BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472457.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 = 14,810,368 number of mapped reads = 14,679,037 (99.11%) number of supplementary alignments = 56,976 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,364,430 number of mapped paired reads (second in pair) = 7,314,607 number of mapped paired reads (both in pair) = 14,607,100 number of mapped paired reads (singletons) = 71,937 number of mapped bases = 1,440,006,270 bp number of sequenced bases = 1,439,793,006 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,007,383 duplication rate = 46.21% >>>>>>> Insert size mean insert size = 19,604.4599 std insert size = 1,379,719.8122 median insert size = 218 >>>>>>> Mapping quality mean mapping quality = 55.1702 >>>>>>> ACTG content number of A's = 392,084,274 bp (27.23%) number of C's = 327,972,034 bp (22.78%) number of T's = 394,033,967 bp (27.37%) number of G's = 325,507,367 bp (22.61%) number of N's = 195,364 bp (0.01%) GC percentage = 45.39% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 6,992,602 number of insertions = 89,797 mapped reads with insertion percentage = 0.61% number of deletions = 76,678 mapped reads with deletion percentage = 0.51% homopolymer indels = 45.57% >>>>>>> Coverage mean coverageData = 0.4652X std coverageData = 15.9167X There is a 4.33% of reference with a coverageData >= 1X There is a 1.88% of reference with a coverageData >= 2X There is a 0.8% 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 0.41% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% 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 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 197405995 0.7919980066970425 25.026982355210922 chr2 243199373 96316260 0.3960382743256497 14.52643788776135 chr3 198022430 125523186 0.6338836767127846 15.501566262803362 chr4 191154276 50016416 0.2616547065889334 9.457725073313256 chr5 180915260 69883951 0.3862800241394783 11.896112855493058 chr6 171115067 106459920 0.6221539801635352 14.742971185885462 chr7 159138663 50552332 0.31766216359377103 10.58208511197352 chr8 146364022 86925874 0.593901922154066 17.098941107703194 chr9 141213431 69796106 0.4942596855394017 15.217446917234161 chr10 135534747 46367094 0.342104847843926 11.511471741432489 chr11 135006516 55696706 0.41254828026226525 14.744537359154748 chr12 133851895 62797372 0.4691556440048906 12.706251862318009 chr13 115169878 23996136 0.20835427124443076 6.676718076681482 chr14 107349540 49578639 0.46184305028228345 21.358863913466397 chr15 102531392 40817485 0.39809744317135576 12.40474040601109 chr16 90354753 79508901 0.8799636804939304 32.98923515877996 chr17 81195210 66921808 0.8242088172442684 24.1869280400157 chr18 78077248 23932352 0.306521459362912 9.506637268155846 chr19 59128983 25620412 0.43329701780935415 9.718548008496267 chr20 63025520 34408938 0.5459524649697456 21.393082834900845 chr21 48129895 13689186 0.2844216884329376 17.31036917770848 chr22 51304566 20498314 0.3995417094065273 11.354604773286075 chrMT 16571 1565 0.09444209764045622 0.3633036014142945 chrX 155270560 42002757 0.27051333491680585 7.499835541319499 chrY 59373566 1288565 0.02170267152220569 0.6893728534226243