BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926980.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 30,470,902 number of mapped reads = 29,992,708 (98.43%) number of supplementary alignments = 484,889 (1.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,064,918 number of mapped paired reads (second in pair) = 14,927,790 number of mapped paired reads (both in pair) = 29,727,938 number of mapped paired reads (singletons) = 264,770 number of mapped bases = 2,861,548,111 bp number of sequenced bases = 2,859,402,961 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,280,880 duplication rate = 5.46% >>>>>>> Insert size mean insert size = 157,182.4078 std insert size = 3,922,433.2677 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 53.3759 >>>>>>> ACTG content number of A's = 805,971,052 bp (28.19%) number of C's = 592,780,857 bp (20.73%) number of T's = 815,208,857 bp (28.51%) number of G's = 645,185,602 bp (22.56%) number of N's = 256,593 bp (0.01%) GC percentage = 43.29% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 26,171,039 number of insertions = 466,129 mapped reads with insertion percentage = 1.53% number of deletions = 1,485,150 mapped reads with deletion percentage = 4.82% homopolymer indels = 52.65% >>>>>>> Coverage mean coverageData = 0.9244X std coverageData = 4.6785X There is a 33.56% of reference with a coverageData >= 1X There is a 19.78% of reference with a coverageData >= 2X There is a 11.89% of reference with a coverageData >= 3X There is a 7.63% of reference with a coverageData >= 4X There is a 5.04% of reference with a coverageData >= 5X There is a 3.42% of reference with a coverageData >= 6X There is a 2.37% of reference with a coverageData >= 7X There is a 1.68% of reference with a coverageData >= 8X There is a 1.21% of reference with a coverageData >= 9X There is a 0.88% of reference with a coverageData >= 10X There is a 0.65% of reference with a coverageData >= 11X There is a 0.49% of reference with a coverageData >= 12X There is a 0.37% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.22% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 243592459 0.9772993063074454 4.362424978704872 chr2 243199373 242728016 0.9980618494439951 6.403242880843195 chr3 198022430 183422721 0.926272448025206 1.936186544326746 chr4 191154276 161360896 0.8441396100393799 3.0740730937669447 chr5 180915260 166464488 0.9201240846128734 1.909478704334099 chr6 171115067 161693804 0.9449419436571298 2.5514305542271187 chr7 159138663 143722011 0.9031244091827012 2.7269036746922706 chr8 146364022 141176442 0.9645570002168976 2.318403022660493 chr9 141213431 121746459 0.8621450391641571 4.323004318825411 chr10 135534747 138785436 1.0239841743313247 6.164490100212608 chr11 135006516 138453740 1.025533760163102 3.2483291858980206 chr12 133851895 126541050 0.9453810870589467 2.2844902521205137 chr13 115169878 80577710 0.6996422276317771 1.725491052920375 chr14 107349540 85573194 0.7971454186017006 1.8881641106435407 chr15 102531392 86086303 0.8396092291422319 2.0147967639801143 chr16 90354753 98071962 1.0854101056532135 7.440699650929621 chr17 81195210 84814375 1.0445736269417862 2.802731621052479 chr18 78077248 73637101 0.9431313588306801 4.645673547861124 chr19 59128983 58586922 0.9908325668310581 3.1639753317741985 chr20 63025520 71018533 1.1268218493080264 2.443154064647207 chr21 48129895 35459055 0.736736595830928 2.8534479327432494 chr22 51304566 44957045 0.8762776591853443 2.27643873741649 chrMT 16571 16729894 1009.5886790175608 714.7509782484483 chrX 155270560 150910308 0.9719183597972468 2.3060079379790825 chrY 59373566 5438187 0.09159273000378654 3.023604017677126