BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080635.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 = 3,322,126 number of mapped reads = 2,914,576 (87.73%) number of supplementary alignments = 19,506 (0.59%) number of secondary alignments = 0 number of mapped bases = 197,038,069 bp number of sequenced bases = 196,955,735 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 129,016 duplication rate = 3.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1093 >>>>>>> ACTG content number of A's = 55,265,411 bp (28.06%) number of C's = 35,316,708 bp (17.93%) number of T's = 62,993,712 bp (31.98%) number of G's = 43,212,857 bp (21.94%) number of N's = 167,047 bp (0.08%) GC percentage = 39.87% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,776,274 number of insertions = 16,483 mapped reads with insertion percentage = 0.56% number of deletions = 49,666 mapped reads with deletion percentage = 1.69% homopolymer indels = 48.35% >>>>>>> Coverage mean coverageData = 0.0636X std coverageData = 0.4533X There is a 5.2% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% 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 24627968 0.09880805071294085 0.6002854599890287 chr2 243199373 14631540 0.06016273734389932 0.4451879998776597 chr3 198022430 13341710 0.06737474133612036 0.30217015688040133 chr4 191154276 7953009 0.04160518491357212 0.2545767406359005 chr5 180915260 8166173 0.045138110516492636 0.246245679783002 chr6 171115067 11522435 0.06733734908335103 0.49920555168302577 chr7 159138663 12555519 0.07889672291641661 1.0581377471181543 chr8 146364022 21702981 0.1482808459581686 0.6453192894297772 chr9 141213431 6364624 0.04507095362621704 0.3733747313868455 chr10 135534747 9526204 0.07028606472405191 0.42504728511488843 chr11 135006516 7633212 0.05653958213394678 0.34025432903306646 chr12 133851895 5882302 0.04394634831281245 0.24887654440832088 chr13 115169878 4463607 0.038756722482592196 0.22616908408455147 chr14 107349540 4108526 0.03827241364983958 0.2500021678349482 chr15 102531392 2962448 0.028893082813115423 0.19729739365681886 chr16 90354753 4933296 0.05459918638701829 0.2988277561295134 chr17 81195210 3067759 0.03778251204720082 0.24355526104650285 chr18 78077248 6007491 0.0769429142789459 0.5856164032985904 chr19 59128983 2774606 0.04692463592685164 0.41965541339786505 chr20 63025520 4861754 0.07713945081294053 0.3294212983091433 chr21 48129895 3066197 0.06370670453363757 0.324686594714201 chr22 51304566 2013460 0.03924523988761546 0.2290095319001997 chrMT 16571 39065 2.357431657715286 2.861718399192525 chrX 155270560 14392257 0.09269147351564908 0.37402811654124135 chrY 59373566 439926 0.007409458950132792 0.1448034426215174