BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231762.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 = 2,781,333 number of mapped reads = 2,487,939 (89.45%) number of supplementary alignments = 19,003 (0.68%) number of secondary alignments = 0 number of mapped bases = 163,753,059 bp number of sequenced bases = 163,689,266 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 145,756 duplication rate = 2.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.0195 >>>>>>> ACTG content number of A's = 45,318,333 bp (27.69%) number of C's = 32,461,845 bp (19.83%) number of T's = 45,787,798 bp (27.97%) number of G's = 40,109,406 bp (24.5%) number of N's = 11,884 bp (0.01%) GC percentage = 44.33% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 1,108,866 number of insertions = 13,562 mapped reads with insertion percentage = 0.54% number of deletions = 37,949 mapped reads with deletion percentage = 1.51% homopolymer indels = 44.6% >>>>>>> Coverage mean coverageData = 0.0529X std coverageData = 7.3507X There is a 4.44% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 0.01% 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 13993290 0.056141444879288786 1.15078474189594 chr2 243199373 16450327 0.0676413215917296 26.149788955268395 chr3 198022430 12960921 0.0654517824066698 0.2879620788730978 chr4 191154276 6467835 0.03383568045320629 0.24079750320527088 chr5 180915260 8208180 0.04537030209613053 0.24647034184854438 chr6 171115067 13785223 0.0805611290792996 0.47860334277512506 chr7 159138663 10832746 0.0680711135545986 1.0482381579445856 chr8 146364022 8688838 0.05936457526426815 0.6772715095041495 chr9 141213431 7648872 0.054165329358791654 0.5318998261292114 chr10 135534747 6909071 0.05097638172445919 0.4414455195746169 chr11 135006516 6072353 0.04497822164376125 0.4864822670570277 chr12 133851895 5865107 0.04381788543225331 0.248399453150837 chr13 115169878 4096844 0.035572183205751076 0.20970627683095547 chr14 107349540 5482204 0.051068723722523635 0.3944282125100702 chr15 102531392 3412334 0.0332808707015311 0.21795985973641646 chr16 90354753 4905513 0.05429169841236797 0.3341299025395347 chr17 81195210 4324481 0.05326029700520511 0.30167890365415045 chr18 78077248 3468679 0.044426245658658464 1.131306819718636 chr19 59128983 4886868 0.08264759094537445 0.766606415412429 chr20 63025520 3965583 0.06292027420003833 0.3095085902479156 chr21 48129895 2564933 0.053291888544531416 0.2981852513101859 chr22 51304566 1904087 0.03711340234317546 0.21531513353382864 chrMT 16571 165412 9.98201677629594 7.7576148485395775 chrX 155270560 6155747 0.039645293995204244 0.29172147705644647 chrY 59373566 537611 0.009054719738410188 0.16431820269093905