BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549081.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 = 9,625,940 number of mapped reads = 8,437,711 (87.66%) number of secondary alignments = 0 number of mapped bases = 334,959,530 bp number of sequenced bases = 334,929,675 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 304,348 duplication rate = 2.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0824 >>>>>>> ACTG content number of A's = 100,084,774 bp (29.88%) number of C's = 67,149,867 bp (20.05%) number of T's = 101,721,677 bp (30.37%) number of G's = 65,887,732 bp (19.67%) number of N's = 85,625 bp (0.03%) GC percentage = 39.72% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 1,343,971 number of insertions = 8,030 mapped reads with insertion percentage = 0.1% number of deletions = 24,108 mapped reads with deletion percentage = 0.29% homopolymer indels = 45.96% >>>>>>> Coverage mean coverageData = 0.1082X std coverageData = 0.8585X There is a 9.17% of reference with a coverageData >= 1X There is a 1.21% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.04% 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 25708704 0.10314399176562132 2.1285910543847573 chr2 243199373 29392657 0.12085827622590128 0.637660345786657 chr3 198022430 23584190 0.11909857888321035 0.40241638768149324 chr4 191154276 24234292 0.12677870726784055 0.4109543564311431 chr5 180915260 22397992 0.12380377420898601 0.4104697385575378 chr6 171115067 21600433 0.126233378385084 0.5577440132235256 chr7 159138663 19527186 0.1227054798116533 1.006248750872633 chr8 146364022 17514119 0.11966136732700608 0.6275009992392129 chr9 141213431 14309583 0.10133301697060246 0.6199626563869317 chr10 135534747 15314513 0.11299326068760802 0.7771010849844097 chr11 135006516 15468495 0.11457591424698346 0.6734982289892513 chr12 133851895 15556524 0.11622191826271866 0.42266691157596215 chr13 115169878 12214715 0.10605824380572844 0.35895158339828614 chr14 107349540 9646723 0.08986273252777795 0.4868474786162453 chr15 102531392 9754485 0.09513657046614563 0.34390299531783125 chr16 90354753 8880038 0.0982796997962022 0.4699705494117991 chr17 81195210 7385695 0.09096220084904023 0.4156802750744585 chr18 78077248 9390255 0.12026877535437724 1.38613594666124 chr19 59128983 5108652 0.08639844186056778 1.6779393863383147 chr20 63025520 6663105 0.105720746135851 0.3941771455293196 chr21 48129895 4421745 0.09187107098405263 0.4087285879352033 chr22 51304566 2972850 0.057945134941790565 0.32634637510632736 chrMT 16571 22928 1.383621990223885 1.7902557612119496 chrX 155270560 11389401 0.07335196704384914 0.4396000255466825 chrY 59373566 2500250 0.04211049071905164 0.3623921021540325