BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819057.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 = 990,235 number of mapped reads = 902,219 (91.11%) number of supplementary alignments = 3,795 (0.38%) number of secondary alignments = 0 number of mapped bases = 51,347,234 bp number of sequenced bases = 51,333,697 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,047 duplication rate = 1.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9567 >>>>>>> ACTG content number of A's = 12,566,510 bp (24.48%) number of C's = 10,789,591 bp (21.02%) number of T's = 15,252,721 bp (29.71%) number of G's = 12,723,813 bp (24.79%) number of N's = 1,062 bp (0%) GC percentage = 45.81% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 254,885 number of insertions = 3,344 mapped reads with insertion percentage = 0.37% number of deletions = 8,047 mapped reads with deletion percentage = 0.89% homopolymer indels = 40.9% >>>>>>> Coverage mean coverageData = 0.0166X std coverageData = 0.1558X There is a 1.55% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5767209 0.02313819310404045 0.2215234419823048 chr2 243199373 4291365 0.017645460788256226 0.17474576506310976 chr3 198022430 3367454 0.017005417012608118 0.1371999511002108 chr4 191154276 3240830 0.01695400211711717 0.14290495189165403 chr5 180915260 2561605 0.014159142794256271 0.12611310211159796 chr6 171115067 2674414 0.015629330875930405 0.13657195153575438 chr7 159138663 2182878 0.013716830082957276 0.13772981898313352 chr8 146364022 3224182 0.02202851463046021 0.16557987362725707 chr9 141213431 1897950 0.013440293791884429 0.15268369312488267 chr10 135534747 2452236 0.018093042959677345 0.1689591628139185 chr11 135006516 1637023 0.012125511038296849 0.13674408917133624 chr12 133851895 2318124 0.017318574384023476 0.13949596719478358 chr13 115169878 1535389 0.013331515381131167 0.12053440966742228 chr14 107349540 1788310 0.016658757922949647 0.1447911305162744 chr15 102531392 1466839 0.01430624291143926 0.12575648852724106 chr16 90354753 1543356 0.01708107154030956 0.1441157836238095 chr17 81195210 1162392 0.01431601691774675 0.1279262651669243 chr18 78077248 1252075 0.016036361834884345 0.2429136748171852 chr19 59128983 1002935 0.01696181718532179 0.16813243975478154 chr20 63025520 1662495 0.02637812428997016 0.17404253465129665 chr21 48129895 664291 0.013802045485451402 0.13077017422043416 chr22 51304566 622682 0.012136970420917312 0.11548660510699182 chrMT 16571 2364 0.14265886186711726 0.3790381675306623 chrX 155270560 2879946 0.018547920481513044 0.1548898677022752 chrY 59373566 148890 0.0025076816171021293 0.06521388690267833