BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472451.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 = 15,545,878 number of mapped reads = 15,424,376 (99.22%) number of supplementary alignments = 55,122 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,734,317 number of mapped paired reads (second in pair) = 7,690,059 number of mapped paired reads (both in pair) = 15,356,682 number of mapped paired reads (singletons) = 67,694 number of mapped bases = 1,508,887,832 bp number of sequenced bases = 1,508,722,743 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,397,981 duplication rate = 46.61% >>>>>>> Insert size mean insert size = 15,652.7734 std insert size = 1,224,127.7809 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 54.8592 >>>>>>> ACTG content number of A's = 406,070,057 bp (26.91%) number of C's = 349,243,296 bp (23.15%) number of T's = 407,702,076 bp (27.02%) number of G's = 345,523,041 bp (22.9%) number of N's = 184,273 bp (0.01%) GC percentage = 46.05% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 7,450,946 number of insertions = 93,101 mapped reads with insertion percentage = 0.6% number of deletions = 70,681 mapped reads with deletion percentage = 0.45% homopolymer indels = 45.58% >>>>>>> Coverage mean coverageData = 0.4874X std coverageData = 15.1609X There is a 4.46% of reference with a coverageData >= 1X There is a 2% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.63% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.22% 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 0.21% 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 0.2% 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 0.18% 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 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 135962827 0.5454864122484975 15.521764840994301 chr2 243199373 109710514 0.45111347388218803 13.53513413380268 chr3 198022430 105613188 0.5333395211845446 14.642026209601436 chr4 191154276 37053595 0.1938413085773713 7.405183971531735 chr5 180915260 55524476 0.3069087483278083 9.975592805066016 chr6 171115067 131374857 0.7677573886582413 16.804205422328828 chr7 159138663 88175948 0.5540824984812145 18.003529345806417 chr8 146364022 125683639 0.8587058300433968 25.916727880796174 chr9 141213431 56924907 0.40311255520730177 10.829315822878693 chr10 135534747 32286650 0.2382167725594382 9.837538263563163 chr11 135006516 40508293 0.30004694736363685 10.773242574676969 chr12 133851895 99662516 0.7445730671201928 20.040375672869732 chr13 115169878 41822895 0.3631409160648759 11.443801044066534 chr14 107349540 26922153 0.25078964474370363 7.566966607637763 chr15 102531392 29446083 0.287190902470143 9.574330920968523 chr16 90354753 102818684 1.137944386832644 28.554364871057267 chr17 81195210 65755592 0.8098457039522405 17.235867401122615 chr18 78077248 16995209 0.21767172172871666 9.630199187453321 chr19 59128983 46072863 0.7791925492782448 18.093095585336865 chr20 63025520 51918428 0.8237683401898152 23.056066186378008 chr21 48129895 11637679 0.24179730705832622 12.613288690841209 chr22 51304566 11400740 0.22221686857267245 8.501646523291967 chrMT 16571 7965 0.4806589825598938 0.861839470372241 chrX 155270560 85280627 0.5492388705238134 15.772570270317718 chrY 59373566 327504 0.005515990061974718 0.33477386174165347