BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525146.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,211,074 number of mapped reads = 1,075,430 (88.8%) number of supplementary alignments = 33,083 (2.73%) number of secondary alignments = 0 number of mapped bases = 81,999,938 bp number of sequenced bases = 81,966,740 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,020 duplication rate = 1.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5193 >>>>>>> ACTG content number of A's = 21,828,610 bp (26.63%) number of C's = 15,894,654 bp (19.39%) number of T's = 24,539,260 bp (29.94%) number of G's = 19,701,122 bp (24.04%) number of N's = 3,094 bp (0%) GC percentage = 43.43% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 602,663 number of insertions = 7,687 mapped reads with insertion percentage = 0.7% number of deletions = 19,387 mapped reads with deletion percentage = 1.78% homopolymer indels = 41.45% >>>>>>> Coverage mean coverageData = 0.0265X std coverageData = 0.2796X There is a 2.4% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 6520377 0.026159922787113137 0.4076455682711165 chr2 243199373 7059353 0.02902701973660105 0.4012419494825883 chr3 198022430 5390403 0.027221173884190795 0.1767075306912464 chr4 191154276 5238470 0.027404409200869773 0.18522660809703304 chr5 180915260 4969169 0.02746683170894484 0.17965149733237065 chr6 171115067 4745994 0.027735687354755265 0.19949749055664057 chr7 159138663 4560770 0.028659094616121036 0.4099818422076664 chr8 146364022 4195511 0.028664906461780614 0.3669373768852499 chr9 141213431 3440462 0.024363560715410987 0.27687277719014813 chr10 135534747 3849756 0.028404199551868424 0.28028233753322873 chr11 135006516 3725287 0.02759338667772154 0.2807542205130106 chr12 133851895 3728787 0.02785755853512571 0.1797517843244642 chr13 115169878 2616937 0.02272240837139725 0.16020348538007467 chr14 107349540 2492691 0.023220323067988928 0.18571811873214644 chr15 102531392 2372133 0.023135675364672703 0.16271589295180294 chr16 90354753 2390252 0.026454081502497163 0.1876935043471786 chr17 81195210 2245693 0.027657949280505585 0.2200102107166166 chr18 78077248 2214923 0.028368353864111604 0.46118183787424033 chr19 59128983 1703124 0.028803539543374185 0.33773118170348204 chr20 63025520 1689484 0.02680634765091982 0.1791606372129819 chr21 48129895 1066051 0.02214945617479531 0.170523705049502 chr22 51304566 919214 0.017916806858867103 0.14331102009144467 chrMT 16571 1281 0.07730372337215617 0.28180538276079475 chrX 155270560 4664754 0.030042746029897746 0.23219384639796548 chrY 59373566 199062 0.003352704130993244 0.08981687779115088