BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819003.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 = 1,214,765 number of mapped reads = 1,191,761 (98.11%) number of supplementary alignments = 19,870 (1.64%) number of secondary alignments = 0 number of mapped bases = 109,974,919 bp number of sequenced bases = 109,908,150 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 410,120 duplication rate = 29.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2128 >>>>>>> ACTG content number of A's = 32,321,505 bp (29.41%) number of C's = 23,674,770 bp (21.54%) number of T's = 31,081,746 bp (28.28%) number of G's = 22,825,455 bp (20.77%) number of N's = 4,674 bp (0%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 730,711 number of insertions = 15,522 mapped reads with insertion percentage = 1.26% number of deletions = 35,894 mapped reads with deletion percentage = 2.95% homopolymer indels = 42.67% >>>>>>> Coverage mean coverageData = 0.0355X std coverageData = 0.4844X There is a 2.05% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% 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 11095058 0.044513662415308484 0.9254249869331941 chr2 243199373 9088394 0.0373701374633067 0.656300655835837 chr3 198022430 5756555 0.02907021694461582 0.26755950429157965 chr4 191154276 5934946 0.03104793742620751 0.3250099666502006 chr5 180915260 5718549 0.03160899196673625 0.28854167802664243 chr6 171115067 4692281 0.027421787468896588 0.318705350616295 chr7 159138663 5336256 0.03353211532259762 0.4999324997739999 chr8 146364022 9991474 0.06826454933029921 0.44991701075282076 chr9 141213431 4703435 0.03330727797414681 0.4193672896597975 chr10 135534747 5850646 0.043167129680774775 0.6068166743013305 chr11 135006516 3781408 0.028009077724811444 0.3205251310222233 chr12 133851895 5228859 0.039064512310415925 0.3147525958357612 chr13 115169878 2284616 0.019836922984324077 0.21427112097836165 chr14 107349540 2634346 0.02453989090218738 0.2599113064583692 chr15 102531392 2877987 0.028069325343793246 0.2685479781963606 chr16 90354753 3556716 0.03936390595854985 0.5491137849576867 chr17 81195210 3846359 0.04737174766836615 0.3783894219795382 chr18 78077248 2483540 0.03180875432494752 0.4823319295778643 chr19 59128983 2247898 0.0380168554564857 0.8121048033672534 chr20 63025520 3157067 0.05009188341484529 0.3717426460512651 chr21 48129895 1485228 0.030858741744605924 0.3033046732194983 chr22 51304566 879151 0.017135921196565623 0.2216181569713 chrMT 16571 13879 0.8375475227807616 1.3893024576954334 chrX 155270560 6874678 0.04427547630407207 0.4023681171331153 chrY 59373566 455593 0.007673330586207337 0.46597136919484056