BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238669.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 = 2,778,756 number of mapped reads = 1,686,729 (60.7%) number of supplementary alignments = 10,496 (0.38%) number of secondary alignments = 0 number of mapped bases = 103,581,270 bp number of sequenced bases = 103,514,323 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 205,374 duplication rate = 10.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6298 >>>>>>> ACTG content number of A's = 26,021,978 bp (25.14%) number of C's = 18,231,805 bp (17.61%) number of T's = 34,587,891 bp (33.41%) number of G's = 24,667,448 bp (23.83%) number of N's = 5,201 bp (0.01%) GC percentage = 41.44% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 692,252 number of insertions = 7,206 mapped reads with insertion percentage = 0.42% number of deletions = 38,899 mapped reads with deletion percentage = 2.28% homopolymer indels = 41.6% >>>>>>> Coverage mean coverageData = 0.0335X std coverageData = 0.4197X There is a 2.54% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% 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 8085020 0.03243731135979798 0.41297478792424436 chr2 243199373 8779121 0.036098452441322704 1.024537154801275 chr3 198022430 6481991 0.032733620125760504 0.2384809580236001 chr4 191154276 6892057 0.036054945482883155 0.25649145380288474 chr5 180915260 5696412 0.031486630812679925 0.23177046038425173 chr6 171115067 6448989 0.037688025450149286 0.3951126710550917 chr7 159138663 5659877 0.03556569405135696 0.349999955040112 chr8 146364022 5010934 0.034236104826362315 0.38101904449765306 chr9 141213431 4258348 0.030155403560727875 0.2607345752552639 chr10 135534747 4817409 0.03554371927960289 0.303377608826689 chr11 135006516 5132048 0.038013335593372395 0.2752145312558175 chr12 133851895 4954555 0.037015202511701456 0.2509610624214539 chr13 115169878 3599412 0.031253067750927024 0.2864854023219116 chr14 107349540 3082155 0.028711394571415957 0.2201203604069882 chr15 102531392 2756797 0.026887345877446 0.28234988733874145 chr16 90354753 3590515 0.03973797593138238 0.2829408662800876 chr17 81195210 2443819 0.030098068592962567 0.22874867031684476 chr18 78077248 3075751 0.039393691232559834 0.7532236705593134 chr19 59128983 2094860 0.03542864926325555 0.3397859879721417 chr20 63025520 1943327 0.0308339701124243 0.2273573531411531 chr21 48129895 1467816 0.030496970749676475 0.2346993116926862 chr22 51304566 1140643 0.02223277748806997 0.18948261784258405 chrMT 16571 15368 0.9274032949127995 1.2955979327607385 chrX 155270560 5856873 0.03772043457562078 0.2600468443982218 chrY 59373566 297173 0.005005139829398153 0.17555576547233284