BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081107.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,325,418 number of mapped reads = 2,113,157 (90.87%) number of supplementary alignments = 21,330 (0.92%) number of secondary alignments = 0 number of mapped bases = 142,318,202 bp number of sequenced bases = 142,267,377 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,594 duplication rate = 3.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5497 >>>>>>> ACTG content number of A's = 39,429,910 bp (27.72%) number of C's = 26,928,496 bp (18.93%) number of T's = 44,269,871 bp (31.12%) number of G's = 31,637,544 bp (22.24%) number of N's = 1,556 bp (0%) GC percentage = 41.17% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,264,971 number of insertions = 11,407 mapped reads with insertion percentage = 0.53% number of deletions = 31,212 mapped reads with deletion percentage = 1.46% homopolymer indels = 46.68% >>>>>>> Coverage mean coverageData = 0.046X std coverageData = 0.3617X There is a 3.87% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 11773480 0.0472355091945789 0.5128014872798111 chr2 243199373 9607809 0.03950589543666299 0.42825746732112213 chr3 198022430 11764169 0.05940826501321088 0.27986133555351334 chr4 191154276 8478635 0.044354932452570404 0.26374450317243253 chr5 180915260 8307423 0.04591886278692024 0.24672869047908644 chr6 171115067 11230410 0.0656307489275623 0.4321711917184184 chr7 159138663 7077902 0.04447631937186754 0.32138839735758806 chr8 146364022 10818952 0.07391811083190923 0.428836071341781 chr9 141213431 7519382 0.053248348593697155 0.4226097220272041 chr10 135534747 6571257 0.04848392862680446 0.36203049376909185 chr11 135006516 6204653 0.04595817434471089 0.3079038056863187 chr12 133851895 6858870 0.05124223306662935 0.273129431699702 chr13 115169878 3697490 0.03210466194988936 0.20514371545207677 chr14 107349540 3940666 0.036708736711866675 0.2811167019396071 chr15 102531392 3747952 0.03655419015475768 0.2185253063367581 chr16 90354753 3680227 0.04073086227129634 0.29244131630404796 chr17 81195210 3270000 0.0402733116891994 0.23586969745610092 chr18 78077248 3440327 0.04406311810580209 0.7630938594060068 chr19 59128983 2957333 0.0500149478302375 0.4389450425404289 chr20 63025520 2245910 0.0356349301045037 0.23313842218751185 chr21 48129895 2590469 0.053822452760389355 0.31212450083531984 chr22 51304566 1354911 0.02640916989727581 0.18472594221557515 chrMT 16571 306438 18.492426528272283 9.091721923274525 chrX 155270560 4503981 0.029007308275309885 0.22345107589369803 chrY 59373566 369556 0.006224251378130126 0.15993747279025206