BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472759.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 = 13,859,802 number of mapped reads = 13,732,880 (99.08%) number of supplementary alignments = 93,215 (0.67%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,891,264 number of mapped paired reads (second in pair) = 6,841,616 number of mapped paired reads (both in pair) = 13,655,040 number of mapped paired reads (singletons) = 77,840 number of mapped bases = 1,354,909,948 bp number of sequenced bases = 1,354,715,012 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,319,669 duplication rate = 46.09% >>>>>>> Insert size mean insert size = 49,743.2259 std insert size = 2,161,106.3124 median insert size = 241 >>>>>>> Mapping quality mean mapping quality = 54.9989 >>>>>>> ACTG content number of A's = 377,101,802 bp (27.84%) number of C's = 302,156,056 bp (22.3%) number of T's = 375,562,890 bp (27.72%) number of G's = 299,633,151 bp (22.12%) number of N's = 261,113 bp (0.02%) GC percentage = 44.42% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 8,366,359 number of insertions = 76,507 mapped reads with insertion percentage = 0.55% number of deletions = 78,034 mapped reads with deletion percentage = 0.56% homopolymer indels = 46.25% >>>>>>> Coverage mean coverageData = 0.4377X std coverageData = 14.3297X There is a 4.15% of reference with a coverageData >= 1X There is a 1.79% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% 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 0.16% of reference with a coverageData >= 43X There is a 0.16% 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 0.15% of reference with a coverageData >= 48X There is a 0.15% 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 154063517 0.6181068531821231 22.308964631104885 chr2 243199373 110969542 0.45629041157108574 15.868072973262132 chr3 198022430 151431473 0.7647187896845827 19.559394903428576 chr4 191154276 42028759 0.2198682649400948 7.721015551836343 chr5 180915260 69099742 0.381945348336011 12.141767146585353 chr6 171115067 95056490 0.5555120987680179 15.100784712767197 chr7 159138663 61641889 0.387347033322757 12.64574524077643 chr8 146364022 48394332 0.33064363317373174 10.058241424779709 chr9 141213431 78484690 0.5557877139887636 13.950253150444269 chr10 135534747 28053069 0.2069806423883316 6.458719610681407 chr11 135006516 68385869 0.506537543713816 19.5093256519688 chr12 133851895 64476296 0.48169879104064983 13.795549236932933 chr13 115169878 33396430 0.2899753874880375 10.925801224543312 chr14 107349540 32193573 0.2998948388600454 10.417046676837144 chr15 102531392 34258305 0.33412503557934725 10.850319965487484 chr16 90354753 50346675 0.5572111408461268 14.572050058998055 chr17 81195210 55988577 0.6895551720353947 15.909371315540113 chr18 78077248 24404273 0.3125657425835501 10.589536739883197 chr19 59128983 42495258 0.7186874497739966 19.72556958334737 chr20 63025520 27214050 0.43179413672429834 11.240423939688817 chr21 48129895 8910301 0.1851302812939858 9.364348725728911 chr22 51304566 10415110 0.2030055180663647 6.420602648067753 chrMT 16571 3151 0.19015146943455435 0.58730729655648 chrX 155270560 61741387 0.3976374336512987 12.401332116160278 chrY 59373566 1457190 0.02454274011434651 0.9528414419502094