BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124851.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 139,184,794 number of mapped reads = 134,676,192 (96.76%) number of supplementary alignments = 2,409,945 (1.73%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 68,041,508 number of mapped paired reads (second in pair) = 66,634,684 number of mapped paired reads (both in pair) = 132,652,322 number of mapped paired reads (singletons) = 2,023,870 number of mapped bases = 18,138,071,882 bp number of sequenced bases = 18,121,403,082 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,976,218 duplication rate = 28.8% >>>>>>> Insert size mean insert size = 54,065.3044 std insert size = 2,187,695.8971 median insert size = 250 >>>>>>> Mapping quality mean mapping quality = 53.719 >>>>>>> ACTG content number of A's = 5,211,777,147 bp (28.76%) number of C's = 3,591,170,943 bp (19.82%) number of T's = 5,280,031,937 bp (29.14%) number of G's = 4,038,383,188 bp (22.29%) number of N's = 39,867 bp (0%) GC percentage = 42.1% >>>>>>> Mismatches and indels general error rate = 0.0142 number of mismatches = 244,831,132 number of insertions = 3,961,445 mapped reads with insertion percentage = 2.69% number of deletions = 7,408,656 mapped reads with deletion percentage = 5.23% homopolymer indels = 44.31% >>>>>>> Coverage mean coverageData = 5.8591X std coverageData = 86.9844X There is a 53.19% of reference with a coverageData >= 1X There is a 45.99% of reference with a coverageData >= 2X There is a 39.93% of reference with a coverageData >= 3X There is a 35.45% of reference with a coverageData >= 4X There is a 31.49% of reference with a coverageData >= 5X There is a 28.22% of reference with a coverageData >= 6X There is a 25.34% of reference with a coverageData >= 7X There is a 22.86% of reference with a coverageData >= 8X There is a 20.67% of reference with a coverageData >= 9X There is a 18.74% of reference with a coverageData >= 10X There is a 17.03% of reference with a coverageData >= 11X There is a 15.5% of reference with a coverageData >= 12X There is a 14.14% of reference with a coverageData >= 13X There is a 12.91% of reference with a coverageData >= 14X There is a 11.82% of reference with a coverageData >= 15X There is a 10.83% of reference with a coverageData >= 16X There is a 9.93% of reference with a coverageData >= 17X There is a 9.13% of reference with a coverageData >= 18X There is a 8.39% of reference with a coverageData >= 19X There is a 7.73% of reference with a coverageData >= 20X There is a 7.13% of reference with a coverageData >= 21X There is a 6.58% of reference with a coverageData >= 22X There is a 6.07% of reference with a coverageData >= 23X There is a 5.62% of reference with a coverageData >= 24X There is a 5.2% of reference with a coverageData >= 25X There is a 4.82% of reference with a coverageData >= 26X There is a 4.46% of reference with a coverageData >= 27X There is a 4.14% of reference with a coverageData >= 28X There is a 3.85% of reference with a coverageData >= 29X There is a 3.57% of reference with a coverageData >= 30X There is a 3.32% of reference with a coverageData >= 31X There is a 3.09% of reference with a coverageData >= 32X There is a 2.88% of reference with a coverageData >= 33X There is a 2.68% of reference with a coverageData >= 34X There is a 2.5% of reference with a coverageData >= 35X There is a 2.34% of reference with a coverageData >= 36X There is a 2.18% of reference with a coverageData >= 37X There is a 2.04% of reference with a coverageData >= 38X There is a 1.91% of reference with a coverageData >= 39X There is a 1.78% of reference with a coverageData >= 40X There is a 1.67% of reference with a coverageData >= 41X There is a 1.56% of reference with a coverageData >= 42X There is a 1.46% of reference with a coverageData >= 43X There is a 1.37% of reference with a coverageData >= 44X There is a 1.29% of reference with a coverageData >= 45X There is a 1.21% of reference with a coverageData >= 46X There is a 1.14% of reference with a coverageData >= 47X There is a 1.07% of reference with a coverageData >= 48X There is a 1.01% of reference with a coverageData >= 49X There is a 0.95% of reference with a coverageData >= 50X There is a 0.89% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1896643846 7.609384636197155 53.86554763496462 chr2 243199373 1490779560 6.129865968034383 77.34539019372944 chr3 198022430 1237966726 6.251648997540329 12.64026353441784 chr4 191154276 919939376 4.8125492939535395 140.8197084929446 chr5 180915260 956507327 5.287046139723095 11.361260107723757 chr6 171115067 1073433723 6.273168937250862 31.51733673563564 chr7 159138663 1308865973 8.22468876089527 46.143571550898685 chr8 146364022 1180349806 8.064480531971169 23.21509457775046 chr9 141213431 677287273 4.796195859018538 71.92812220534269 chr10 135534747 980808853 7.236586002554755 301.3812436026701 chr11 135006516 620807381 4.5983512455058095 19.182713263062844 chr12 133851895 853226400 6.3744065782557655 11.459330350342832 chr13 115169878 381668325 3.313959618851033 7.356330691476834 chr14 107349540 553644762 5.157402276712131 11.809841319838887 chr15 102531392 467585139 4.56040954754618 9.266589924272887 chr16 90354753 541210042 5.989834779361303 67.1719456378285 chr17 81195210 427217956 5.261615260309075 70.75391009344429 chr18 78077248 253508408 3.24689220603677 56.1339949377426 chr19 59128983 322044446 5.446473618529851 26.0407154221718 chr20 63025520 431490955 6.8462894871791615 44.90520412319333 chr21 48129895 176277441 3.6625353327697887 61.36715476314008 chr22 51304566 160262173 3.1237409356508348 9.671949837486423 chrMT 16571 30753080 1855.8373061372276 767.8707789954259 chrX 155270560 816785689 5.260402802694857 15.477760805825689 chrY 59373566 379007222 6.383433698423976 190.30138255825474