BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708625.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 2,835,272 number of mapped reads = 1,851,104 (65.29%) number of supplementary alignments = 600 (0.02%) number of secondary alignments = 0 number of mapped bases = 89,484,303 bp number of sequenced bases = 89,460,432 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,021 duplication rate = 3.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.3024 >>>>>>> ACTG content number of A's = 26,692,763 bp (29.84%) number of C's = 16,349,156 bp (18.28%) number of T's = 28,827,758 bp (32.22%) number of G's = 17,583,352 bp (19.65%) number of N's = 7,403 bp (0.01%) GC percentage = 37.93% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 645,977 number of insertions = 4,654 mapped reads with insertion percentage = 0.25% number of deletions = 15,671 mapped reads with deletion percentage = 0.84% homopolymer indels = 44.36% >>>>>>> Coverage mean coverageData = 0.0289X std coverageData = 0.3862X There is a 2.14% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 7935286 0.03183657464187421 0.6578976050655106 chr2 243199373 4795989 0.019720400348236095 0.3140647813784785 chr3 198022430 5751187 0.029043108904380176 0.22180751368712656 chr4 191154276 8463224 0.04427431170830832 0.2781325577028022 chr5 180915260 3903829 0.021578218443264543 0.19284671642513726 chr6 171115067 4853261 0.028362557927175402 0.26903763775236245 chr7 159138663 6505892 0.040881906868854366 0.5960544704629231 chr8 146364022 4737215 0.03236597994007025 0.8674115576302535 chr9 141213431 4496437 0.031841425905160536 0.2816100744950367 chr10 135534747 4436569 0.032733812532958796 0.29751777499244586 chr11 135006516 3373966 0.02499113450198211 0.2699434231433228 chr12 133851895 4282060 0.03199103008590203 0.23742798857407957 chr13 115169878 2969653 0.02578497999277207 0.20970733543580417 chr14 107349540 3592085 0.0334615779443489 0.2549992158384975 chr15 102531392 3369333 0.03286147719519891 0.23438210664273218 chr16 90354753 1794258 0.019857926013034422 0.1992617500624929 chr17 81195210 1549323 0.0190814581303503 0.20130004039938496 chr18 78077248 1841525 0.023585936328083694 0.5670674902371917 chr19 59128983 1467532 0.024819165247607928 0.4333246668924726 chr20 63025520 1018204 0.016155424025061593 0.17713592198542755 chr21 48129895 1233009 0.025618360480528787 0.2191371360454701 chr22 51304566 838937 0.016352092326441275 0.16270292436483155 chrMT 16571 2786 0.16812503771649268 0.5709354349047487 chrX 155270560 5991499 0.038587475951654966 0.27644091988885366 chrY 59373566 281244 0.0047368554551700665 0.09533735519755365