BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472667.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 = 20,902,604 number of mapped reads = 20,707,747 (99.07%) number of supplementary alignments = 135,128 (0.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,393,047 number of mapped paired reads (second in pair) = 10,314,700 number of mapped paired reads (both in pair) = 20,575,526 number of mapped paired reads (singletons) = 132,221 number of mapped bases = 2,038,956,837 bp number of sequenced bases = 2,038,694,744 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,597,122 duplication rate = 49.36% >>>>>>> Insert size mean insert size = 21,076.243 std insert size = 1,419,135.7549 median insert size = 218 >>>>>>> Mapping quality mean mapping quality = 54.8585 >>>>>>> ACTG content number of A's = 540,063,304 bp (26.49%) number of C's = 482,707,154 bp (23.68%) number of T's = 541,339,240 bp (26.55%) number of G's = 474,201,381 bp (23.26%) number of N's = 383,665 bp (0.02%) GC percentage = 46.94% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 11,979,213 number of insertions = 127,399 mapped reads with insertion percentage = 0.61% number of deletions = 103,738 mapped reads with deletion percentage = 0.5% homopolymer indels = 46.48% >>>>>>> Coverage mean coverageData = 0.6586X std coverageData = 47.1823X There is a 3.47% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.81% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.37% 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 0.27% 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 0.24% 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 0.2% 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 0.19% 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 0.18% 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 0.17% 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 0.16% 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 0.15% 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 0.14% 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 242793301 0.9740930635434606 62.596025599629634 chr2 243199373 219466067 0.9024121414984075 66.4027331874208 chr3 198022430 193715439 0.9782499841053359 35.49448058080796 chr4 191154276 32440969 0.1697109250122137 23.697584770062086 chr5 180915260 59695677 0.329964852052834 16.705129973111518 chr6 171115067 113772389 0.6648882006398653 23.785738481333645 chr7 159138663 77833096 0.48908979460258506 18.150573324941444 chr8 146364022 80493916 0.5499569832810416 19.246937056062045 chr9 141213431 123582208 0.8751448578570405 38.11614254445127 chr10 135534747 31046865 0.22906941346930024 13.068259661202777 chr11 135006516 39566099 0.2930680693959986 17.404928306322798 chr12 133851895 248962819 1.85998725681097 153.69835793092216 chr13 115169878 63905841 0.5548832916190117 24.145249229744998 chr14 107349540 16208580 0.1509888165333545 7.1073590850061645 chr15 102531392 16057932 0.15661478584041852 6.668369790752182 chr16 90354753 148443447 1.6428958308369235 65.12897455022663 chr17 81195210 63493068 0.7819804641185114 32.93623318741629 chr18 78077248 20254239 0.259412818955914 16.59089327569767 chr19 59128983 53680594 0.9078558648641056 29.411706599565928 chr20 63025520 87288369 1.384968644447519 41.32739528778926 chr21 48129895 5815313 0.12082538305973865 5.6144215680623235 chr22 51304566 23894062 0.4657297364137141 23.889728974032828 chrMT 16571 5063 0.3055337638042363 0.666612566914003 chrX 155270560 74912185 0.48246225813831034 16.110724687488197 chrY 59373566 1629299 0.027441488018422205 1.4745020975029501