BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013218.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 = 1,890,674 number of mapped reads = 1,429,768 (75.62%) number of supplementary alignments = 12,394 (0.66%) number of secondary alignments = 0 number of mapped bases = 90,019,995 bp number of sequenced bases = 89,979,218 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,676 duplication rate = 6.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5162 >>>>>>> ACTG content number of A's = 23,534,792 bp (26.16%) number of C's = 16,152,996 bp (17.95%) number of T's = 29,009,665 bp (32.24%) number of G's = 21,280,571 bp (23.65%) number of N's = 1,194 bp (0%) GC percentage = 41.6% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 709,722 number of insertions = 5,663 mapped reads with insertion percentage = 0.39% number of deletions = 24,268 mapped reads with deletion percentage = 1.68% homopolymer indels = 45.95% >>>>>>> Coverage mean coverageData = 0.0291X std coverageData = 0.2681X There is a 2.22% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 5441666 0.02183210608731041 0.3030801591429685 chr2 243199373 12610009 0.051850499631016726 0.43238103995574 chr3 198022430 6971981 0.03520803678653979 0.23612386699937538 chr4 191154276 3582804 0.01874299688697521 0.17685848741302107 chr5 180915260 2846410 0.015733388106674916 0.15704779885843195 chr6 171115067 3276356 0.019147092406538346 0.2432596336416922 chr7 159138663 6205915 0.03899690297134142 0.3228102894018783 chr8 146364022 8583588 0.05864547778005171 0.3553419164379745 chr9 141213431 2051336 0.014526493588276316 0.21092310814870813 chr10 135534747 8061780 0.059481278258482304 0.38175215393672846 chr11 135006516 3853088 0.02854001506119897 0.24526542288672007 chr12 133851895 4935746 0.03687468152766907 0.24520838089820102 chr13 115169878 854311 0.007417833680435087 0.10612352973886464 chr14 107349540 3160345 0.029439762853199 0.22394062476619167 chr15 102531392 1705946 0.0166382799133362 0.16619068250770958 chr16 90354753 2032979 0.02249996743392127 0.19059922956960718 chr17 81195210 3637627 0.04480100488686463 0.3132664377155271 chr18 78077248 2198368 0.028156320263747002 0.33143083137037477 chr19 59128983 2291779 0.03875897882431024 0.3009446692437345 chr20 63025520 1522146 0.024151264440182327 0.197228885069119 chr21 48129895 981256 0.020387661348523614 0.18488514892931313 chr22 51304566 541746 0.01055941102786056 0.12475035151218744 chrMT 16571 12772 0.7707440709673526 1.2221330572766722 chrX 155270560 2454990 0.015811046215071293 0.17079978326815165 chrY 59373566 205051 0.003453573935579345 0.07654028102682205