BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068188.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 = 1,248,551 number of mapped reads = 1,139,837 (91.29%) number of supplementary alignments = 7,486 (0.6%) number of secondary alignments = 0 number of mapped bases = 77,553,200 bp number of sequenced bases = 77,518,050 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,899 duplication rate = 2.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6483 >>>>>>> ACTG content number of A's = 22,573,676 bp (29.12%) number of C's = 14,375,687 bp (18.54%) number of T's = 24,431,457 bp (31.52%) number of G's = 16,061,748 bp (20.72%) number of N's = 75,482 bp (0.1%) GC percentage = 39.26% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 644,066 number of insertions = 5,407 mapped reads with insertion percentage = 0.47% number of deletions = 20,228 mapped reads with deletion percentage = 1.75% homopolymer indels = 46.87% >>>>>>> Coverage mean coverageData = 0.0251X std coverageData = 0.2734X There is a 2.11% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 9436165 0.037858140381523867 0.5597284315760462 chr2 243199373 10941085 0.04498812996528573 0.2757055447912687 chr3 198022430 7218535 0.036453117962444964 0.22025979021325123 chr4 191154276 2315697 0.012114283020276251 0.1329112364652439 chr5 180915260 4243529 0.02345589310708229 0.17446521350404198 chr6 171115067 2969577 0.01735426956879256 0.17457945303900388 chr7 159138663 8308903 0.05221171802857235 0.43925475440403167 chr8 146364022 1128363 0.007709292110051472 0.35709851543418974 chr9 141213431 3168054 0.022434509080088847 0.19182619906974657 chr10 135534747 3898691 0.028765250876957773 0.2648317931178748 chr11 135006516 2447814 0.018131080428740193 0.19944232662152026 chr12 133851895 795274 0.005941447448315916 0.09369211774181438 chr13 115169878 2431181 0.021109521362868856 0.16515017000745516 chr14 107349540 651755 0.006071334818947524 0.09738342330976274 chr15 102531392 1714616 0.016722839381718334 0.1466827553607226 chr16 90354753 1968048 0.02178134447448492 0.1836267019108519 chr17 81195210 1313116 0.016172333318677297 0.15097881003690858 chr18 78077248 1295667 0.016594680693663794 0.2307151983459055 chr19 59128983 1328487 0.022467611188239107 0.3799103523300786 chr20 63025520 1026929 0.016293860010992374 0.14905565698619938 chr21 48129895 1768052 0.03673500638220798 0.2325742854292348 chr22 51304566 503607 0.009816026900997466 0.1119281578879634 chrMT 16571 17509 1.056604912196005 1.2651707962957046 chrX 155270560 6441902 0.041488238337003484 0.26239429254616137 chrY 59373566 220644 0.003716199225763196 0.10245921082300964