BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240070.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 = 1,248,720 number of mapped reads = 951,765 (76.22%) number of supplementary alignments = 4,769 (0.38%) number of secondary alignments = 0 number of mapped bases = 59,215,474 bp number of sequenced bases = 59,186,063 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,803 duplication rate = 6.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5844 >>>>>>> ACTG content number of A's = 15,905,347 bp (26.87%) number of C's = 10,394,349 bp (17.56%) number of T's = 19,194,047 bp (32.43%) number of G's = 13,651,676 bp (23.07%) number of N's = 40,644 bp (0.07%) GC percentage = 40.63% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 547,179 number of insertions = 4,129 mapped reads with insertion percentage = 0.43% number of deletions = 16,616 mapped reads with deletion percentage = 1.72% homopolymer indels = 50.34% >>>>>>> Coverage mean coverageData = 0.0191X std coverageData = 0.2246X There is a 1.52% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.06% 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% 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 4678523 0.01877035644376589 0.3368643384269908 chr2 243199373 4914491 0.02020766311761832 0.23783306836495074 chr3 198022430 4065178 0.02052887645101618 0.17729237536251355 chr4 191154276 3677574 0.0192387744441563 0.1964616339715166 chr5 180915260 3492069 0.01930223575391042 0.17033038751818427 chr6 171115067 3685750 0.021539599432234685 0.20310879946357974 chr7 159138663 3438191 0.021605001168069383 0.29723178096809294 chr8 146364022 3088352 0.021100486019713233 0.3186248132390346 chr9 141213431 2446381 0.017323996610492384 0.2055979842987343 chr10 135534747 2922107 0.021559836607803605 0.20340768102149318 chr11 135006516 2447428 0.01812822130748119 0.1946917450646285 chr12 133851895 2664931 0.019909550029157227 0.1767499813400513 chr13 115169878 1695437 0.01472118430133268 0.1499454470783415 chr14 107349540 1828121 0.01702961186419616 0.16624873100876514 chr15 102531392 2022397 0.019724661496841864 0.22546175113375821 chr16 90354753 1905270 0.02108654981326771 0.19376598583178664 chr17 81195210 1434310 0.017664958314659203 0.16791217835084982 chr18 78077248 1754752 0.022474562628027054 0.33728876665448687 chr19 59128983 1010829 0.017095321933746094 0.22574821652091134 chr20 63025520 1135042 0.018009244509208332 0.16607484131945272 chr21 48129895 776955 0.016142877519263236 0.16246357902273822 chr22 51304566 527932 0.010290156240674564 0.12122777294756067 chrMT 16571 30006 1.8107537263894755 2.2009078379045763 chrX 155270560 3415509 0.021997144854761907 0.19331777698786315 chrY 59373566 157939 0.002660089508519667 0.07414754904098039