BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708549.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 = 4,758,021 number of mapped reads = 3,929,831 (82.59%) number of supplementary alignments = 117 (0%) number of secondary alignments = 0 number of mapped bases = 195,973,188 bp number of sequenced bases = 195,955,267 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,239 duplication rate = 0.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3631 >>>>>>> ACTG content number of A's = 60,832,138 bp (31.04%) number of C's = 37,097,824 bp (18.93%) number of T's = 60,510,113 bp (30.88%) number of G's = 37,506,197 bp (19.14%) number of N's = 8,995 bp (0%) GC percentage = 38.07% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 306,156 number of insertions = 13,204 mapped reads with insertion percentage = 0.34% number of deletions = 10,508 mapped reads with deletion percentage = 0.27% homopolymer indels = 47.43% >>>>>>> Coverage mean coverageData = 0.0633X std coverageData = 0.2598X There is a 5.95% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.02% 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 14755115 0.059197906672417075 0.25207598225031164 chr2 243199373 17259415 0.07096817227402967 0.27404874668872453 chr3 198022430 14898061 0.07523420957918757 0.28207262704879343 chr4 191154276 15204979 0.07954297083053481 0.2895237256042825 chr5 180915260 13721590 0.07584539855841901 0.2829495731866831 chr6 171115067 12832858 0.07499548826989035 0.2817752534384454 chr7 159138663 10771360 0.06768537448376075 0.2686575348146669 chr8 146364022 10624470 0.07258935532667994 0.27730137055190685 chr9 141213431 8003197 0.056674474540598055 0.24589563852771498 chr10 135534747 8514864 0.06282421436917575 0.25773925107137013 chr11 135006516 8488422 0.06287416527362279 0.25927853605157614 chr12 133851895 8990316 0.06716614658313205 0.26738561638590186 chr13 115169878 7461354 0.06478563778629687 0.26292029070279477 chr14 107349540 6304547 0.05872914779141112 0.25090507057670897 chr15 102531392 5547307 0.054103498370528316 0.24125935198328333 chr16 90354753 3583523 0.0396605920664738 0.2052883848792933 chr17 81195210 3140323 0.03867621008677729 0.2027286781702454 chr18 78077248 5148468 0.06594069504089078 0.2638957849703897 chr19 59128983 1529443 0.025866215219700294 0.16438885378513618 chr20 63025520 3001932 0.04763042018534714 0.2245670707389991 chr21 48129895 2457191 0.05105332143359133 0.23523403480149602 chr22 51304566 1053620 0.020536573684299366 0.1471028301300953 chrMT 16571 139 0.008388147969344034 0.09120190207988221 chrX 155270560 12407160 0.07990671251523791 0.29195394696955 chrY 59373566 273534 0.004606999687369291 0.07032154286969004