BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238660.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 = 3,065,938 number of mapped reads = 2,693,817 (87.86%) number of supplementary alignments = 24,718 (0.81%) number of secondary alignments = 0 number of mapped bases = 160,407,126 bp number of sequenced bases = 160,337,255 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,253,776 duplication rate = 24.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.0379 >>>>>>> ACTG content number of A's = 39,131,844 bp (24.41%) number of C's = 26,485,250 bp (16.52%) number of T's = 56,060,240 bp (34.96%) number of G's = 38,656,355 bp (24.11%) number of N's = 3,566 bp (0%) GC percentage = 40.63% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 948,357 number of insertions = 10,082 mapped reads with insertion percentage = 0.37% number of deletions = 42,752 mapped reads with deletion percentage = 1.57% homopolymer indels = 42.09% >>>>>>> Coverage mean coverageData = 0.0518X std coverageData = 0.9914X There is a 1.36% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.58% of reference with a coverageData >= 3X There is a 0.47% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.3% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 17531773 0.07033793107380061 0.842555794542145 chr2 243199373 13649630 0.05612526805321986 1.9873617969971535 chr3 198022430 6666361 0.03366467626924889 0.5418812649354472 chr4 191154276 10515243 0.055009195818355644 0.6845032014862311 chr5 180915260 13587510 0.07510427810235576 0.8125339919552396 chr6 171115067 12735760 0.07442804554434707 1.0426976418316323 chr7 159138663 6259350 0.03933267932507388 0.7110741690406841 chr8 146364022 3009525 0.020561917873505826 0.8477554852491233 chr9 141213431 8297511 0.058758653063248636 0.9382451142328093 chr10 135534747 8029566 0.059243597510828715 0.7663666308678412 chr11 135006516 7633735 0.05654345602104124 0.7735186526318643 chr12 133851895 5939002 0.044369950832597475 0.6675045771450249 chr13 115169878 6944656 0.06029923900761621 0.8578031307452608 chr14 107349540 3869153 0.036042567113003 0.6616888524579404 chr15 102531392 5030240 0.04906048676292232 0.7511879682009182 chr16 90354753 3509925 0.03884604720240893 0.6583025978938997 chr17 81195210 2347450 0.028911188233887195 0.47620587923198554 chr18 78077248 5851639 0.07494678859582755 2.5192101024645517 chr19 59128983 5577800 0.09433275725374814 0.9418293801252596 chr20 63025520 2239111 0.03552705316830389 0.6022181711648108 chr21 48129895 1073435 0.022302874336210372 0.45875945101998067 chr22 51304566 1164828 0.02270417802579209 0.4321159507279123 chrMT 16571 21735 1.3116287490193712 3.42391672373904 chrX 155270560 8464461 0.05451426851297503 0.6995318768432963 chrY 59373566 457727 0.007709272506893051 0.339536599130619