BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779395.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 = 18,785,756 number of mapped reads = 17,608,041 (93.73%) number of supplementary alignments = 63,948 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,875,190 number of mapped paired reads (second in pair) = 8,732,851 number of mapped paired reads (both in pair) = 17,416,998 number of mapped paired reads (singletons) = 191,043 number of mapped bases = 1,397,053,591 bp number of sequenced bases = 1,396,706,800 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 794,239 duplication rate = 4.15% >>>>>>> Insert size mean insert size = 244,144.6628 std insert size = 4,731,780.103 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 52.8883 >>>>>>> ACTG content number of A's = 420,945,872 bp (30.14%) number of C's = 277,936,937 bp (19.9%) number of T's = 413,423,629 bp (29.6%) number of G's = 284,095,340 bp (20.34%) number of N's = 305,022 bp (0.02%) GC percentage = 40.24% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 4,649,973 number of insertions = 137,191 mapped reads with insertion percentage = 0.77% number of deletions = 161,648 mapped reads with deletion percentage = 0.91% homopolymer indels = 46.65% >>>>>>> Coverage mean coverageData = 0.4513X std coverageData = 1.6791X There is a 17.78% of reference with a coverageData >= 1X There is a 9.56% of reference with a coverageData >= 2X There is a 5.63% of reference with a coverageData >= 3X There is a 3.57% of reference with a coverageData >= 4X There is a 2.36% of reference with a coverageData >= 5X There is a 1.6% of reference with a coverageData >= 6X There is a 1.11% of reference with a coverageData >= 7X There is a 0.78% of reference with a coverageData >= 8X There is a 0.56% of reference with a coverageData >= 9X There is a 0.41% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% 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 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% 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 92576477 0.371419243123972 2.261167356480608 chr2 243199373 110488198 0.4543111959421047 1.4536239721944564 chr3 198022430 94936181 0.4794213514095348 1.490084744021862 chr4 191154276 69230978 0.36217331596600016 1.1867619526683268 chr5 180915260 117595067 0.6500008180625559 1.6434485155472331 chr6 171115067 72689286 0.42479769475822954 1.3394546675549026 chr7 159138663 140615828 0.8836056892095417 3.1522575305588454 chr8 146364022 94451781 0.6453210270485734 1.721551312910061 chr9 141213431 87190346 0.6174366374541244 1.8182963882411645 chr10 135534747 33926953 0.25031922625716047 2.0147944602213586 chr11 135006516 68021228 0.5038366296334912 1.4620581074751435 chr12 133851895 72731347 0.5433718140486543 1.4968836596484003 chr13 115169878 76208458 0.6617047731873086 1.8028462215198453 chr14 107349540 27600084 0.25710481852088046 1.0525279967323977 chr15 102531392 41920417 0.4088544608855013 1.4990770402720082 chr16 90354753 29262492 0.3238622322391828 1.2155103431580188 chr17 81195210 19260608 0.23721359917660167 0.983478451572898 chr18 78077248 32386114 0.41479579300745845 1.4135071223628393 chr19 59128983 21093434 0.3567359513015808 1.9317290790016348 chr20 63025520 20137935 0.31952033081202663 1.1896748674129167 chr21 48129895 22262114 0.4625423346549998 1.3828932691251616 chr22 51304566 8674631 0.16908107165354444 0.7911934978239067 chrMT 16571 480 0.028966266368957817 0.19344395977898707 chrX 155270560 35206673 0.22674403312514618 1.0062305104395048 chrY 59373566 8586481 0.144617909592966 0.8301774472547699