BamQC report ----------------------------------- >>>>>>> Input bam file = SRR26104284.sorted.bam outfile = /mainsd2/zhouyj/SRP461548/SRP461548.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 = 178,813,988 number of mapped reads = 175,282,347 (98.02%) number of supplementary alignments = 176,858 (0.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 88,346,542 number of mapped paired reads (second in pair) = 86,935,805 number of mapped paired reads (both in pair) = 173,540,884 number of mapped paired reads (singletons) = 1,741,463 number of mapped bases = 15,153,887,868 bp number of sequenced bases = 15,149,969,783 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,791,370 duplication rate = 33.2% >>>>>>> Insert size mean insert size = 11,545.2059 std insert size = 1,042,147.4043 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 53.2772 >>>>>>> ACTG content number of A's = 4,739,552,612 bp (31.28%) number of C's = 2,835,907,246 bp (18.72%) number of T's = 4,784,342,965 bp (31.58%) number of G's = 2,782,198,897 bp (18.36%) number of N's = 7,968,063 bp (0.05%) GC percentage = 37.08% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 95,457,260 number of insertions = 1,455,282 mapped reads with insertion percentage = 0.82% number of deletions = 1,741,442 mapped reads with deletion percentage = 0.98% homopolymer indels = 44.46% >>>>>>> Coverage mean coverageData = 4.8952X std coverageData = 75.9756X There is a 69.02% of reference with a coverageData >= 1X There is a 57.26% of reference with a coverageData >= 2X There is a 47.72% of reference with a coverageData >= 3X There is a 40.65% of reference with a coverageData >= 4X There is a 34.54% of reference with a coverageData >= 5X There is a 29.62% of reference with a coverageData >= 6X There is a 25.32% of reference with a coverageData >= 7X There is a 21.75% of reference with a coverageData >= 8X There is a 18.64% of reference with a coverageData >= 9X There is a 16.03% of reference with a coverageData >= 10X There is a 13.76% of reference with a coverageData >= 11X There is a 11.84% of reference with a coverageData >= 12X There is a 10.18% of reference with a coverageData >= 13X There is a 8.77% of reference with a coverageData >= 14X There is a 7.56% of reference with a coverageData >= 15X There is a 6.53% of reference with a coverageData >= 16X There is a 5.64% of reference with a coverageData >= 17X There is a 4.88% of reference with a coverageData >= 18X There is a 4.23% of reference with a coverageData >= 19X There is a 3.68% of reference with a coverageData >= 20X There is a 3.2% of reference with a coverageData >= 21X There is a 2.79% of reference with a coverageData >= 22X There is a 2.44% of reference with a coverageData >= 23X There is a 2.14% of reference with a coverageData >= 24X There is a 1.87% of reference with a coverageData >= 25X There is a 1.65% of reference with a coverageData >= 26X There is a 1.46% of reference with a coverageData >= 27X There is a 1.29% of reference with a coverageData >= 28X There is a 1.14% of reference with a coverageData >= 29X There is a 1.02% of reference with a coverageData >= 30X There is a 0.91% of reference with a coverageData >= 31X There is a 0.81% of reference with a coverageData >= 32X There is a 0.73% of reference with a coverageData >= 33X There is a 0.65% of reference with a coverageData >= 34X There is a 0.59% of reference with a coverageData >= 35X There is a 0.53% of reference with a coverageData >= 36X There is a 0.48% of reference with a coverageData >= 37X There is a 0.44% of reference with a coverageData >= 38X There is a 0.4% of reference with a coverageData >= 39X There is a 0.37% of reference with a coverageData >= 40X There is a 0.33% of reference with a coverageData >= 41X There is a 0.31% of reference with a coverageData >= 42X There is a 0.28% of reference with a coverageData >= 43X There is a 0.26% of reference with a coverageData >= 44X There is a 0.24% of reference with a coverageData >= 45X There is a 0.22% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1375031619 5.5166627608923795 86.4139407977901 chr2 243199373 1585204731 6.518128362937843 16.93442217441107 chr3 198022430 1073476287 5.420983304770071 7.444893149294901 chr4 191154276 1419503980 7.425959856634335 13.94328247791363 chr5 180915260 1066758536 5.896454152070975 8.4000404353055 chr6 171115067 1176610164 6.876134198048147 13.590016166705988 chr7 159138663 1181571511 7.424792245489709 48.08706901059121 chr8 146364022 959199376 6.553518842219299 204.20965540846487 chr9 141213431 383716948 2.7172836555469004 22.14950653178629 chr10 135534747 565716587 4.173959811206199 45.04026413055959 chr11 135006516 707417701 5.239878207063724 14.989672849028349 chr12 133851895 537066894 4.012396641825654 5.8098080331664885 chr13 115169878 538403580 4.6748645509548945 11.937057877178786 chr14 107349540 280322676 2.6113076590733413 5.1895895538638985 chr15 102531392 227163614 2.215551838016595 3.957157789359898 chr16 90354753 189160775 2.093534304719974 17.123808612029336 chr17 81195210 122667067 1.5107672854100629 6.947997727018785 chr18 78077248 306038460 3.9196881017117815 24.640954775846325 chr19 59128983 81559567 1.379350072704616 51.14224783395502 chr20 63025520 128833854 2.0441537650145527 4.957118421283968 chr21 48129895 145390612 3.020796367829184 7.095000126840059 chr22 51304566 45745942 0.8916543997273069 3.8477629182589874 chrMT 16571 372669779 22489.275179530505 4514.499083872125 chrX 155270560 667338177 4.297905391723969 7.022143779350847 chrY 59373566 17319431 0.29170272508139394 9.866027777210455