BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819135.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,244,613 number of mapped reads = 1,136,905 (91.35%) number of supplementary alignments = 4,682 (0.38%) number of secondary alignments = 0 number of mapped bases = 65,910,522 bp number of sequenced bases = 65,890,638 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,547 duplication rate = 4.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.628 >>>>>>> ACTG content number of A's = 16,728,747 bp (25.39%) number of C's = 12,918,000 bp (19.61%) number of T's = 20,610,063 bp (31.28%) number of G's = 15,632,825 bp (23.73%) number of N's = 1,003 bp (0%) GC percentage = 43.33% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 342,992 number of insertions = 4,409 mapped reads with insertion percentage = 0.39% number of deletions = 11,952 mapped reads with deletion percentage = 1.04% homopolymer indels = 44.01% >>>>>>> Coverage mean coverageData = 0.0213X std coverageData = 0.2298X There is a 1.85% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 6491589 0.026044424579387507 0.418344918306446 chr2 243199373 4985156 0.020498227189097235 0.2753676980400157 chr3 198022430 3524802 0.017800013867115962 0.14988103974930236 chr4 191154276 3780527 0.019777360355778806 0.18638356797169864 chr5 180915260 3674445 0.02031030992078833 0.16030687232748958 chr6 171115067 2800516 0.016366273578936212 0.1675092022490013 chr7 159138663 3228793 0.020289180134685433 0.2677733340875897 chr8 146364022 5981023 0.04086402463031523 0.2653476646516021 chr9 141213431 2617899 0.0185385977910274 0.18022368940901584 chr10 135534747 3482088 0.025691478215545717 0.2512373374945359 chr11 135006516 2305568 0.017077457209546835 0.19532339010569963 chr12 133851895 3050740 0.022791907428729344 0.16987084319539128 chr13 115169878 1889789 0.01640870888132746 0.14401716698822237 chr14 107349540 1559128 0.01452384425680818 0.1364391691179372 chr15 102531392 1773790 0.01729996994481456 0.147806327074973 chr16 90354753 2081838 0.023040713751937322 0.17855962571385406 chr17 81195210 2133064 0.026270810802755482 0.19402240909451277 chr18 78077248 1494854 0.019145833623644113 0.30862999257404905 chr19 59128983 1297003 0.02193514811509611 0.2748903627472321 chr20 63025520 1722030 0.02732274164497175 0.18830323085976228 chr21 48129895 944696 0.019628050300130512 0.18072433546553934 chr22 51304566 521153 0.010158023751726114 0.11383134544408963 chrMT 16571 92284 5.569006094985215 3.81954954996532 chrX 155270560 4226517 0.0272203371972124 0.19604252175888098 chrY 59373566 251230 0.0042313442989090466 0.14347839687503247