BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013302.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,853,089 number of mapped reads = 1,679,070 (90.61%) number of supplementary alignments = 19,297 (1.04%) number of secondary alignments = 0 number of mapped bases = 110,523,846 bp number of sequenced bases = 110,455,530 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 108,705 duplication rate = 5.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4369 >>>>>>> ACTG content number of A's = 30,598,934 bp (27.7%) number of C's = 20,146,667 bp (18.24%) number of T's = 35,394,242 bp (32.04%) number of G's = 24,303,596 bp (22%) number of N's = 12,091 bp (0.01%) GC percentage = 40.24% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 872,430 number of insertions = 8,151 mapped reads with insertion percentage = 0.48% number of deletions = 39,607 mapped reads with deletion percentage = 2.33% homopolymer indels = 45.18% >>>>>>> Coverage mean coverageData = 0.0357X std coverageData = 0.3349X There is a 2.67% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.16% 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 4103216 0.01646220973708226 0.41868248504356353 chr2 243199373 9110441 0.03746079147991882 0.4456939266399157 chr3 198022430 5017135 0.025336195500681412 0.19939221176414268 chr4 191154276 8305840 0.043450976738809655 0.27029249619284734 chr5 180915260 10931007 0.06042059138626559 0.3147166602219332 chr6 171115067 3062456 0.017897056370845474 0.225181358202384 chr7 159138663 10483501 0.0658765180149842 0.5790076369009434 chr8 146364022 6691152 0.04571582489035454 0.43206450468082847 chr9 141213431 3349328 0.023718197173468576 0.2826189436540825 chr10 135534747 3416007 0.025203920585766836 0.28467361424277965 chr11 135006516 7795847 0.05774422769342481 0.3638348013229523 chr12 133851895 5372071 0.040134441129877164 0.25849179725082105 chr13 115169878 1569731 0.013629700988308766 0.14765741342460273 chr14 107349540 4541505 0.042305770476519976 0.26936339342585996 chr15 102531392 991169 0.009666980820859235 0.1225279002511737 chr16 90354753 4170252 0.046154207294440835 0.2787075823940387 chr17 81195210 4721468 0.058149587888251045 0.32708079132356854 chr18 78077248 4064454 0.05205682966694728 0.4742932021356381 chr19 59128983 2312067 0.03910209313087627 0.45000522296447065 chr20 63025520 3480668 0.05522632736707289 0.30150681992899026 chr21 48129895 2983380 0.06198600682590311 0.32633585363842577 chr22 51304566 1227352 0.023922860978884415 0.19179303077911775 chrMT 16571 6137 0.3703457848047794 0.7368089637598645 chrX 155270560 2629951 0.01693785995233095 0.19225602755815926 chrY 59373566 187711 0.003161524776867874 0.09621537339595176