BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472756.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 = 14,847,526 number of mapped reads = 14,707,888 (99.06%) number of supplementary alignments = 82,666 (0.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,379,794 number of mapped paired reads (second in pair) = 7,328,094 number of mapped paired reads (both in pair) = 14,623,766 number of mapped paired reads (singletons) = 84,122 number of mapped bases = 1,447,515,127 bp number of sequenced bases = 1,447,321,180 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,090,235 duplication rate = 45.91% >>>>>>> Insert size mean insert size = 35,689.2665 std insert size = 1,856,922.0973 median insert size = 227 >>>>>>> Mapping quality mean mapping quality = 55.0124 >>>>>>> ACTG content number of A's = 397,904,297 bp (27.49%) number of C's = 327,718,223 bp (22.64%) number of T's = 395,771,227 bp (27.35%) number of G's = 325,645,981 bp (22.5%) number of N's = 281,452 bp (0.02%) GC percentage = 45.14% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 8,610,639 number of insertions = 84,723 mapped reads with insertion percentage = 0.57% number of deletions = 80,932 mapped reads with deletion percentage = 0.54% homopolymer indels = 43.83% >>>>>>> Coverage mean coverageData = 0.4676X std coverageData = 16.0082X There is a 4.33% of reference with a coverageData >= 1X There is a 1.9% of reference with a coverageData >= 2X There is a 0.86% 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 0.42% 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 0.27% 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 0.25% 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 0.22% 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 0.2% 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 0.19% 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 0.18% 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 0.17% 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 0.16% of reference with a coverageData >= 45X There is a 0.16% 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 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 151294832 0.6069988166649342 22.222254343435115 chr2 243199373 96565579 0.39706343733049015 15.509574300147827 chr3 198022430 159849853 0.8072310444831932 18.2931365378435 chr4 191154276 69544486 0.36381339437052407 13.790076242821943 chr5 180915260 64492513 0.35647912177225954 12.648464333207293 chr6 171115067 81746388 0.4777275866654104 13.661915068106605 chr7 159138663 61467726 0.38625262297195495 14.477275112642028 chr8 146364022 50607428 0.3457641250115414 11.245169216289417 chr9 141213431 95256785 0.6745589589137594 18.211984539519857 chr10 135534747 43270040 0.3192542204693827 12.76955198521389 chr11 135006516 74564756 0.5523048680109632 20.800164009439598 chr12 133851895 83635762 0.6248380869019449 19.42482700853744 chr13 115169878 36660838 0.31831967382999227 13.275596833632111 chr14 107349540 25222602 0.2349577091806821 11.773302124553767 chr15 102531392 38051703 0.3711224655957075 14.16137401431663 chr16 90354753 52592365 0.5820652843796718 15.933815582169544 chr17 81195210 63960385 0.7877359391028116 20.279021014813218 chr18 78077248 23984301 0.3071868132442373 11.467215890322752 chr19 59128983 32902219 0.5564482480613611 13.502122859280343 chr20 63025520 31117267 0.4937248752568801 17.388429654414406 chr21 48129895 8789818 0.18262699305701788 7.972273232929202 chr22 51304566 17928846 0.34945907153760936 14.193083614204953 chrMT 16571 2591 0.15635749200410357 0.502235527323588 chrX 155270560 80689060 0.5196674759207411 18.376962376652603 chrY 59373566 3316984 0.05586634294460265 2.6679263969909215