BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006020.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 = 21,400,944 number of mapped reads = 14,962,746 (69.92%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,538,499 number of mapped paired reads (second in pair) = 7,424,247 number of mapped paired reads (both in pair) = 13,418,298 number of mapped paired reads (singletons) = 1,544,448 number of mapped bases = 577,777,274 bp number of sequenced bases = 577,710,063 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 709,188 duplication rate = 3.89% >>>>>>> Insert size mean insert size = 64,905.5363 std insert size = 2,479,270.575 median insert size = 74 >>>>>>> Mapping quality mean mapping quality = 46.6656 >>>>>>> ACTG content number of A's = 165,900,205 bp (28.72%) number of C's = 120,941,150 bp (20.93%) number of T's = 167,859,490 bp (29.06%) number of G's = 122,936,632 bp (21.28%) number of N's = 72,586 bp (0.01%) GC percentage = 42.21% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 3,096,963 number of insertions = 17,756 mapped reads with insertion percentage = 0.12% number of deletions = 52,449 mapped reads with deletion percentage = 0.35% homopolymer indels = 45.06% >>>>>>> Coverage mean coverageData = 0.1866X std coverageData = 0.9333X There is a 11.95% of reference with a coverageData >= 1X There is a 4.2% of reference with a coverageData >= 2X There is a 1.38% of reference with a coverageData >= 3X There is a 0.52% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 45798133 0.1837433054981235 1.3563423346145351 chr2 243199373 50097801 0.20599477861318335 0.8800153784736974 chr3 198022430 39932921 0.20165857473822535 0.6333430131357936 chr4 191154276 38130159 0.19947322025901215 0.7088333663427292 chr5 180915260 35822098 0.19800484492021292 0.6252450901040295 chr6 171115067 32808672 0.19173455952888124 1.0543784314609344 chr7 159138663 31894492 0.20041950459267086 1.1654724147224798 chr8 146364022 29744095 0.20321998940422667 1.8091643778533766 chr9 141213431 23204404 0.1643215084831414 0.7453679502250242 chr10 135534747 26846397 0.19807759703126165 1.0582143658642975 chr11 135006516 26007104 0.19263591692122475 0.726253389273361 chr12 133851895 26279810 0.19633498651625367 0.6329863966851037 chr13 115169878 18803926 0.16327121576007922 0.5635377885189328 chr14 107349540 18101321 0.16862038719495212 0.6505676510093303 chr15 102531392 16467985 0.16061407807669284 0.5665982395633918 chr16 90354753 16347348 0.1809240516655499 0.739520759223783 chr17 81195210 15111714 0.18611583121713707 0.653123393814011 chr18 78077248 14831659 0.18996134443673016 1.2219080438806291 chr19 59128983 11148556 0.18854638511201857 1.2389092561741977 chr20 63025520 11903080 0.18886127397282879 0.6511306134806163 chr21 48129895 7480057 0.1554139480254424 0.6456052864591102 chr22 51304566 6381386 0.12438241851612193 0.5572468322804516 chrMT 16571 26392 1.5926618791865308 1.661605068739156 chrX 155270560 33143291 0.21345508768693822 0.714138148946789 chrY 59373566 1464473 0.024665404129507733 0.4563121586951987