BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238066.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 = 2,491,945 number of mapped reads = 2,274,804 (91.29%) number of supplementary alignments = 16,426 (0.66%) number of secondary alignments = 0 number of mapped bases = 153,385,419 bp number of sequenced bases = 153,318,381 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,475 duplication rate = 2.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2192 >>>>>>> ACTG content number of A's = 41,863,707 bp (27.31%) number of C's = 29,187,441 bp (19.04%) number of T's = 47,667,682 bp (31.09%) number of G's = 34,578,505 bp (22.55%) number of N's = 21,046 bp (0.01%) GC percentage = 41.59% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,121,607 number of insertions = 10,622 mapped reads with insertion percentage = 0.46% number of deletions = 37,592 mapped reads with deletion percentage = 1.63% homopolymer indels = 46.64% >>>>>>> Coverage mean coverageData = 0.0495X std coverageData = 0.4251X There is a 4.24% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 11939531 0.04790171014257975 0.7958952234860924 chr2 243199373 13911887 0.05720363020837229 0.4706966391508115 chr3 198022430 10587609 0.05346671586648038 0.2614459685206185 chr4 191154276 9817138 0.05135714568059152 0.27730338307566105 chr5 180915260 9347270 0.051666564777343826 0.25943946624073333 chr6 171115067 9015182 0.05268491055787624 0.3278675464613299 chr7 159138663 8435393 0.05300655944306884 0.566349499467297 chr8 146364022 7853908 0.05366009961109158 0.5135661235053028 chr9 141213431 6262793 0.04434983949933204 0.40998975596622056 chr10 135534747 7193184 0.053072619082691765 0.4242113971764438 chr11 135006516 6131804 0.04541857816699751 0.32698213851064284 chr12 133851895 6871816 0.05133895190650831 0.26229893071678895 chr13 115169878 4779562 0.04150010474092888 0.2289017520024991 chr14 107349540 5037170 0.04692307018735246 0.27992671206390957 chr15 102531392 4679375 0.045638461633291785 0.24164090970462154 chr16 90354753 4348216 0.048123821444124804 0.2974384510247583 chr17 81195210 3910530 0.048162077541273676 0.2759904782142366 chr18 78077248 4292476 0.05497729633093625 0.7952554381509139 chr19 59128983 2885365 0.04879781206451665 0.5325414318536287 chr20 63025520 2961119 0.04698285710296401 0.25260957170723236 chr21 48129895 1926935 0.040036135545278045 0.26076811137459793 chr22 51304566 1680014 0.03274589633990862 0.20386820127927163 chrMT 16571 74987 4.525194617102167 3.3796081837457796 chrX 155270560 9054987 0.058317474993327775 0.3115252322663001 chrY 59373566 387168 0.006520881700115503 0.1626858395688722