BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237804.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 = 2,493,173 number of mapped reads = 1,450,250 (58.17%) number of supplementary alignments = 8,746 (0.35%) number of secondary alignments = 0 number of mapped bases = 89,804,755 bp number of sequenced bases = 89,764,917 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,836 duplication rate = 7.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6819 >>>>>>> ACTG content number of A's = 24,324,941 bp (27.1%) number of C's = 17,542,755 bp (19.54%) number of T's = 27,192,987 bp (30.29%) number of G's = 20,628,606 bp (22.98%) number of N's = 75,628 bp (0.08%) GC percentage = 42.52% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 747,492 number of insertions = 6,566 mapped reads with insertion percentage = 0.45% number of deletions = 24,853 mapped reads with deletion percentage = 1.7% homopolymer indels = 46.49% >>>>>>> Coverage mean coverageData = 0.029X std coverageData = 0.2853X There is a 1.96% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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% 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 7406518 0.029715143618438567 0.39287844626720925 chr2 243199373 8072697 0.03319374100524511 0.3209551551400627 chr3 198022430 5964959 0.030122643177341073 0.24842397315360817 chr4 191154276 5358555 0.028032619055824836 0.24837662909979705 chr5 180915260 5349545 0.029569340916846924 0.24501548002756812 chr6 171115067 5503451 0.03216228177031307 0.2789730969118398 chr7 159138663 4767646 0.02995906783507412 0.3214302425105183 chr8 146364022 4530836 0.030955940798073997 0.2910351965152829 chr9 141213431 3572137 0.0252960145129538 0.253485186280918 chr10 135534747 4427003 0.03266323284611289 0.35036054172095976 chr11 135006516 3790807 0.028078696586763263 0.26248324372043486 chr12 133851895 4171588 0.03116569997010502 0.24978486339246864 chr13 115169878 2991953 0.02597860701041986 0.2267133319522045 chr14 107349540 2730469 0.02543531159984477 0.2336656217866283 chr15 102531392 2341755 0.02283939537268742 0.21410456881975481 chr16 90354753 2740982 0.030335781007558064 0.2632253130233704 chr17 81195210 2224786 0.02740045872164134 0.24673409835092386 chr18 78077248 2347689 0.03006879801911051 0.3997013029989432 chr19 59128983 1652627 0.02794952519308509 0.31680108456719774 chr20 63025520 1848205 0.02932470846730023 0.25047098876868695 chr21 48129895 1181954 0.024557585259639567 0.2264836947171763 chr22 51304566 987193 0.019241815630990818 0.20125120319350945 chrMT 16571 39237 2.3678112364974955 2.513691701364754 chrX 155270560 5502064 0.03543533300839515 0.28080045786155955 chrY 59373566 300099 0.005054421019616709 0.12258567791774133