BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472683.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 = 27,768,862 number of mapped reads = 27,525,991 (99.13%) number of supplementary alignments = 165,360 (0.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,800,034 number of mapped paired reads (second in pair) = 13,725,957 number of mapped paired reads (both in pair) = 27,361,336 number of mapped paired reads (singletons) = 164,655 number of mapped bases = 2,707,851,494 bp number of sequenced bases = 2,707,438,937 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,462,015 duplication rate = 50.54% >>>>>>> Insert size mean insert size = 27,365.9932 std insert size = 1,636,387.8968 median insert size = 229 >>>>>>> Mapping quality mean mapping quality = 54.5824 >>>>>>> ACTG content number of A's = 730,928,659 bp (27%) number of C's = 626,794,387 bp (23.15%) number of T's = 731,705,224 bp (27.03%) number of G's = 617,486,599 bp (22.81%) number of N's = 524,068 bp (0.02%) GC percentage = 45.96% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 17,255,455 number of insertions = 183,636 mapped reads with insertion percentage = 0.66% number of deletions = 148,666 mapped reads with deletion percentage = 0.53% homopolymer indels = 46.78% >>>>>>> Coverage mean coverageData = 0.8747X std coverageData = 42.038X There is a 5.16% of reference with a coverageData >= 1X There is a 2.41% of reference with a coverageData >= 2X There is a 1.14% of reference with a coverageData >= 3X There is a 0.82% of reference with a coverageData >= 4X There is a 0.6% of reference with a coverageData >= 5X There is a 0.52% of reference with a coverageData >= 6X There is a 0.45% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.22% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 257655310 1.0337198317351435 37.81032069766371 chr2 243199373 258296979 1.062079132087236 52.571474627680104 chr3 198022430 235053563 1.1870047398165955 34.31835164442458 chr4 191154276 99326013 0.5196117768247047 35.13860149886521 chr5 180915260 82606145 0.45660131157537515 18.438632446890807 chr6 171115067 196565656 1.1487337698906432 31.51351355116355 chr7 159138663 131066368 0.8235985242630824 29.025267230358313 chr8 146364022 120424570 0.8227743973857182 28.420561469699482 chr9 141213431 180058746 1.2750822972355937 40.74879411792695 chr10 135534747 43711301 0.32250992433696724 11.581786124148833 chr11 135006516 74869931 0.5545653144623034 29.79367144665958 chr12 133851895 118303344 0.8838376475730881 30.705828395265577 chr13 115169878 90939218 0.7896093976933796 39.949646418583136 chr14 107349540 48351598 0.45041271718537407 24.070596250288542 chr15 102531392 34498261 0.3364653529720927 16.905741454383758 chr16 90354753 144696329 1.601424653332847 62.8439111632058 chr17 81195210 79307032 0.9767452045508596 27.260656434340074 chr18 78077248 15587698 0.1996445622673586 11.339803736479318 chr19 59128983 57085993 0.9654485855100873 29.628620568468513 chr20 63025520 138656717 2.2000090915552937 62.666319550786376 chr21 48129895 14032460 0.29155392921592704 20.016731088137337 chr22 51304566 39215867 0.7643738181120175 33.225774035943644 chrMT 16571 11469 0.6921127270532859 1.4699928915135478 chrX 155270560 245807017 1.5830883652380723 110.96174007999566 chrY 59373566 1723909 0.029034958082187617 2.405077386899923