 0.005489957240286091 0.10765859297332016 chr12 133851895 769302 0.005747412093045078 0.10688253432716158 chr13 115169878 543064 0.00471533016645203 0.1470574366334868 chr14 107349540 533357 0.004968414396559128 0.11908196920170942 chr15 102531392 466752 0.004552283850783963 0.09764285309438789 chr16 90354753 475301 0.00526038735339136 0.12411866438939402 chr17 81195210 470739 0.0057976203276030695 0.12092949560872358 chr18 78077248 400233 0.005126115613091281 0.11468885400871014 chr19 59128983 353229 0.00597387240703937 0.10978983586649892 chr20 63025520 358032 0.005680746465876045 0.1160928245145386 chr21 48129895 203574 0.00422967887214381 0.08669237933460672 chr22 51304566 191588 0.0037343264924997125 0.08519412029021058 chrMT 16571 7518 0.45368414700380183 0.8636001897925657 chrX 155270560 721420 0.004646212392098025 0.10347213210378728 chrY 59373566 76343 0.0012858078963961842 0.04899175622954148