BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472715.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 = 15,893,226 number of mapped reads = 15,749,524 (99.1%) number of supplementary alignments = 53,594 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,902,587 number of mapped paired reads (second in pair) = 7,846,937 number of mapped paired reads (both in pair) = 15,661,186 number of mapped paired reads (singletons) = 88,338 number of mapped bases = 1,551,684,769 bp number of sequenced bases = 1,551,480,980 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,634,896 duplication rate = 46.64% >>>>>>> Insert size mean insert size = 24,948.7004 std insert size = 1,552,321.9812 median insert size = 248 >>>>>>> Mapping quality mean mapping quality = 55.2052 >>>>>>> ACTG content number of A's = 433,570,813 bp (27.95%) number of C's = 344,726,015 bp (22.22%) number of T's = 429,903,043 bp (27.71%) number of G's = 342,983,849 bp (22.11%) number of N's = 297,260 bp (0.02%) GC percentage = 44.33% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 9,694,778 number of insertions = 91,987 mapped reads with insertion percentage = 0.58% number of deletions = 80,366 mapped reads with deletion percentage = 0.5% homopolymer indels = 44.42% >>>>>>> Coverage mean coverageData = 0.5012X std coverageData = 16.8907X There is a 4.62% of reference with a coverageData >= 1X There is a 1.98% of reference with a coverageData >= 2X There is a 0.9% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 146419446 0.5874386407245902 20.410413747741657 chr2 243199373 113006091 0.4646644010879091 14.160329107831997 chr3 198022430 199145677 1.0056723220697776 25.888590174036512 chr4 191154276 59438994 0.31094776033155547 11.596833323489273 chr5 180915260 74420424 0.411355150472105 13.508220757950731 chr6 171115067 96258805 0.562538452560697 15.112888435235382 chr7 159138663 72597426 0.45618974441176496 15.313760895743084 chr8 146364022 72077261 0.492452038520778 17.313502226167824 chr9 141213431 98041847 0.694281318042616 16.795507954096696 chr10 135534747 37796015 0.2788658689863493 10.030684009119607 chr11 135006516 79645501 0.589938199723634 27.90886080844364 chr12 133851895 91673755 0.6848894817663956 21.019929820588857 chr13 115169878 29473368 0.2559121231334464 9.674250567304764 chr14 107349540 42547652 0.3963468497396449 13.483295123016086 chr15 102531392 29743027 0.2900870301263441 8.462085723616084 chr16 90354753 48234333 0.5338328244890449 23.384785701433586 chr17 81195210 52035558 0.640869800078108 14.692901682624289 chr18 78077248 32322654 0.41398300821258455 17.10086429907752 chr19 59128983 30424192 0.5145394095481061 14.05732555108251 chr20 63025520 38163703 0.6055277766847461 17.58106233080075 chr21 48129895 5369024 0.11155278855272799 4.3552308066171594 chr22 51304566 16138657 0.3145657055163472 9.960977944804899 chrMT 16571 3532 0.21314344336491461 0.7171770842202484 chrX 155270560 81217471 0.5230706387611406 14.789890713096726 chrY 59373566 5490356 0.09247138701421437 6.426120549997603