BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618614.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 29,708,384 number of mapped reads = 28,584,759 (96.22%) number of supplementary alignments = 37,504 (0.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,428,030 number of mapped paired reads (second in pair) = 14,156,729 number of mapped paired reads (both in pair) = 28,132,690 number of mapped paired reads (singletons) = 452,069 number of mapped bases = 2,750,091,383 bp number of sequenced bases = 2,748,277,847 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,214,567 duplication rate = 13.39% >>>>>>> Insert size mean insert size = 27,688.109 std insert size = 1,658,556.1728 median insert size = 223 >>>>>>> Mapping quality mean mapping quality = 52.5381 >>>>>>> ACTG content number of A's = 747,760,177 bp (27.21%) number of C's = 609,605,786 bp (22.18%) number of T's = 752,116,406 bp (27.37%) number of G's = 638,640,903 bp (23.24%) number of N's = 154,575 bp (0.01%) GC percentage = 45.42% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 31,644,350 number of insertions = 477,069 mapped reads with insertion percentage = 1.65% number of deletions = 1,328,571 mapped reads with deletion percentage = 4.54% homopolymer indels = 53.12% >>>>>>> Coverage mean coverageData = 0.8884X std coverageData = 3.7008X There is a 21.12% of reference with a coverageData >= 1X There is a 13.31% of reference with a coverageData >= 2X There is a 9.3% of reference with a coverageData >= 3X There is a 6.92% of reference with a coverageData >= 4X There is a 5.36% of reference with a coverageData >= 5X There is a 4.27% of reference with a coverageData >= 6X There is a 3.47% of reference with a coverageData >= 7X There is a 2.87% of reference with a coverageData >= 8X There is a 2.41% of reference with a coverageData >= 9X There is a 2.04% of reference with a coverageData >= 10X There is a 1.75% of reference with a coverageData >= 11X There is a 1.51% of reference with a coverageData >= 12X There is a 1.32% of reference with a coverageData >= 13X There is a 1.15% of reference with a coverageData >= 14X There is a 1.01% of reference with a coverageData >= 15X There is a 0.9% of reference with a coverageData >= 16X There is a 0.8% of reference with a coverageData >= 17X There is a 0.71% of reference with a coverageData >= 18X There is a 0.64% of reference with a coverageData >= 19X There is a 0.57% of reference with a coverageData >= 20X There is a 0.52% of reference with a coverageData >= 21X There is a 0.47% of reference with a coverageData >= 22X There is a 0.43% of reference with a coverageData >= 23X There is a 0.39% of reference with a coverageData >= 24X There is a 0.35% of reference with a coverageData >= 25X There is a 0.32% of reference with a coverageData >= 26X There is a 0.3% of reference with a coverageData >= 27X There is a 0.27% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.15% of reference with a coverageData >= 36X There is a 0.14% of reference with a coverageData >= 37X There is a 0.13% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.1% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.07% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 259936270 1.0428711028166304 4.602241994935364 chr2 243199373 234885510 0.9658146199250275 3.7792391555545053 chr3 198022430 180306385 0.9105351600826229 3.2014202057933585 chr4 191154276 137575800 0.7197108161995811 3.2976937707306146 chr5 180915260 162003502 0.8954662088759124 3.1985165302373972 chr6 171115067 149790751 0.8753802550888169 3.2964827886261494 chr7 159138663 142445860 0.8951052956879498 3.3422473120464424 chr8 146364022 139317806 0.9518582783957659 3.4195985673711813 chr9 141213431 126302872 0.8944111838766952 4.178694741145717 chr10 135534747 147536194 1.0885488575117936 3.855846289572361 chr11 135006516 152562859 1.1300407085536524 4.40640177436009 chr12 133851895 128263222 0.9582473374769928 3.5097130355257455 chr13 115169878 74830361 0.6497389968581889 2.5819275739969667 chr14 107349540 89409601 0.8328829448174626 3.257511016324978 chr15 102531392 94719929 0.9238139378815807 3.5527770276647552 chr16 90354753 102818353 1.1379407234946457 4.8156246466284305 chr17 81195210 94478284 1.1635943056246791 4.210787441690413 chr18 78077248 70330033 0.9007749991393139 4.104444293643897 chr19 59128983 65708034 1.1112660943280557 4.621431455834043 chr20 63025520 82111999 1.3028373109813294 4.323600759148692 chr21 48129895 34874634 0.7245940179175542 5.75086375712183 chr22 51304566 51688647 1.0074862927404942 4.049265677149574 chrMT 16571 33576 2.0261903325085995 2.8678878668787955 chrX 155270560 3768474 0.024270370378003402 0.7980818628041776 chrY 59373566 24392427 0.41082974534492334 2.502260534176652