BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068180.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 = 5,087,565 number of mapped reads = 4,669,882 (91.79%) number of supplementary alignments = 31,967 (0.63%) number of secondary alignments = 0 number of mapped bases = 297,289,032 bp number of sequenced bases = 297,157,698 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 631,465 duplication rate = 11.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6769 >>>>>>> ACTG content number of A's = 77,327,803 bp (26.02%) number of C's = 52,991,360 bp (17.83%) number of T's = 97,147,649 bp (32.69%) number of G's = 69,657,155 bp (23.44%) number of N's = 33,731 bp (0.01%) GC percentage = 41.27% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 1,771,668 number of insertions = 18,884 mapped reads with insertion percentage = 0.4% number of deletions = 74,331 mapped reads with deletion percentage = 1.58% homopolymer indels = 45.31% >>>>>>> Coverage mean coverageData = 0.096X std coverageData = 1.0152X There is a 6.79% of reference with a coverageData >= 1X There is a 1.75% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 29025244 0.11645003684865443 2.3233389158572524 chr2 243199373 27653084 0.11370540827833467 1.3063846681223745 chr3 198022430 20501563 0.10353151913144384 0.4389576579225392 chr4 191154276 16561618 0.08664006030396097 0.4367896804029048 chr5 180915260 18625839 0.10295338823270077 0.4390933072346734 chr6 171115067 16254269 0.09499028510446716 0.5621933022922392 chr7 159138663 28153361 0.1769108805444721 1.7228168484612432 chr8 146364022 12415026 0.08482293551621586 1.0741667496515022 chr9 141213431 11561167 0.08187016573515589 0.6973912399361938 chr10 135534747 11604490 0.08562003660950501 0.6551771641834716 chr11 135006516 12794911 0.09477254416372022 0.5689149182111807 chr12 133851895 9453059 0.07062327358159554 0.4127260733821204 chr13 115169878 8015135 0.06959402179795658 0.37974150459541034 chr14 107349540 7510479 0.06996284287757544 0.4406192165107045 chr15 102531392 5788171 0.0564526715876441 0.3776400766166224 chr16 90354753 7364099 0.08150206553052057 0.44044208126707607 chr17 81195210 8201214 0.10100613078037485 0.4674249627096259 chr18 78077248 7663306 0.09815030878137508 1.2711655823159422 chr19 59128983 6819585 0.1153340486170716 1.4583811209828843 chr20 63025520 4917279 0.07802044314747424 0.41639685516718056 chr21 48129895 4832190 0.10039893085160481 0.45747824509307766 chr22 51304566 3194436 0.06226416572747151 0.33194518277763535 chrMT 16571 305342 18.42628688672983 11.56383127581824 chrX 155270560 16869147 0.10864356385395918 0.5484002443281009 chrY 59373566 1205018 0.020295530169099157 0.39225902090750975