BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975277.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 65,653,560 number of mapped reads = 65,512,127 (99.78%) number of supplementary alignments = 108,326 (0.16%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 32,769,623 number of mapped paired reads (second in pair) = 32,742,504 number of mapped paired reads (both in pair) = 65,451,120 number of mapped paired reads (singletons) = 61,007 number of mapped bases = 6,054,665,423 bp number of sequenced bases = 6,052,886,429 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,166,741 duplication rate = 48.21% >>>>>>> Insert size mean insert size = 59,568.0748 std insert size = 2,328,680.9701 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 56.2105 >>>>>>> ACTG content number of A's = 1,680,520,304 bp (27.76%) number of C's = 1,286,039,495 bp (21.25%) number of T's = 1,694,535,388 bp (28%) number of G's = 1,391,523,291 bp (22.99%) number of N's = 267,951 bp (0%) GC percentage = 44.24% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 30,649,331 number of insertions = 595,210 mapped reads with insertion percentage = 0.9% number of deletions = 1,150,771 mapped reads with deletion percentage = 1.73% homopolymer indels = 47.26% >>>>>>> Coverage mean coverageData = 1.9558X std coverageData = 27.3758X There is a 11.3% of reference with a coverageData >= 1X There is a 5.86% of reference with a coverageData >= 2X There is a 3.58% of reference with a coverageData >= 3X There is a 2.8% of reference with a coverageData >= 4X There is a 2.33% of reference with a coverageData >= 5X There is a 2.09% of reference with a coverageData >= 6X There is a 1.92% of reference with a coverageData >= 7X There is a 1.81% of reference with a coverageData >= 8X There is a 1.72% of reference with a coverageData >= 9X There is a 1.64% of reference with a coverageData >= 10X There is a 1.58% of reference with a coverageData >= 11X There is a 1.52% of reference with a coverageData >= 12X There is a 1.48% of reference with a coverageData >= 13X There is a 1.43% of reference with a coverageData >= 14X There is a 1.39% of reference with a coverageData >= 15X There is a 1.36% of reference with a coverageData >= 16X There is a 1.32% of reference with a coverageData >= 17X There is a 1.29% of reference with a coverageData >= 18X There is a 1.26% of reference with a coverageData >= 19X There is a 1.23% of reference with a coverageData >= 20X There is a 1.21% of reference with a coverageData >= 21X There is a 1.18% of reference with a coverageData >= 22X There is a 1.16% of reference with a coverageData >= 23X There is a 1.14% of reference with a coverageData >= 24X There is a 1.12% of reference with a coverageData >= 25X There is a 1.1% of reference with a coverageData >= 26X There is a 1.08% of reference with a coverageData >= 27X There is a 1.06% of reference with a coverageData >= 28X There is a 1.04% of reference with a coverageData >= 29X There is a 1.02% of reference with a coverageData >= 30X There is a 1.01% of reference with a coverageData >= 31X There is a 0.99% of reference with a coverageData >= 32X There is a 0.97% of reference with a coverageData >= 33X There is a 0.96% of reference with a coverageData >= 34X There is a 0.94% of reference with a coverageData >= 35X There is a 0.93% of reference with a coverageData >= 36X There is a 0.92% of reference with a coverageData >= 37X There is a 0.9% of reference with a coverageData >= 38X There is a 0.89% of reference with a coverageData >= 39X There is a 0.88% of reference with a coverageData >= 40X There is a 0.87% of reference with a coverageData >= 41X There is a 0.86% of reference with a coverageData >= 42X There is a 0.84% of reference with a coverageData >= 43X There is a 0.83% of reference with a coverageData >= 44X There is a 0.82% of reference with a coverageData >= 45X There is a 0.81% of reference with a coverageData >= 46X There is a 0.8% of reference with a coverageData >= 47X There is a 0.79% of reference with a coverageData >= 48X There is a 0.78% of reference with a coverageData >= 49X There is a 0.77% of reference with a coverageData >= 50X There is a 0.76% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 576003270 2.3109401601049573 28.335406427640976 chr2 243199373 376246655 1.5470708265353956 20.856145138617244 chr3 198022430 521348275 2.632773847891878 34.31489963485873 chr4 191154276 363143140 1.8997385127811632 27.71240414254897 chr5 180915260 241968256 1.337467364555096 19.017587554083526 chr6 171115067 594824803 3.4761684837490083 47.641392876500504 chr7 159138663 268284339 1.685852664226543 24.447381589689343 chr8 146364022 178161246 1.2172475418856692 18.45859844849247 chr9 141213431 275776415 1.9529049966925596 27.473197468730227 chr10 135534747 217945912 1.6080445555411707 21.99958255247226 chr11 135006516 221402773 1.6399413862364984 22.110798739856353 chr12 133851895 409309997 3.0579320300246775 33.27859071342444 chr13 115169878 144525250 1.2548875844081384 25.74517674592935 chr14 107349540 239486601 2.2309047714596635 29.141739684769128 chr15 102531392 250196082 2.4401900444304903 30.367788505190102 chr16 90354753 205310142 2.272267204360572 26.825420521057303 chr17 81195210 185328192 2.2825015416549816 25.302001613110946 chr18 78077248 91049895 1.1661514376121453 18.708939290640803 chr19 59128983 258220417 4.367070155764391 40.640209762330805 chr20 63025520 162981304 2.5859573074526003 32.840475777011896 chr21 48129895 71870258 1.4932560729667081 23.75458888795771 chr22 51304566 69773324 1.3599827352598597 18.917830016590937 chrMT 16571 152670 9.213083096976646 19.388703119768177 chrX 155270560 120897235 0.7786230371037497 13.488853381209983 chrY 59373566 10458972 0.17615536179854854 4.6045580553319