BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089602.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 9,562,002 number of mapped reads = 6,145,659 (64.27%) number of supplementary alignments = 186 (0%) number of secondary alignments = 0 number of mapped bases = 286,358,699 bp number of sequenced bases = 286,302,638 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,811,289 duplication rate = 22.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1089 >>>>>>> ACTG content number of A's = 92,480,738 bp (32.3%) number of C's = 55,368,147 bp (19.34%) number of T's = 73,858,388 bp (25.8%) number of G's = 64,385,474 bp (22.49%) number of N's = 209,891 bp (0.07%) GC percentage = 41.83% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 2,988,384 number of insertions = 15,808 mapped reads with insertion percentage = 0.26% number of deletions = 38,320 mapped reads with deletion percentage = 0.62% homopolymer indels = 40.61% >>>>>>> Coverage mean coverageData = 0.0925X std coverageData = 0.843X There is a 3.46% of reference with a coverageData >= 1X There is a 1.58% of reference with a coverageData >= 2X There is a 1% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.29% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 23437098 0.09403024917639022 0.8910296681502174 chr2 243199373 24775770 0.1018743169210391 0.9544352131422057 chr3 198022430 19162248 0.09676806814258365 0.8314935190935187 chr4 191154276 19278161 0.10085131969530203 0.8740692995660241 chr5 180915260 17983838 0.0994047599964757 0.8377620817242667 chr6 171115067 17010255 0.09940828296552051 0.8824803274219433 chr7 159138663 15539262 0.09764605097882467 0.8739519220019192 chr8 146364022 14453742 0.09875201434407152 0.912526946349261 chr9 141213431 11832190 0.08378940952153482 0.7729568386866392 chr10 135534747 13126187 0.09684739367979195 0.8400042428869094 chr11 135006516 12867485 0.0953101034027128 0.8730841872241514 chr12 133851895 13280363 0.09921684709805566 0.8413709910075666 chr13 115169878 9286433 0.08063248100340958 0.7600444399297106 chr14 107349540 8769316 0.08168936727628269 0.8067448053261016 chr15 102531392 5131016 0.050043366230705225 0.5536109630713631 chr16 90354753 8146691 0.0901633918472446 0.7970451630684995 chr17 81195210 7936212 0.09774236682188518 0.8089447530649656 chr18 78077248 7429252 0.09515258529603912 0.875763014700145 chr19 59128983 5687662 0.09619076316600947 0.8255522234956643 chr20 63025520 6187670 0.09817721456324359 0.8574087130530681 chr21 48129895 3734621 0.07759462180418221 0.7621608870993586 chr22 51304566 3338480 0.06507179107606134 0.6589626004688426 chrMT 16571 101888 6.148572807917446 11.912713606480398 chrX 155270560 17060391 0.10987524615097673 0.925031697599267 chrY 59373566 802468 0.01351557694883949 0.283720141624054