BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124893.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,462,718 number of mapped reads = 4,404,432 (98.69%) number of supplementary alignments = 15,909 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,206,575 number of mapped paired reads (second in pair) = 2,197,857 number of mapped paired reads (both in pair) = 4,385,268 number of mapped paired reads (singletons) = 19,164 number of mapped bases = 380,895,041 bp number of sequenced bases = 380,694,385 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 363,723 duplication rate = 5.7% >>>>>>> Insert size mean insert size = 32,031.087 std insert size = 1,669,259.9082 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 52.6886 >>>>>>> ACTG content number of A's = 107,659,742 bp (28.28%) number of C's = 70,270,543 bp (18.46%) number of T's = 113,499,581 bp (29.81%) number of G's = 89,123,238 bp (23.41%) number of N's = 141,281 bp (0.04%) GC percentage = 41.87% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 2,946,584 number of insertions = 51,614 mapped reads with insertion percentage = 1.14% number of deletions = 120,335 mapped reads with deletion percentage = 2.68% homopolymer indels = 48.02% >>>>>>> Coverage mean coverageData = 0.123X std coverageData = 1.2066X There is a 8.6% of reference with a coverageData >= 1X There is a 2.24% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 35982405 0.14436234844927429 1.2131330442239345 chr2 243199373 28663663 0.11786076027424626 1.3513638952846974 chr3 198022430 30751387 0.1552924433863376 0.5158212875167913 chr4 191154276 26130474 0.13669834934793715 0.8565769683168851 chr5 180915260 22283572 0.12317132341406689 0.4572894532991135 chr6 171115067 20316476 0.11872990705137614 1.6200782068796575 chr7 159138663 18523478 0.11639835129191704 1.9219401545654844 chr8 146364022 25641685 0.1751911750553015 0.6816859984343152 chr9 141213431 19294670 0.13663480777547285 1.6356574155116794 chr10 135534747 17647994 0.1302101076707658 2.601468452725221 chr11 135006516 15891150 0.11770654091984716 1.1483529085126336 chr12 133851895 13749868 0.10272449261924906 0.4144335045143498 chr13 115169878 7934467 0.06889359559797398 0.32499416174151907 chr14 107349540 14822184 0.13807403366609675 0.5702636228217135 chr15 102531392 9691440 0.09452168561214891 0.4055597187907954 chr16 90354753 12327703 0.1364366852953491 1.5543990064231787 chr17 81195210 11980870 0.14755636447026863 1.2854032961729465 chr18 78077248 11066866 0.1417425214577235 1.6269868691202771 chr19 59128983 4062158 0.06869994702936122 0.7102323789985183 chr20 63025520 9918591 0.15737420333858412 0.5628590776588704 chr21 48129895 4847112 0.10070896684898233 0.7281564344584415 chr22 51304566 2795799 0.054494155549430046 0.31519547046154905 chrMT 16571 81929 4.944119244463219 3.9714516468782124 chrX 155270560 15255173 0.09824897263203018 0.5894248478984466 chrY 59373566 1233927 0.020782430349559938 1.3190194027278632