BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779273.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 11,734,440 number of mapped reads = 11,333,821 (96.59%) number of supplementary alignments = 25,901 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,727,862 number of mapped paired reads (second in pair) = 5,605,959 number of mapped paired reads (both in pair) = 11,193,638 number of mapped paired reads (singletons) = 140,183 number of mapped bases = 901,926,327 bp number of sequenced bases = 901,757,920 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 193,231 duplication rate = 1.46% >>>>>>> Insert size mean insert size = 47,324.5298 std insert size = 2,009,278.7499 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 52.916 >>>>>>> ACTG content number of A's = 274,561,539 bp (30.45%) number of C's = 175,179,910 bp (19.43%) number of T's = 273,803,400 bp (30.36%) number of G's = 178,042,855 bp (19.74%) number of N's = 170,216 bp (0.02%) GC percentage = 39.17% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 3,389,723 number of insertions = 64,189 mapped reads with insertion percentage = 0.56% number of deletions = 81,153 mapped reads with deletion percentage = 0.71% homopolymer indels = 46.58% >>>>>>> Coverage mean coverageData = 0.2913X std coverageData = 1.0347X There is a 18.15% of reference with a coverageData >= 1X There is a 6.19% of reference with a coverageData >= 2X There is a 2.3% of reference with a coverageData >= 3X There is a 0.96% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.22% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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% 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 70032487 0.28097216656483276 1.2742277814733056 chr2 243199373 63200616 0.25987162392889884 0.7070231518648508 chr3 198022430 69469325 0.35081543540294907 0.7952178849539105 chr4 191154276 69119796 0.3615916810566142 0.8241732012516418 chr5 180915260 39761018 0.21977702710097535 0.6396762893731905 chr6 171115067 41881019 0.24475354353220105 0.6962305737228607 chr7 159138663 93156726 0.5853808511637426 2.791985982942777 chr8 146364022 75714053 0.5172996202577708 1.0240230282477376 chr9 141213431 38515534 0.2727469598837238 0.7778751677622184 chr10 135534747 19331015 0.14262774253749114 1.1646488892226114 chr11 135006516 44584385 0.33023876417935266 0.8196745215226253 chr12 133851895 32700961 0.2443070454848622 0.6791515014006844 chr13 115169878 14774762 0.12828668621147624 0.4872807938992238 chr14 107349540 32530529 0.3030337065254308 0.788920268517859 chr15 102531392 16900314 0.16483063060335706 0.5554580724257075 chr16 90354753 19389697 0.21459520784700722 0.622407788906957 chr17 81195210 15621057 0.19238889831062694 0.5955371108349873 chr18 78077248 19677758 0.2520293491901764 0.7097331238296705 chr19 59128983 12714476 0.21502950591928835 0.9463214044406509 chr20 63025520 22591197 0.3584452298053233 0.8223269564213656 chr21 48129895 11827730 0.2457460171064159 0.6793040207550729 chr22 51304566 4854761 0.09462629505529781 0.48024302583305306 chrMT 16571 1238 0.07470882867660371 0.3662369404848281 chrX 155270560 72919840 0.46963081732944095 0.9956946487371894 chrY 59373566 656033 0.011049243698786763 0.1420077480677417