BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038456.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 15,120,310 number of mapped reads = 13,668,611 (90.4%) number of supplementary alignments = 154,716 (1.02%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,950,891 number of mapped paired reads (second in pair) = 6,717,720 number of mapped paired reads (both in pair) = 13,392,864 number of mapped paired reads (singletons) = 275,747 number of mapped bases = 1,856,353,106 bp number of sequenced bases = 1,855,146,875 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,602,012 duplication rate = 14.19% >>>>>>> Insert size mean insert size = 96,162.7435 std insert size = 3,065,437.7644 median insert size = 256 >>>>>>> Mapping quality mean mapping quality = 53.3855 >>>>>>> ACTG content number of A's = 517,477,738 bp (27.89%) number of C's = 383,374,804 bp (20.67%) number of T's = 523,629,410 bp (28.23%) number of G's = 430,517,609 bp (23.21%) number of N's = 147,314 bp (0.01%) GC percentage = 43.87% >>>>>>> Mismatches and indels general error rate = 0.0131 number of mismatches = 23,624,739 number of insertions = 292,176 mapped reads with insertion percentage = 2.03% number of deletions = 653,571 mapped reads with deletion percentage = 4.62% homopolymer indels = 48.19% >>>>>>> Coverage mean coverageData = 0.5997X std coverageData = 5.4284X There is a 20.95% of reference with a coverageData >= 1X There is a 12.34% of reference with a coverageData >= 2X There is a 7.43% of reference with a coverageData >= 3X There is a 4.9% of reference with a coverageData >= 4X There is a 3.27% of reference with a coverageData >= 5X There is a 2.28% of reference with a coverageData >= 6X There is a 1.61% of reference with a coverageData >= 7X There is a 1.17% of reference with a coverageData >= 8X There is a 0.86% of reference with a coverageData >= 9X There is a 0.64% of reference with a coverageData >= 10X There is a 0.49% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% 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 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% 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 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 165073005 0.6622772065229879 4.011222474273008 chr2 243199373 167097915 0.6870820139820015 6.551972261460339 chr3 198022430 125434986 0.6334382726239649 1.7616296241232179 chr4 191154276 76899779 0.40229170180843876 5.2434041223680765 chr5 180915260 127855577 0.7067152710058842 1.86674493781135 chr6 171115067 105687848 0.6176419753849028 3.6819106375369284 chr7 159138663 91037981 0.5720670218273732 6.761860825597551 chr8 146364022 117552338 0.8031505037487969 2.8460349714567283 chr9 141213431 77887467 0.5515584916281795 8.272327094830986 chr10 135534747 102852888 0.7588673036000133 15.14052699499991 chr11 135006516 88288818 0.6539596799905569 3.270315459486984 chr12 133851895 79778964 0.5960241653657574 1.8144344037853999 chr13 115169878 57273417 0.4972951087088935 1.4744363055383418 chr14 107349540 61896060 0.5765843058107188 1.660008580464988 chr15 102531392 40039895 0.3905135219465274 1.3209307341378145 chr16 90354753 60125822 0.6654417172719181 7.292664605779963 chr17 81195210 48496289 0.5972801720692636 7.114106478385892 chr18 78077248 79177082 1.0140864852203808 7.1276911489854315 chr19 59128983 26936683 0.4555580298074804 2.255063071691555 chr20 63025520 57132881 0.906503920951386 2.6911491194694923 chr21 48129895 19341312 0.4018565176591389 2.7275924882894556 chr22 51304566 13261585 0.25848742195772595 1.087618380811716 chrMT 16571 1277666 77.10252851366846 42.735025867980596 chrX 155270560 62794623 0.4044206641619635 1.5703274062024652 chrY 59373566 3152225 0.05309138750399462 5.024077475430869