BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080992.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 = 3,118,966 number of mapped reads = 2,820,745 (90.44%) number of supplementary alignments = 16,519 (0.53%) number of secondary alignments = 0 number of mapped bases = 186,833,174 bp number of sequenced bases = 186,768,015 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,248 duplication rate = 2.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8379 >>>>>>> ACTG content number of A's = 51,336,573 bp (27.49%) number of C's = 37,051,004 bp (19.84%) number of T's = 55,846,495 bp (29.9%) number of G's = 42,531,470 bp (22.77%) number of N's = 2,473 bp (0%) GC percentage = 42.61% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,403,473 number of insertions = 13,628 mapped reads with insertion percentage = 0.48% number of deletions = 36,787 mapped reads with deletion percentage = 1.29% homopolymer indels = 45.95% >>>>>>> Coverage mean coverageData = 0.0604X std coverageData = 0.5783X There is a 5.01% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 16092773 0.06456462549796416 1.0875468455969746 chr2 243199373 15323590 0.06300834500917896 0.6751663941428314 chr3 198022430 11253053 0.05682716346830003 0.27543629998106267 chr4 191154276 11401227 0.05964411175400544 0.33519190812266686 chr5 180915260 11095751 0.06133120555999533 0.2941076578076407 chr6 171115067 11119006 0.06497970164135225 0.497026237985866 chr7 159138663 9101609 0.057192946254676025 0.9156716208827542 chr8 146364022 8703726 0.05946629425091912 0.5231738075659879 chr9 141213431 7938174 0.05621401550678278 0.5409919106324597 chr10 135534747 9761697 0.0720235748844538 0.5351106764943598 chr11 135006516 9270526 0.06866724862376272 0.5179364685638889 chr12 133851895 7386825 0.05518655525945299 0.28548499990044734 chr13 115169878 6201260 0.05384446096226654 0.2660216100659045 chr14 107349540 5673975 0.05285514032011688 0.3250438516822497 chr15 102531392 5893504 0.05747999598015796 0.299242967788216 chr16 90354753 4889171 0.05411083354961969 0.33321580597106654 chr17 81195210 4808039 0.059215796104228315 0.36537017983351217 chr18 78077248 5825947 0.07461772986670842 1.1513970449979556 chr19 59128983 3617921 0.061186930950596595 0.7835743161371258 chr20 63025520 3985295 0.06323303639541569 0.31863149144383807 chr21 48129895 2488820 0.051710480565145635 0.32863838494247055 chr22 51304566 2082324 0.04058749858638313 0.23361689324737878 chrMT 16571 56331 3.399372397562006 2.5220355399740053 chrX 155270560 12354239 0.07956588164556114 0.4195531064423189 chrY 59373566 508391 0.008562581536706082 0.21686788804458648