BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472505.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 = 13,625,580 number of mapped reads = 12,934,124 (94.93%) number of supplementary alignments = 80,399 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,305,685 number of mapped paired reads (second in pair) = 6,628,439 number of mapped paired reads (both in pair) = 12,432,790 number of mapped paired reads (singletons) = 501,334 number of mapped bases = 1,242,585,609 bp number of sequenced bases = 1,242,423,590 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,340,234 duplication rate = 41.82% >>>>>>> Insert size mean insert size = 53,755.2196 std insert size = 2,231,954.6097 median insert size = 238 >>>>>>> Mapping quality mean mapping quality = 54.0359 >>>>>>> ACTG content number of A's = 366,243,740 bp (29.48%) number of C's = 276,627,154 bp (22.27%) number of T's = 328,132,937 bp (26.41%) number of G's = 271,251,787 bp (21.83%) number of N's = 167,972 bp (0.01%) GC percentage = 44.1% >>>>>>> Mismatches and indels general error rate = 0.0186 number of mismatches = 22,933,690 number of insertions = 67,851 mapped reads with insertion percentage = 0.52% number of deletions = 66,098 mapped reads with deletion percentage = 0.5% homopolymer indels = 45.2% >>>>>>> Coverage mean coverageData = 0.4014X std coverageData = 12.9272X There is a 4.57% of reference with a coverageData >= 1X There is a 1.85% of reference with a coverageData >= 2X There is a 0.81% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.33% 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 0.29% of reference with a coverageData >= 12X There is a 0.28% 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 0.25% 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 0.16% 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 0.15% of reference with a coverageData >= 41X There is a 0.15% 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 0.14% of reference with a coverageData >= 46X There is a 0.14% 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 133099303 0.5339978791868286 17.393731683359977 chr2 243199373 88999612 0.36595329544702404 11.84805281901738 chr3 198022430 148622897 0.7505356691158673 17.575673758042743 chr4 191154276 44124975 0.2308343602002395 7.301252964434488 chr5 180915260 67151014 0.3711738523328546 13.998438089122615 chr6 171115067 75625694 0.441958124003189 11.293735145633649 chr7 159138663 40616728 0.2552285361351817 8.543112644791913 chr8 146364022 54156872 0.3700149207432958 12.236146067159623 chr9 141213431 75420691 0.5340900682457039 13.36123984298348 chr10 135534747 35218649 0.2598495941413459 9.50482310920544 chr11 135006516 65453437 0.48481687357964265 15.341818012768302 chr12 133851895 62152261 0.46433605590716515 13.15313142839725 chr13 115169878 33361300 0.28967035981404793 10.55094408548386 chr14 107349540 27898830 0.2598877461421819 7.846471124086258 chr15 102531392 35647221 0.3476712868581751 13.768255800998208 chr16 90354753 34822388 0.3853963056044213 10.10303466452297 chr17 81195210 52067378 0.6412616951172366 14.648249416646328 chr18 78077248 34598161 0.44312731155688273 17.705178809897863 chr19 59128983 19692177 0.3330376407793112 7.477135519155065 chr20 63025520 23810253 0.37778748989298305 10.507114444923369 chr21 48129895 4486697 0.09322058566718253 2.96077967440856 chr22 51304566 15433882 0.30082862410335953 10.372857109288928 chrMT 16571 1535 0.09263170599239635 0.34081571500777785 chrX 155270560 67182995 0.43268340759510365 17.22301331134732 chrY 59373566 2940659 0.049528084602498024 3.9154517292384208