BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004121.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 = 4,727,572 number of mapped reads = 3,892,601 (82.34%) number of supplementary alignments = 25,164 (0.53%) number of secondary alignments = 0 number of mapped bases = 257,511,654 bp number of sequenced bases = 257,386,372 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 298,797 duplication rate = 5.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5531 >>>>>>> ACTG content number of A's = 71,099,033 bp (27.62%) number of C's = 45,408,414 bp (17.64%) number of T's = 84,641,496 bp (32.88%) number of G's = 56,209,310 bp (21.84%) number of N's = 28,119 bp (0.01%) GC percentage = 39.48% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 2,542,384 number of insertions = 22,943 mapped reads with insertion percentage = 0.58% number of deletions = 75,816 mapped reads with deletion percentage = 1.93% homopolymer indels = 48.15% >>>>>>> Coverage mean coverageData = 0.0832X std coverageData = 0.8181X There is a 6.07% of reference with a coverageData >= 1X There is a 1.49% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 15855183 0.06361140821390371 1.4917953089794846 chr2 243199373 20652927 0.0849217937745259 0.9247139346673685 chr3 198022430 18488536 0.09336586769488689 0.3939508935634178 chr4 191154276 24651873 0.12896323072574112 0.4740601951015279 chr5 180915260 16452581 0.09094081394792236 0.3991619386296034 chr6 171115067 16268225 0.0950718442578759 0.4831498671670941 chr7 159138663 19215080 0.12074425936329501 1.2994645722799867 chr8 146364022 13434670 0.09178942896226232 1.5812894941600604 chr9 141213431 7583199 0.05370026736337849 0.6664710975272082 chr10 135534747 12872017 0.0949720812184052 0.6111513874930926 chr11 135006516 10496214 0.07774598079399368 0.5662261176909733 chr12 133851895 11265648 0.08416502433529238 0.3846246875945906 chr13 115169878 7456221 0.06474106884093427 0.3261859069494207 chr14 107349540 5614014 0.05229658180184098 0.3577700351475344 chr15 102531392 6313784 0.061579033277925264 0.3240588084695231 chr16 90354753 8588514 0.09505326189093782 0.46206435082857367 chr17 81195210 5439435 0.06699206763551692 0.38342666371170847 chr18 78077248 8759999 0.11219656461252323 1.4605696667894585 chr19 59128983 5546988 0.09381165916552293 0.9964807720251693 chr20 63025520 5259710 0.083453654963894 0.4165949221230935 chr21 48129895 5594367 0.11623476427696341 0.4689888907197793 chr22 51304566 2943753 0.05737799243833385 0.3033728579800622 chrMT 16571 323538 19.524349767666404 11.579002465407886 chrX 155270560 7899846 0.05087793848363785 0.3923540928880821 chrY 59373566 535332 0.009016335653479193 0.1835567879986152