BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238493.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 = 4,026,485 number of mapped reads = 3,269,545 (81.2%) number of supplementary alignments = 26,775 (0.66%) number of secondary alignments = 0 number of mapped bases = 194,832,784 bp number of sequenced bases = 194,726,233 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,774,506 duplication rate = 23.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.2921 >>>>>>> ACTG content number of A's = 46,851,632 bp (24.06%) number of C's = 32,437,096 bp (16.66%) number of T's = 67,665,047 bp (34.75%) number of G's = 47,760,522 bp (24.53%) number of N's = 11,936 bp (0.01%) GC percentage = 41.18% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,269,649 number of insertions = 12,386 mapped reads with insertion percentage = 0.38% number of deletions = 64,260 mapped reads with deletion percentage = 1.95% homopolymer indels = 40.87% >>>>>>> Coverage mean coverageData = 0.0629X std coverageData = 1.3501X There is a 1.27% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.26% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.19% of reference with a coverageData >= 11X There is a 0.16% of reference with a coverageData >= 12X There is a 0.15% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% 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 19563929 0.07849099401040209 1.2290677339228584 chr2 243199373 16078051 0.06611057751370107 2.552264702701052 chr3 198022430 5438046 0.027461767841148097 0.6207621828257952 chr4 191154276 3890515 0.020352749001544698 0.5036900317593788 chr5 180915260 7831885 0.043290350410462884 0.7894537479550381 chr6 171115067 17899183 0.1046031966314223 1.4925415512645717 chr7 159138663 16811595 0.10564117281794683 2.0104745140428353 chr8 146364022 5160300 0.03525661518101764 0.8169401611609709 chr9 141213431 14917864 0.10564054633018582 1.4666846595247724 chr10 135534747 4493610 0.03315467139950466 0.7638296847320161 chr11 135006516 5581402 0.04134172309135064 0.8082647003639459 chr12 133851895 14880982 0.11117498187082073 1.3768256507878671 chr13 115169878 6609593 0.05738994531191567 1.042753442255491 chr14 107349540 1555810 0.014492935880302794 0.6505078675065993 chr15 102531392 4803848 0.04685246056154197 0.9476667343158504 chr16 90354753 5903940 0.06534177565622917 1.1265617876986609 chr17 81195210 1658109 0.0204212662298675 0.5139413384539044 chr18 78077248 23590188 0.30213908154139857 3.3584986354312143 chr19 59128983 1479587 0.02502304157675095 0.7528443924375574 chr20 63025520 8297689 0.1316560180701405 1.519062863408601 chr21 48129895 2749741 0.057131664218257695 0.9626415771636576 chr22 51304566 962852 0.01876737442823315 0.5204594677998228 chrMT 16571 25981 1.5678595136081106 4.065436925136681 chrX 155270560 4281883 0.027576914773798717 0.6391004443460723 chrY 59373566 366201 0.006167744750247947 0.386800143603431