BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617422.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,580,457 (95.56%) number of supplementary alignments = 507,121 (1.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,396,536 number of mapped paired reads (second in pair) = 15,183,921 number of mapped paired reads (both in pair) = 30,110,520 number of mapped paired reads (singletons) = 469,937 number of mapped bases = 3,016,928,884 bp number of sequenced bases = 3,016,247,415 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,474,469 duplication rate = 4.3% >>>>>>> Insert size mean insert size = 62,060.2766 std insert size = 2,395,468.7396 median insert size = 214 >>>>>>> Mapping quality mean mapping quality = 53.9379 >>>>>>> ACTG content number of A's = 897,414,879 bp (29.75%) number of C's = 608,409,427 bp (20.17%) number of T's = 890,839,826 bp (29.53%) number of G's = 619,237,862 bp (20.53%) number of N's = 345,421 bp (0.01%) GC percentage = 40.7% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 24,926,334 number of insertions = 251,774 mapped reads with insertion percentage = 0.81% number of deletions = 299,639 mapped reads with deletion percentage = 0.96% homopolymer indels = 44.9% >>>>>>> Coverage mean coverageData = 0.9746X std coverageData = 3.002X There is a 29.9% of reference with a coverageData >= 1X There is a 17.21% of reference with a coverageData >= 2X There is a 11.07% of reference with a coverageData >= 3X There is a 7.68% of reference with a coverageData >= 4X There is a 5.6% of reference with a coverageData >= 5X There is a 4.23% of reference with a coverageData >= 6X There is a 3.28% of reference with a coverageData >= 7X There is a 2.6% of reference with a coverageData >= 8X There is a 2.1% of reference with a coverageData >= 9X There is a 1.72% of reference with a coverageData >= 10X There is a 1.43% of reference with a coverageData >= 11X There is a 1.2% of reference with a coverageData >= 12X There is a 1.01% of reference with a coverageData >= 13X There is a 0.87% of reference with a coverageData >= 14X There is a 0.75% of reference with a coverageData >= 15X There is a 0.65% of reference with a coverageData >= 16X There is a 0.57% of reference with a coverageData >= 17X There is a 0.5% of reference with a coverageData >= 18X There is a 0.44% of reference with a coverageData >= 19X There is a 0.39% of reference with a coverageData >= 20X There is a 0.34% of reference with a coverageData >= 21X There is a 0.31% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.16% of reference with a coverageData >= 28X There is a 0.15% of reference with a coverageData >= 29X There is a 0.14% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.11% of reference with a coverageData >= 33X There is a 0.1% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.08% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 194084775 0.7786731853318031 2.7940050539061265 chr2 243199373 300712615 1.236485979756206 3.1912044915904327 chr3 198022430 254321117 1.2843045962015516 3.497517032076276 chr4 191154276 143781591 0.7521756458118677 2.317414377388694 chr5 180915260 192204541 1.062400932900851 2.909178887819144 chr6 171115067 137723809 0.8048607958059006 2.6580002705260237 chr7 159138663 225581797 1.4175172314976656 3.3125067636785333 chr8 146364022 133277752 0.9105909374367971 3.3239501953333384 chr9 141213431 120546086 0.8536446225146955 2.6722349796881675 chr10 135534747 97050400 0.7160554923970899 2.4956865848364633 chr11 135006516 224220108 1.660809527149045 3.9293547351641496 chr12 133851895 143773360 1.0741227085354301 2.8697836404824613 chr13 115169878 130040796 1.129121592019052 2.8177476193053046 chr14 107349540 87868998 0.8185316676717944 2.988467268737659 chr15 102531392 69492186 0.6777649717269029 2.4392991836022793 chr16 90354753 76720490 0.8491029796739082 3.421642086608091 chr17 81195210 94002505 1.1577346126698853 3.813948228768426 chr18 78077248 43113549 0.5521909404388843 2.0451443663018662 chr19 59128983 43748826 0.7398880173535202 2.4031655592282517 chr20 63025520 103908942 1.6486804392887198 4.922258852089942 chr21 48129895 41357232 0.8592836531224513 2.579498291533172 chr22 51304566 24830374 0.483979807957054 2.18144708080841 chrMT 16571 200784 12.116589222135055 5.7266306102719975 chrX 155270560 131898254 0.8494736800073369 2.6318456573982445 chrY 59373566 2467997 0.04156726917834108 0.6490800318987763