BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536745.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 18,832,078 number of mapped reads = 15,292,702 (81.21%) number of supplementary alignments = 335 (0%) number of secondary alignments = 0 number of mapped bases = 762,544,459 bp number of sequenced bases = 762,477,663 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 114,948 duplication rate = 0.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5234 >>>>>>> ACTG content number of A's = 239,941,395 bp (31.47%) number of C's = 140,991,432 bp (18.49%) number of T's = 238,441,021 bp (31.27%) number of G's = 143,087,372 bp (18.77%) number of N's = 16,443 bp (0%) GC percentage = 37.26% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 2,585,348 number of insertions = 50,660 mapped reads with insertion percentage = 0.33% number of deletions = 39,939 mapped reads with deletion percentage = 0.26% homopolymer indels = 49.05% >>>>>>> Coverage mean coverageData = 0.2463X std coverageData = 0.556X There is a 19.83% of reference with a coverageData >= 1X There is a 3.92% of reference with a coverageData >= 2X There is a 0.72% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.02% 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 57989945 0.23265717360038193 0.5437560927457613 chr2 243199373 72380349 0.29761733390653106 0.6074423639650105 chr3 198022430 62877249 0.3175258934051057 0.6217552785864342 chr4 191154276 66371385 0.3472137081568607 0.6413153008683157 chr5 180915260 56450788 0.31202889131629913 0.6110920393404735 chr6 171115067 51894161 0.30327055302500044 0.6018713648208054 chr7 159138663 43896189 0.2758361052712878 0.5852963692903971 chr8 146364022 44177991 0.3018364103167375 0.600653456697667 chr9 141213431 31999420 0.22660323294602197 0.5382239537318346 chr10 135534747 31696594 0.23386323213485616 0.5249623095349815 chr11 135006516 34993142 0.25919594873480034 0.5642547444544586 chr12 133851895 34335802 0.2565208509001684 0.5608711737759795 chr13 115169878 34036956 0.2955369632326953 0.6044165000412347 chr14 107349540 23723105 0.2209893493721538 0.5239946849697131 chr15 102531392 18672866 0.18211852619732305 0.47361830121321974 chr16 90354753 12303510 0.13616892959687465 0.5257811195938238 chr17 81195210 9366744 0.11536079529814629 0.3752853430114136 chr18 78077248 24804398 0.3176904749511663 0.6155159709483757 chr19 59128983 3398826 0.057481556887254426 0.255422275283883 chr20 63025520 11583570 0.18379174023474934 0.47611330911115207 chr21 48129895 10108843 0.21003251721201552 0.5244649584048294 chr22 51304566 2889465 0.056319841005964266 0.25429797346684213 chrMT 16571 2787 0.16818538410476133 0.4153144716276725 chrX 155270560 19576187 0.1260779055604617 0.37135528557437397 chrY 59373566 3014187 0.050766480827511694 0.2441297866108036