BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068106.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 = 4,916,590 number of mapped reads = 4,657,207 (94.72%) number of supplementary alignments = 31,602 (0.64%) number of secondary alignments = 0 number of mapped bases = 305,541,849 bp number of sequenced bases = 305,398,832 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 607,838 duplication rate = 10.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.386 >>>>>>> ACTG content number of A's = 83,463,721 bp (27.33%) number of C's = 54,454,856 bp (17.83%) number of T's = 99,907,919 bp (32.71%) number of G's = 67,536,158 bp (22.11%) number of N's = 36,178 bp (0.01%) GC percentage = 39.94% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,708,068 number of insertions = 20,216 mapped reads with insertion percentage = 0.43% number of deletions = 80,890 mapped reads with deletion percentage = 1.72% homopolymer indels = 45.67% >>>>>>> Coverage mean coverageData = 0.0987X std coverageData = 1.0715X There is a 6.94% of reference with a coverageData >= 1X There is a 1.9% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 30265777 0.1214270876380284 2.754196722514635 chr2 243199373 25325003 0.10413268211838687 1.0553066804486326 chr3 198022430 17914342 0.0904662264774753 0.40383034646685473 chr4 191154276 24057350 0.12585305703545968 0.49188869168847044 chr5 180915260 17325396 0.0957652549596977 0.41928569231901763 chr6 171115067 23151672 0.13529885126947938 0.6399407088185594 chr7 159138663 19057038 0.11975115060505441 0.5489334507025808 chr8 146364022 11235782 0.07676601016061174 1.7809494152726477 chr9 141213431 6935889 0.049116354945019355 0.7269795531562923 chr10 135534747 16062673 0.11851332116331763 0.7085862255873546 chr11 135006516 15569367 0.11532307818387078 0.5638549140476623 chr12 133851895 17070133 0.12753000620573957 0.5160335881996477 chr13 115169878 6679763 0.05799921920556345 0.3466819474661409 chr14 107349540 9671790 0.09009624074774797 0.46441672495461056 chr15 102531392 5860721 0.05716025975732388 0.3480769674614332 chr16 90354753 4346225 0.04810178607870247 0.36806574639027334 chr17 81195210 6975362 0.08590854066391355 0.40839528875108116 chr18 78077248 7184410 0.0920166909571403 1.4199426138678375 chr19 59128983 6558314 0.11091538645269783 1.6266966757810415 chr20 63025520 4878540 0.07740578736994157 0.4423417146738028 chr21 48129895 5915055 0.12289773331107412 0.4852964803166308 chr22 51304566 3835681 0.07476295579617612 0.3573928393503495 chrMT 16571 263911 15.926075674370889 10.00364039594409 chrX 155270560 18578596 0.1196530494898711 0.5265980557021861 chrY 59373566 823059 0.013862381114181352 0.3746175065961171