BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006142.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 7,062,110 number of mapped reads = 6,110,781 (86.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,114,216 number of mapped paired reads (second in pair) = 2,996,565 number of mapped paired reads (both in pair) = 5,518,914 number of mapped paired reads (singletons) = 591,867 number of mapped bases = 235,994,143 bp number of sequenced bases = 235,968,804 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 246,976 duplication rate = 3.57% >>>>>>> Insert size mean insert size = 69,287.5428 std insert size = 2,585,940.1989 median insert size = 112 >>>>>>> Mapping quality mean mapping quality = 47.0861 >>>>>>> ACTG content number of A's = 63,235,108 bp (26.8%) number of C's = 52,069,947 bp (22.07%) number of T's = 65,366,297 bp (27.7%) number of G's = 55,287,578 bp (23.43%) number of N's = 9,874 bp (0%) GC percentage = 45.5% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 1,165,554 number of insertions = 7,423 mapped reads with insertion percentage = 0.12% number of deletions = 19,894 mapped reads with deletion percentage = 0.33% homopolymer indels = 45.44% >>>>>>> Coverage mean coverageData = 0.0762X std coverageData = 0.4137X There is a 5.48% of reference with a coverageData >= 1X There is a 1.48% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 20033499 0.08037492111203205 0.44274286506929356 chr2 243199373 20356720 0.08370383422000023 0.4662437330513972 chr3 198022430 16017072 0.08088514013286273 0.3717915896724394 chr4 191154276 14388328 0.07527076192635104 0.3722917104722707 chr5 180915260 14247022 0.07874969751031505 0.36723703861358503 chr6 171115067 13499368 0.07889058653145956 0.4033897014590326 chr7 159138663 12935081 0.08128182527208991 0.5417035401245814 chr8 146364022 11848413 0.0809516767720417 0.4353296706798567 chr9 141213431 10144243 0.0718362476441777 0.3799485578352681 chr10 135534747 11430538 0.08433658713363001 0.3954408854188414 chr11 135006516 10965337 0.08122079826132243 0.5604988742793566 chr12 133851895 10903814 0.08146178281599972 0.37497485324688595 chr13 115169878 7311695 0.0634861747444067 0.3349086991523093 chr14 107349540 7313881 0.06813146101976776 0.35227858720926875 chr15 102531392 7235021 0.07056395957249854 0.3531218761253048 chr16 90354753 7614910 0.08427791286198304 0.4355611640986783 chr17 81195210 7300166 0.08990882590241468 0.4300364477205264 chr18 78077248 6165271 0.0789637334553595 0.48131092595938074 chr19 59128983 5473253 0.09256463957785305 0.47447115223980996 chr20 63025520 5614889 0.08908913405236482 0.400687685951197 chr21 48129895 3173104 0.06592792275985643 0.37580738872124736 chr22 51304566 3372245 0.06572991963327397 0.36782744588128874 chrMT 16571 64349 3.883229738700139 5.252225408310659 chrX 155270560 7094308 0.04568997497014244 0.2969061910248927 chrY 59373566 1491616 0.0251225604337122 0.2408241059608727