BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960919.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 223,184,190 number of mapped reads = 218,576,341 (97.94%) number of supplementary alignments = 455,388 (0.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 109,835,602 number of mapped paired reads (second in pair) = 108,740,739 number of mapped paired reads (both in pair) = 216,553,236 number of mapped paired reads (singletons) = 2,023,105 number of mapped bases = 21,363,586,999 bp number of sequenced bases = 21,357,460,256 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,843,842 duplication rate = 12.03% >>>>>>> Insert size mean insert size = 18,566.9934 std insert size = 1,260,347.1742 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 53.5629 >>>>>>> ACTG content number of A's = 6,517,533,322 bp (30.52%) number of C's = 4,169,377,524 bp (19.52%) number of T's = 6,515,570,481 bp (30.51%) number of G's = 4,151,779,269 bp (19.44%) number of N's = 3,199,660 bp (0.01%) GC percentage = 38.96% >>>>>>> Mismatches and indels general error rate = 0.0142 number of mismatches = 298,202,303 number of insertions = 2,588,128 mapped reads with insertion percentage = 1.16% number of deletions = 2,809,028 mapped reads with deletion percentage = 1.25% homopolymer indels = 40.28% >>>>>>> Coverage mean coverageData = 6.9011X std coverageData = 102.9845X There is a 89.43% of reference with a coverageData >= 1X There is a 85.14% of reference with a coverageData >= 2X There is a 78.81% of reference with a coverageData >= 3X There is a 70.93% of reference with a coverageData >= 4X There is a 62.13% of reference with a coverageData >= 5X There is a 53.07% of reference with a coverageData >= 6X There is a 44.31% of reference with a coverageData >= 7X There is a 36.25% of reference with a coverageData >= 8X There is a 29.12% of reference with a coverageData >= 9X There is a 23.04% of reference with a coverageData >= 10X There is a 17.98% of reference with a coverageData >= 11X There is a 13.88% of reference with a coverageData >= 12X There is a 10.63% of reference with a coverageData >= 13X There is a 8.09% of reference with a coverageData >= 14X There is a 6.13% of reference with a coverageData >= 15X There is a 4.64% of reference with a coverageData >= 16X There is a 3.51% of reference with a coverageData >= 17X There is a 2.66% of reference with a coverageData >= 18X There is a 2.03% of reference with a coverageData >= 19X There is a 1.56% of reference with a coverageData >= 20X There is a 1.21% of reference with a coverageData >= 21X There is a 0.96% of reference with a coverageData >= 22X There is a 0.77% of reference with a coverageData >= 23X There is a 0.63% of reference with a coverageData >= 24X There is a 0.53% of reference with a coverageData >= 25X There is a 0.45% of reference with a coverageData >= 26X There is a 0.4% of reference with a coverageData >= 27X There is a 0.35% of reference with a coverageData >= 28X There is a 0.32% of reference with a coverageData >= 29X There is a 0.3% of reference with a coverageData >= 30X There is a 0.28% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1777653197 7.131991045270054 274.27156169006116 chr2 243199373 1798237823 7.3940890587740125 55.377684207822085 chr3 198022430 1583527494 7.996707716393542 9.500905572384816 chr4 191154276 1404861190 7.349357908164189 57.10305204355498 chr5 180915260 1158801438 6.40521666331519 9.277262201773855 chr6 171115067 1120182619 6.546370454917334 27.01339980530783 chr7 159138663 1173916118 7.376687071953093 68.27995331173453 chr8 146364022 1249245700 8.535196579935471 120.96851839485443 chr9 141213431 912093385 6.4589704997678306 97.87090501150539 chr10 135534747 1022036561 7.5407715262861705 199.3052819089843 chr11 135006516 1042441554 7.721416601847573 43.43115286354797 chr12 133851895 965117677 7.210340032914738 11.70823037448167 chr13 115169878 732899726 6.363640725572359 4.780319458815598 chr14 107349540 454473859 4.233589254318184 7.2522488577794055 chr15 102531392 575483023 5.612749537234411 5.060269105569786 chr16 90354753 707132620 7.826180654823991 85.50946554390023 chr17 81195210 410495900 5.055666461112669 25.72240565473986 chr18 78077248 820318611 10.506500062604665 101.01908049937407 chr19 59128983 399041722 6.74866540491657 115.08579345149951 chr20 63025520 403849263 6.407710130753384 18.76566840720438 chr21 48129895 283822131 5.897002912638808 22.661557018415564 chr22 51304566 223102909 4.348597530286096 5.6382657769933004 chrMT 16571 4890514 295.12485667732784 59.28540149660614 chrX 155270560 1080458195 6.958551543834195 29.25299033887843 chrY 59373566 59503770 1.0021929624371897 53.19777913244824