BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708586.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 6,782,186 number of mapped reads = 6,562,919 (96.77%) number of supplementary alignments = 174 (0%) number of secondary alignments = 0 number of mapped bases = 327,369,429 bp number of sequenced bases = 327,341,486 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,922 duplication rate = 1.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7468 >>>>>>> ACTG content number of A's = 101,370,618 bp (30.97%) number of C's = 62,083,566 bp (18.97%) number of T's = 100,861,626 bp (30.81%) number of G's = 63,013,664 bp (19.25%) number of N's = 12,012 bp (0%) GC percentage = 38.22% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 469,969 number of insertions = 20,410 mapped reads with insertion percentage = 0.31% number of deletions = 16,602 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.87% >>>>>>> Coverage mean coverageData = 0.1057X std coverageData = 0.3426X There is a 9.56% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.09% 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 25322156 0.10159315109590038 0.33903396720405193 chr2 243199373 29001737 0.11925087076601962 0.3617043569895244 chr3 198022430 24039714 0.12139894455390736 0.36375125542932213 chr4 191154276 26074436 0.13640519346791907 0.3855719560694302 chr5 180915260 22110744 0.12221602533694505 0.36565364984150284 chr6 171115067 21780572 0.12728611443666735 0.37392862152994344 chr7 159138663 17951612 0.11280484366014813 0.3526025799617622 chr8 146364022 17947367 0.12262143903096623 0.36631153748297063 chr9 141213431 13393197 0.09484364840621995 0.3245621829010149 chr10 135534747 13672237 0.10087624983724654 0.3320042752145729 chr11 135006516 15727738 0.11649614008260165 0.3624254608038346 chr12 133851895 15993410 0.11948586906446114 0.363981571274548 chr13 115169878 13121676 0.11393322826998219 0.3569588120805836 chr14 107349540 10055008 0.09366605576512019 0.32296217066495087 chr15 102531392 8791725 0.08574666576261834 0.3100575505853609 chr16 90354753 6113872 0.06766519521114733 0.2729835291186345 chr17 81195210 5278367 0.06500835455687595 0.2683453143796296 chr18 78077248 9022925 0.11556407572152133 0.3559117568897969 chr19 59128983 2784804 0.04709710633785127 0.2261148558917524 chr20 63025520 5194539 0.08241961351528714 0.30201246279293004 chr21 48129895 3947247 0.08201237505296864 0.30456176720934175 chr22 51304566 1948343 0.03797601562402848 0.20444159254613134 chrMT 16571 432 0.026069639732062035 0.1593424413529005 chrX 155270560 17659043 0.11373078708545908 0.35306393385537477 chrY 59373566 436528 0.007352228094233046 0.09175756609948901