BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472669.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 = 15,413,320 number of mapped reads = 15,306,892 (99.31%) number of supplementary alignments = 83,883 (0.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,669,174 number of mapped paired reads (second in pair) = 7,637,718 number of mapped paired reads (both in pair) = 15,233,062 number of mapped paired reads (singletons) = 73,830 number of mapped bases = 1,500,342,049 bp number of sequenced bases = 1,500,166,070 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,324,034 duplication rate = 49.01% >>>>>>> Insert size mean insert size = 20,862.2852 std insert size = 1,413,465.3014 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 54.6248 >>>>>>> ACTG content number of A's = 409,651,130 bp (27.31%) number of C's = 342,642,906 bp (22.84%) number of T's = 409,626,503 bp (27.31%) number of G's = 337,959,667 bp (22.53%) number of N's = 285,864 bp (0.02%) GC percentage = 45.37% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 8,779,756 number of insertions = 92,242 mapped reads with insertion percentage = 0.6% number of deletions = 79,671 mapped reads with deletion percentage = 0.51% homopolymer indels = 46.65% >>>>>>> Coverage mean coverageData = 0.4847X std coverageData = 20.0562X There is a 3.09% of reference with a coverageData >= 1X There is a 1.46% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 179224081 0.719051692954458 26.27967196931465 chr2 243199373 99452919 0.4089357541230174 18.09803685074498 chr3 198022430 137113917 0.6924160914498423 19.849740161882426 chr4 191154276 32670940 0.1709139899125249 10.188767391255412 chr5 180915260 84818349 0.4688291579162532 21.890043172640905 chr6 171115067 90979497 0.5316860671304883 15.228981857478777 chr7 159138663 73776712 0.46360017489904387 19.87871563463252 chr8 146364022 96425537 0.6588062809588547 28.770815184848505 chr9 141213431 107323517 0.7600092727723612 31.935761406439784 chr10 135534747 23840410 0.17589887853629152 7.828856833484101 chr11 135006516 38651206 0.286291411297511 14.152471577747365 chr12 133851895 70974646 0.5302475994082863 17.202347940881232 chr13 115169878 35094962 0.30472344513554145 12.7633265981525 chr14 107349540 24920118 0.2321399607301531 12.41712546361953 chr15 102531392 18842072 0.1837688110193608 9.11345245893289 chr16 90354753 89732455 0.9931127253482724 37.59175154365386 chr17 81195210 49160200 0.6054568982579145 16.27866316812337 chr18 78077248 10720126 0.1373015350131193 7.184501923592903 chr19 59128983 39376595 0.6659440599544897 18.826986719699526 chr20 63025520 63585198 1.0088801805998586 26.159048453855736 chr21 48129895 12413469 0.25791597924740955 18.51123053131491 chr22 51304566 14283791 0.27841169146621375 10.114270667702234 chrMT 16571 9403 0.5674370888902299 1.0337199693469032 chrX 155270560 106273593 0.684441358361817 23.135521996858273 chrY 59373566 678336 0.011424882244734971 0.5457024550843638