BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053620.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 = 13,737,323 number of mapped reads = 11,050,960 (80.44%) number of supplementary alignments = 320 (0%) number of secondary alignments = 0 number of mapped bases = 523,201,772 bp number of sequenced bases = 523,097,637 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,759,538 duplication rate = 17.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1472 >>>>>>> ACTG content number of A's = 154,998,811 bp (29.63%) number of C's = 97,407,586 bp (18.62%) number of T's = 160,324,145 bp (30.65%) number of G's = 110,056,769 bp (21.04%) number of N's = 310,326 bp (0.06%) GC percentage = 39.66% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 3,018,116 number of insertions = 23,344 mapped reads with insertion percentage = 0.21% number of deletions = 70,274 mapped reads with deletion percentage = 0.63% homopolymer indels = 48.61% >>>>>>> Coverage mean coverageData = 0.169X std coverageData = 1.1174X There is a 6.81% of reference with a coverageData >= 1X There is a 3.06% of reference with a coverageData >= 2X There is a 1.82% of reference with a coverageData >= 3X There is a 1.2% of reference with a coverageData >= 4X There is a 0.84% of reference with a coverageData >= 5X There is a 0.61% of reference with a coverageData >= 6X There is a 0.46% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.27% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% 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 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 41425275 0.1661992850160241 1.1495930682693967 chr2 243199373 44326619 0.1822645282888949 1.308805936711738 chr3 198022430 36302649 0.18332594443972836 1.0987043471730635 chr4 191154276 35527498 0.18585772049378588 1.181285463337581 chr5 180915260 32897973 0.181841891059936 1.0874441394972727 chr6 171115067 31770260 0.18566605826709578 1.1374942899213263 chr7 159138663 28293083 0.1777888695721919 1.1861907754846255 chr8 146364022 26652526 0.1820975239393189 1.139488007473243 chr9 141213431 21514904 0.15235734906830498 1.0608179145059131 chr10 135534747 24129935 0.1780350466142826 1.1730279494566729 chr11 135006516 23631974 0.17504321050696545 1.146249344809561 chr12 133851895 23764543 0.177543567836675 1.0600092032203434 chr13 115169878 17219009 0.14950965737760008 0.9957845706957431 chr14 107349540 16082179 0.14981134525588094 1.1055340836647416 chr15 102531392 14645761 0.14284172597598208 0.9351265514210405 chr16 90354753 14079931 0.15582944485499287 1.0144806530105628 chr17 81195210 12752473 0.15705942505721704 0.9629908712003539 chr18 78077248 13889317 0.1778919897381629 1.244283834833774 chr19 59128983 8656469 0.14639976134884647 1.0180424829413937 chr20 63025520 10638545 0.16879741730016667 1.0616424028983515 chr21 48129895 6795218 0.14118497453609655 1.040200152630887 chr22 51304566 5254172 0.10241139160986178 0.775764988549091 chrMT 16571 48859 2.9484641844185626 6.3801421945519605 chrX 155270560 31622209 0.20365875540089506 1.230942416452637 chrY 59373566 1280391 0.021565000828820017 0.4714163321950291