BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080639.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 = 3,231,563 number of mapped reads = 2,541,760 (78.65%) number of supplementary alignments = 18,200 (0.56%) number of secondary alignments = 0 number of mapped bases = 168,366,719 bp number of sequenced bases = 168,299,213 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,086 duplication rate = 3.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6912 >>>>>>> ACTG content number of A's = 45,650,206 bp (27.12%) number of C's = 29,859,793 bp (17.74%) number of T's = 54,467,496 bp (32.36%) number of G's = 38,188,835 bp (22.69%) number of N's = 132,883 bp (0.08%) GC percentage = 40.43% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,532,821 number of insertions = 14,740 mapped reads with insertion percentage = 0.58% number of deletions = 41,128 mapped reads with deletion percentage = 1.6% homopolymer indels = 46.97% >>>>>>> Coverage mean coverageData = 0.0544X std coverageData = 0.4146X There is a 4.59% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.11% 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% 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 19831818 0.07956577167364409 0.5596489624994825 chr2 243199373 11723828 0.04820665388804271 0.48131972626053404 chr3 198022430 10463226 0.05283859005265212 0.26344728638377357 chr4 191154276 7495080 0.03920958587397752 0.24589627635273772 chr5 180915260 7655581 0.04231583891817639 0.23361831628494956 chr6 171115067 10252690 0.05991693297236064 0.4505380479587082 chr7 159138663 10555718 0.06633031722781282 0.8684455450104067 chr8 146364022 19437185 0.13280029295724055 0.6034910453499457 chr9 141213431 5657658 0.04006458847388249 0.3708611655640869 chr10 135534747 8193554 0.06045353078351192 0.41238657402548085 chr11 135006516 7032153 0.052087508131829725 0.3055425869962347 chr12 133851895 5428997 0.0405597320829862 0.236742626549744 chr13 115169878 3740992 0.032482382242342914 0.20155851572995556 chr14 107349540 3438160 0.03202771059848044 0.22953690850315783 chr15 102531392 3046447 0.0297123343453681 0.19440119953714852 chr16 90354753 4348036 0.04812182929657281 0.2720260711755563 chr17 81195210 2913369 0.035881045199587513 0.22530622964543018 chr18 78077248 5208740 0.06671264847859391 0.5520686024561601 chr19 59128983 2718256 0.04597163458739008 0.41244260256018006 chr20 63025520 4143065 0.06573630808599437 0.30703673579734 chr21 48129895 2531248 0.052592011680058726 0.277376382270624 chr22 51304566 1625992 0.03169292963125348 0.19925230931328794 chrMT 16571 30883 1.8636775089010922 2.7244897965830037 chrX 155270560 10516506 0.06773019946601597 0.3441138892344752 chrY 59373566 377537 0.00635867146669277 0.1342507641456554