BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004030.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 = 1,186,882 number of mapped reads = 1,035,984 (87.29%) number of supplementary alignments = 8,921 (0.75%) number of secondary alignments = 0 number of mapped bases = 69,190,553 bp number of sequenced bases = 69,162,165 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,753 duplication rate = 1.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2016 >>>>>>> ACTG content number of A's = 19,851,542 bp (28.7%) number of C's = 12,579,635 bp (18.19%) number of T's = 21,295,619 bp (30.79%) number of G's = 15,421,161 bp (22.3%) number of N's = 14,208 bp (0.02%) GC percentage = 40.49% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 608,061 number of insertions = 6,322 mapped reads with insertion percentage = 0.61% number of deletions = 17,412 mapped reads with deletion percentage = 1.66% homopolymer indels = 46.47% >>>>>>> Coverage mean coverageData = 0.0224X std coverageData = 0.2637X There is a 2.07% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 6179442 0.024792082664460043 0.5330818090431234 chr2 243199373 5994115 0.0246469179836249 0.25781582692790356 chr3 198022430 4965350 0.02507468472132172 0.16609283447545137 chr4 191154276 4495598 0.023518166028365487 0.1658237547690117 chr5 180915260 5250164 0.02902001743799832 0.1805709675309559 chr6 171115067 4131472 0.02414440804327301 0.1771660592312277 chr7 159138663 4121312 0.02589761609345681 0.30058067721505627 chr8 146364022 4162773 0.028441231274718592 0.43164388613701804 chr9 141213431 2296768 0.01626451523580643 0.2086496959327875 chr10 135534747 3000150 0.022135652047957855 0.2085644723793947 chr11 135006516 3127819 0.02316791139177312 0.23788167976792857 chr12 133851895 2885056 0.021554091557687696 0.15795276135504163 chr13 115169878 1583893 0.013752667168753969 0.12252538669046578 chr14 107349540 1838436 0.017125699839980683 0.14434494299686043 chr15 102531392 1574378 0.01535508266580444 0.13150592859510093 chr16 90354753 1677675 0.01856764524606691 0.15984434776468154 chr17 81195210 1669293 0.02055900834544304 0.16421466403817656 chr18 78077248 1915414 0.024532293966098805 0.4279402670976703 chr19 59128983 1106221 0.01870860860231606 0.35672765462147954 chr20 63025520 1375519 0.021824794146878917 0.16492298293306082 chr21 48129895 923369 0.01918493692953205 0.1546612797084085 chr22 51304566 568102 0.011073127487327345 0.10921708160431555 chrMT 16571 26544 1.6018345302033674 1.9075506695361233 chrX 155270560 4148621 0.026718658063705058 0.18912887902233305 chrY 59373566 173069 0.0029149167156306563 0.06995904070499198