BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068186.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 = 787,021 number of mapped reads = 668,093 (84.89%) number of supplementary alignments = 2,999 (0.38%) number of secondary alignments = 0 number of mapped bases = 45,667,817 bp number of sequenced bases = 45,644,705 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,123 duplication rate = 2.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3472 >>>>>>> ACTG content number of A's = 13,174,435 bp (28.86%) number of C's = 8,500,548 bp (18.62%) number of T's = 14,130,437 bp (30.96%) number of G's = 9,790,736 bp (21.45%) number of N's = 48,549 bp (0.11%) GC percentage = 40.07% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 418,140 number of insertions = 3,507 mapped reads with insertion percentage = 0.52% number of deletions = 13,191 mapped reads with deletion percentage = 1.95% homopolymer indels = 47.38% >>>>>>> Coverage mean coverageData = 0.0148X std coverageData = 0.1942X There is a 1.34% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5306813 0.021291072329966233 0.4195525472942212 chr2 243199373 3901961 0.01604428889707705 0.18963834902581014 chr3 198022430 2391382 0.01207631882913466 0.1192870491552567 chr4 191154276 2491842 0.013035763845533855 0.1251982765234063 chr5 180915260 2711178 0.014985900028554806 0.13208100511525828 chr6 171115067 3342277 0.01953233609755709 0.1765502317196856 chr7 159138663 2581531 0.016221897000605064 0.1638450396447914 chr8 146364022 1760418 0.01202766893082509 0.2033187142374957 chr9 141213431 1708868 0.012101313507494906 0.17458219602513936 chr10 135534747 2394637 0.017668067067701833 0.19316500420961905 chr11 135006516 2008957 0.01488044473349716 0.15629737499239962 chr12 133851895 2363390 0.017656754131123806 0.14364742598015426 chr13 115169878 1236152 0.010733292606249006 0.11030379588786239 chr14 107349540 1030783 0.009602118462733981 0.11406335334305748 chr15 102531392 859285 0.008380701590396823 0.0972744296189499 chr16 90354753 1357073 0.015019386971264257 0.1415103498210873 chr17 81195210 1437564 0.017705034570389067 0.14776452219661212 chr18 78077248 995580 0.012751217870793807 0.2933023021218637 chr19 59128983 1230633 0.020812686732663743 0.2694250405348138 chr20 63025520 961839 0.015261103756065797 0.13499253745797213 chr21 48129895 823385 0.017107558618193536 0.14591234999012612 chr22 51304566 502697 0.009798289688290123 0.10506379801195308 chrMT 16571 7089 0.42779554643654577 0.7341844397204428 chrX 155270560 2121808 0.013665230549822193 0.13012704149433793 chrY 59373566 140675 0.0023693203807229634 0.07086254045876879