BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549009.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 7,857,909 number of mapped reads = 6,824,909 (86.85%) number of secondary alignments = 0 number of mapped bases = 270,801,147 bp number of sequenced bases = 270,771,788 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 485,528 duplication rate = 6.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3883 >>>>>>> ACTG content number of A's = 81,185,344 bp (29.98%) number of C's = 53,710,187 bp (19.84%) number of T's = 80,914,888 bp (29.88%) number of G's = 54,959,031 bp (20.3%) number of N's = 2,338 bp (0%) GC percentage = 40.13% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 836,862 number of insertions = 8,150 mapped reads with insertion percentage = 0.12% number of deletions = 22,825 mapped reads with deletion percentage = 0.33% homopolymer indels = 43.29% >>>>>>> Coverage mean coverageData = 0.0875X std coverageData = 0.6273X There is a 6.95% of reference with a coverageData >= 1X There is a 1.3% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 21030429 0.08437463030433132 1.0158440825336859 chr2 243199373 24219236 0.09958593108708384 0.5531817525981488 chr3 198022430 19579129 0.09887328925314168 0.37784795673050947 chr4 191154276 19177211 0.10032321223094168 0.42218702167430655 chr5 180915260 16958527 0.09373740501492246 0.37324639163513157 chr6 171115067 16075179 0.09394367943063717 0.4418225034309414 chr7 159138663 14980202 0.0941330140495148 0.7240966564574881 chr8 146364022 14496050 0.0990410744520262 1.4112447923760376 chr9 141213431 11627075 0.08233689187822368 0.5275143722937725 chr10 135534747 12192496 0.08995845176145126 0.5659778457154678 chr11 135006516 12591078 0.09326274296271744 0.48110658201253276 chr12 133851895 13039640 0.09741841906683503 0.39349143904431216 chr13 115169878 9016989 0.07829294566067006 0.33207447261813766 chr14 107349540 8824393 0.08220242955861758 0.43581025395920503 chr15 102531392 7787376 0.0759511389448414 0.32819586403416323 chr16 90354753 7186957 0.07954154885465738 0.3871432113346664 chr17 81195210 6548118 0.08064660464576666 0.3773554756797262 chr18 78077248 7762029 0.0994147360316798 1.078680392542002 chr19 59128983 4471663 0.0756255692745468 0.8370926080736573 chr20 63025520 5389756 0.08551704135086867 0.37570074151679195 chr21 48129895 3552721 0.07381526595892221 0.40620368803135193 chr22 51304566 2615439 0.05097867897371942 0.2915336795420955 chrMT 16571 2502 0.15098666344819262 0.40763438536217106 chrX 155270560 9360804 0.0602870499082376 0.38995284007066405 chrY 59373566 2316148 0.0390097505681232 0.3938212513366937