BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472610.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 34,335,212 number of mapped reads = 34,047,272 (99.16%) number of supplementary alignments = 140,512 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 17,063,453 number of mapped paired reads (second in pair) = 16,983,819 number of mapped paired reads (both in pair) = 33,866,140 number of mapped paired reads (singletons) = 181,132 number of mapped bases = 3,329,535,056 bp number of sequenced bases = 3,329,168,496 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,703,417 duplication rate = 51.18% >>>>>>> Insert size mean insert size = 16,056.817 std insert size = 1,261,334.7877 median insert size = 191 >>>>>>> Mapping quality mean mapping quality = 54.9257 >>>>>>> ACTG content number of A's = 877,924,856 bp (26.37%) number of C's = 792,867,823 bp (23.82%) number of T's = 873,667,241 bp (26.24%) number of G's = 784,060,444 bp (23.55%) number of N's = 648,132 bp (0.02%) GC percentage = 47.37% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 19,643,475 number of insertions = 174,093 mapped reads with insertion percentage = 0.51% number of deletions = 145,780 mapped reads with deletion percentage = 0.42% homopolymer indels = 46.15% >>>>>>> Coverage mean coverageData = 1.0755X std coverageData = 43.6704X There is a 6.56% of reference with a coverageData >= 1X There is a 3.34% of reference with a coverageData >= 2X There is a 1.43% of reference with a coverageData >= 3X There is a 1.01% of reference with a coverageData >= 4X There is a 0.67% of reference with a coverageData >= 5X There is a 0.56% of reference with a coverageData >= 6X There is a 0.48% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.41% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.38% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.34% of reference with a coverageData >= 15X There is a 0.33% of reference with a coverageData >= 16X There is a 0.32% of reference with a coverageData >= 17X There is a 0.32% of reference with a coverageData >= 18X There is a 0.31% of reference with a coverageData >= 19X There is a 0.3% of reference with a coverageData >= 20X There is a 0.3% of reference with a coverageData >= 21X There is a 0.29% of reference with a coverageData >= 22X There is a 0.29% of reference with a coverageData >= 23X There is a 0.28% of reference with a coverageData >= 24X There is a 0.28% of reference with a coverageData >= 25X There is a 0.28% of reference with a coverageData >= 26X There is a 0.27% of reference with a coverageData >= 27X There is a 0.27% of reference with a coverageData >= 28X There is a 0.26% of reference with a coverageData >= 29X There is a 0.26% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.25% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.25% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.24% of reference with a coverageData >= 38X There is a 0.23% of reference with a coverageData >= 39X There is a 0.23% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.23% of reference with a coverageData >= 42X There is a 0.23% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.22% of reference with a coverageData >= 45X There is a 0.22% of reference with a coverageData >= 46X There is a 0.22% of reference with a coverageData >= 47X There is a 0.22% of reference with a coverageData >= 48X There is a 0.21% of reference with a coverageData >= 49X There is a 0.21% of reference with a coverageData >= 50X There is a 0.21% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 467455828 1.8754449883597282 67.64340594955287 chr2 243199373 240765030 0.9899903401477931 38.1571768333259 chr3 198022430 172225805 0.8697287726445938 25.46725526753702 chr4 191154276 65009828 0.3400908907734818 16.676907324122812 chr5 180915260 170501993 0.9424411904225216 49.1081509261618 chr6 171115067 269796920 1.5766987953199936 39.62542923992444 chr7 159138663 142681162 0.8965838930040527 41.069558903776574 chr8 146364022 162517156 1.1103627365473736 47.36147900769787 chr9 141213431 171676081 1.2157206278771033 47.12605562435983 chr10 135534747 89203100 0.6581566865654016 32.52360632413434 chr11 135006516 108937002 0.8069018090949033 45.80140810265569 chr12 133851895 121919016 0.9108501302876586 26.14315688276374 chr13 115169878 80489158 0.6988733460323714 24.49579588366029 chr14 107349540 54049442 0.5034902059198391 22.60347244353695 chr15 102531392 110585559 1.0785531810589288 57.70175672758522 chr16 90354753 161158397 1.783618367038201 63.465849021945935 chr17 81195210 113012240 1.391858460616088 33.929985487269185 chr18 78077248 36476036 0.467178812449947 17.052677603510414 chr19 59128983 93952192 1.5889363765989346 41.15525025756695 chr20 63025520 183725498 2.915096900430175 78.4632409432358 chr21 48129895 17677848 0.3672945473909719 22.120969513288678 chr22 51304566 92536214 1.803664297637758 91.44257523011447 chrMT 16571 3927 0.23698026673103614 0.6184644286496935 chrX 155270560 200714345 1.292674831597181 36.52012005506762 chrY 59373566 2465279 0.0415214912306261 1.6060808491484906