BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008679.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 = 2,020,323 number of mapped reads = 1,833,114 (90.73%) number of supplementary alignments = 11,690 (0.58%) number of secondary alignments = 0 number of mapped bases = 119,626,617 bp number of sequenced bases = 119,576,981 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,049 duplication rate = 2.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9385 >>>>>>> ACTG content number of A's = 32,890,016 bp (27.51%) number of C's = 22,039,123 bp (18.43%) number of T's = 37,292,037 bp (31.19%) number of G's = 27,333,098 bp (22.86%) number of N's = 22,707 bp (0.02%) GC percentage = 41.29% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 830,187 number of insertions = 9,895 mapped reads with insertion percentage = 0.54% number of deletions = 29,859 mapped reads with deletion percentage = 1.61% homopolymer indels = 48.04% >>>>>>> Coverage mean coverageData = 0.0386X std coverageData = 0.3277X There is a 3.42% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 11523743 0.04623355782933034 0.5717046689780323 chr2 243199373 8755300 0.03600050399800989 0.3706519578945919 chr3 198022430 9291265 0.04692026554769579 0.237464900780214 chr4 191154276 5471861 0.028625365409037463 0.18960320278055898 chr5 180915260 5471012 0.030240743649817048 0.19069659688944623 chr6 171115067 8232589 0.048111420837067494 0.28598944630633266 chr7 159138663 6019015 0.037822455502218216 0.47454345652529734 chr8 146364022 10429115 0.07125463524089273 0.39689782393425416 chr9 141213431 2482585 0.017580374490015756 0.27533097400348383 chr10 135534747 8972138 0.06619806506150043 0.3631892778011858 chr11 135006516 4819313 0.035696891844835106 0.29430070008720394 chr12 133851895 5007058 0.03740744947988969 0.2135666834611442 chr13 115169878 2344375 0.02035579997749064 0.15507247038545924 chr14 107349540 5274026 0.04912946995394671 0.24455650463540154 chr15 102531392 2965682 0.028924624372601904 0.18799138032697998 chr16 90354753 2812309 0.031125191610008606 0.21802957994421016 chr17 81195210 4846684 0.059691747826010916 0.3259938203252109 chr18 78077248 1672661 0.021423155180879325 0.5239942189644294 chr19 59128983 2702697 0.04570849797974709 0.4047490079031098 chr20 63025520 3144075 0.049885744695164755 0.24679348178422647 chr21 48129895 1359409 0.028244586862281748 0.19087112639311604 chr22 51304566 1999039 0.038964153794810386 0.21493036088648781 chrMT 16571 169545 10.23142839901032 6.168207170356422 chrX 155270560 3632497 0.023394628060850686 0.18271382645848055 chrY 59373566 228624 0.0038506024718138036 0.10351435880622019