BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818803.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 = 891,929 number of mapped reads = 868,847 (97.41%) number of supplementary alignments = 6,683 (0.75%) number of secondary alignments = 0 number of mapped bases = 59,029,598 bp number of sequenced bases = 59,006,306 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 524,136 duplication rate = 47.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.786 >>>>>>> ACTG content number of A's = 17,175,539 bp (29.11%) number of C's = 13,483,594 bp (22.85%) number of T's = 16,214,816 bp (27.48%) number of G's = 12,128,816 bp (20.56%) number of N's = 3,541 bp (0.01%) GC percentage = 43.41% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 303,296 number of insertions = 8,028 mapped reads with insertion percentage = 0.91% number of deletions = 15,006 mapped reads with deletion percentage = 1.71% homopolymer indels = 40.63% >>>>>>> Coverage mean coverageData = 0.0191X std coverageData = 0.3807X There is a 0.62% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 4882143 0.01958728520078592 0.4047578873462741 chr2 243199373 5216103 0.02144784723602063 0.5410582928394575 chr3 198022430 3869140 0.019538897689519313 0.3359643155571986 chr4 191154276 3929093 0.020554565046716506 0.35618392657800424 chr5 180915260 3645362 0.020149555101100926 0.3500573160908013 chr6 171115067 3517536 0.02055655332794277 0.3671766744764212 chr7 159138663 3175207 0.019952454922912102 0.355853737695335 chr8 146364022 3005905 0.020537185019416863 0.3624912938825873 chr9 141213431 2495235 0.017669955204190173 0.32881802143508077 chr10 135534747 2845901 0.020997574887567393 0.43291345079645066 chr11 135006516 2838128 0.021022155700988535 0.3650685923927092 chr12 133851895 2680370 0.020024893932207685 0.3610564733861624 chr13 115169878 1862138 0.0161686200622701 0.30443253762303835 chr14 107349540 1840717 0.017146948184407682 0.33512738492365357 chr15 102531392 1701851 0.016598340925674745 0.31808461934276544 chr16 90354753 1678263 0.018574152928070093 0.3981286019180046 chr17 81195210 1636439 0.02015437856494244 0.3743192582504112 chr18 78077248 1633575 0.020922548397197607 0.3772135901598915 chr19 59128983 1178012 0.019922750912188023 0.4222410972190324 chr20 63025520 1308974 0.020768952005473337 0.3706954548457307 chr21 48129895 806125 0.016748945743596574 0.33101492900045704 chr22 51304566 744067 0.014502939173094262 0.3323611637268135 chrMT 16571 132003 7.965904290628206 10.711193131013854 chrX 155270560 1822290 0.011736223531363575 0.25846364318216475 chrY 59373566 585021 0.009853223234056718 0.5188018709616585