BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708561.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 = 4,177,035 number of mapped reads = 3,421,638 (81.92%) number of supplementary alignments = 101 (0%) number of secondary alignments = 0 number of mapped bases = 170,629,935 bp number of sequenced bases = 170,614,750 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,753 duplication rate = 0.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0095 >>>>>>> ACTG content number of A's = 52,980,707 bp (31.05%) number of C's = 32,284,805 bp (18.92%) number of T's = 52,813,847 bp (30.96%) number of G's = 32,529,496 bp (19.07%) number of N's = 5,895 bp (0%) GC percentage = 37.99% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 267,813 number of insertions = 11,590 mapped reads with insertion percentage = 0.34% number of deletions = 9,060 mapped reads with deletion percentage = 0.26% homopolymer indels = 47.82% >>>>>>> Coverage mean coverageData = 0.0551X std coverageData = 0.2475X There is a 5.1% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.03% 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 8269250 0.033176446930497316 0.19190016066335 chr2 243199373 17679411 0.07269513396319488 0.28289478984039373 chr3 198022430 13445364 0.06789818708921004 0.27363652803224564 chr4 191154276 15265536 0.07985976730125566 0.29723323676272295 chr5 180915260 8332598 0.04605801633317167 0.22546971364516055 chr6 171115067 13752546 0.08037016401366924 0.2983708421010648 chr7 159138663 5611565 0.03526210974890495 0.19659468271299513 chr8 146364022 7998974 0.054651231161166096 0.2452525159805505 chr9 141213431 7213177 0.05107996419972262 0.23774824871304187 chr10 135534747 8233907 0.06075126255262055 0.258391039292545 chr11 135006516 9732187 0.07208679468478396 0.28401871320175165 chr12 133851895 8110577 0.06059366585732686 0.25874908211365083 chr13 115169878 6792152 0.058975073326030615 0.2548786598074419 chr14 107349540 6124596 0.05705283879185696 0.25236033279619263 chr15 102531392 4387144 0.042788300387065846 0.21756706458344738 chr16 90354753 2582963 0.028586907874121464 0.1766846323285961 chr17 81195210 3872963 0.04769940246475131 0.22982229034362145 chr18 78077248 5334560 0.06832412945702185 0.27401163061190986 chr19 59128983 1385243 0.023427478872755175 0.15883919174731523 chr20 63025520 3187007 0.05056692907888741 0.23613499851859396 chr21 48129895 2786428 0.05789391395929702 0.25796222814530473 chr22 51304566 642080 0.012515065423221785 0.1149580555368353 chrMT 16571 100 0.006034638826866212 0.07744818888195831 chrX 155270560 9659141 0.06220845084863479 0.2628287798215086 chrY 59373566 230466 0.0038816263789848834 0.0646931790623985