BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231854.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 = 5,254,531 number of mapped reads = 4,890,826 (93.08%) number of supplementary alignments = 35,437 (0.67%) number of secondary alignments = 0 number of mapped bases = 313,144,632 bp number of sequenced bases = 313,025,536 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 518,442 duplication rate = 8.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3232 >>>>>>> ACTG content number of A's = 82,689,738 bp (26.42%) number of C's = 55,965,417 bp (17.88%) number of T's = 102,441,424 bp (32.73%) number of G's = 71,808,613 bp (22.94%) number of N's = 120,344 bp (0.04%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,979,182 number of insertions = 20,545 mapped reads with insertion percentage = 0.42% number of deletions = 68,428 mapped reads with deletion percentage = 1.39% homopolymer indels = 44.49% >>>>>>> Coverage mean coverageData = 0.1012X std coverageData = 1.1142X There is a 7.6% of reference with a coverageData >= 1X There is a 1.67% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 39268491 0.1575462112890784 2.754189887278408 chr2 243199373 23444865 0.0964018315951826 1.400815052309727 chr3 198022430 20621584 0.10413761713761416 0.41073022537102744 chr4 191154276 11404324 0.05966031332723104 0.3623700130795143 chr5 180915260 18415221 0.10178920783133495 0.42598343478866546 chr6 171115067 27808908 0.16251583503163985 0.866892263351142 chr7 159138663 18435809 0.11584745436751595 1.2887182688667245 chr8 146364022 15970596 0.10911558579607768 1.3325576185239272 chr9 141213431 9377103 0.06640376155154816 0.6916248142888085 chr10 135534747 9764291 0.07204271388797442 0.6465275251628468 chr11 135006516 11292559 0.0836445479416712 0.6744714009191277 chr12 133851895 10251395 0.07658759706016863 0.3804719172829174 chr13 115169878 9153597 0.0794790891416938 0.3908894100498026 chr14 107349540 14770461 0.13759221511335773 0.4986405450536891 chr15 102531392 8553080 0.0834191346977909 0.41533033099738875 chr16 90354753 10547063 0.11672947631210945 0.5107282519174622 chr17 81195210 5445186 0.06706289693690058 0.3945575959529551 chr18 78077248 9636660 0.12342468832917881 1.6597283231078297 chr19 59128983 9853214 0.16663932812779816 1.487365043318411 chr20 63025520 8838337 0.14023425748807786 0.48893004382715377 chr21 48129895 5324420 0.11062604645200244 0.4537707494560653 chr22 51304566 2632290 0.05130712927188586 0.27743078236976076 chrMT 16571 379976 22.93017922877316 12.715701611482634 chrX 155270560 11189457 0.07206425351979152 0.4648640331435267 chrY 59373566 765745 0.012897069379326146 0.2731814037638719