BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084799.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,350,420 number of mapped reads = 2,138,234 (90.97%) number of supplementary alignments = 22,156 (0.94%) number of secondary alignments = 0 number of mapped bases = 142,638,174 bp number of sequenced bases = 142,584,078 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,763 duplication rate = 3.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0756 >>>>>>> ACTG content number of A's = 38,474,605 bp (26.98%) number of C's = 26,841,458 bp (18.83%) number of T's = 44,609,856 bp (31.29%) number of G's = 32,638,053 bp (22.89%) number of N's = 20,106 bp (0.01%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,089,461 number of insertions = 11,408 mapped reads with insertion percentage = 0.53% number of deletions = 32,872 mapped reads with deletion percentage = 1.52% homopolymer indels = 47.42% >>>>>>> Coverage mean coverageData = 0.0461X std coverageData = 0.3265X There is a 3.84% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 11884643 0.04768149805331879 0.39720818412483955 chr2 243199373 12743603 0.052399818481439916 0.5705068755725223 chr3 198022430 12505365 0.06315125513811744 0.29315055853186506 chr4 191154276 8463886 0.04427777487959516 0.24893257448090292 chr5 180915260 6192611 0.03422934582743324 0.21440632338565044 chr6 171115067 8622737 0.05039145383965516 0.28542938409772334 chr7 159138663 9071437 0.05700335059368948 0.4302439770796636 chr8 146364022 7976275 0.054496145234380074 0.32000682106999034 chr9 141213431 9565676 0.06773913736293256 0.37282613223286876 chr10 135534747 4290199 0.03165386806676224 0.2227567697121213 chr11 135006516 6321460 0.04682336962165589 0.30329658902418904 chr12 133851895 5652653 0.042230653514468364 0.2403599038900387 chr13 115169878 3929757 0.03412139587401491 0.2166576290387568 chr14 107349540 3203400 0.0298408358340427 0.20758202237112588 chr15 102531392 3584426 0.034959303000587374 0.2328045893232132 chr16 90354753 2806037 0.031055776335308004 0.21355344214891447 chr17 81195210 3950618 0.04865580124738886 0.26107342656412796 chr18 78077248 5377834 0.06887837542634699 0.4700568265314925 chr19 59128983 2624768 0.04439054870942056 0.32725687951800864 chr20 63025520 2892234 0.04588988714412828 0.2515538563917645 chr21 48129895 1179934 0.024515615502589398 0.18663155894536376 chr22 51304566 828882 0.016156105871746387 0.14466184302046275 chrMT 16571 16836 1.0159917928911955 1.2140393838210772 chrX 155270560 8661515 0.05578336936506186 0.28687447098295066 chrY 59373566 291388 0.004907705897267481 0.09976404963791499