BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618610.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 = 47,275,028 number of mapped reads = 44,423,029 (93.97%) number of supplementary alignments = 58,935 (0.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 22,670,836 number of mapped paired reads (second in pair) = 21,752,193 number of mapped paired reads (both in pair) = 42,604,004 number of mapped paired reads (singletons) = 1,819,025 number of mapped bases = 4,232,527,854 bp number of sequenced bases = 4,229,986,423 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,278,372 duplication rate = 38.68% >>>>>>> Insert size mean insert size = 59,625.9089 std insert size = 2,480,000.4271 median insert size = 221 >>>>>>> Mapping quality mean mapping quality = 53.9323 >>>>>>> ACTG content number of A's = 1,131,564,179 bp (26.75%) number of C's = 973,090,950 bp (23%) number of T's = 1,136,426,705 bp (26.87%) number of G's = 985,585,836 bp (23.3%) number of N's = 3,318,753 bp (0.08%) GC percentage = 46.3% >>>>>>> Mismatches and indels general error rate = 0.0145 number of mismatches = 60,288,277 number of insertions = 748,216 mapped reads with insertion percentage = 1.66% number of deletions = 1,804,305 mapped reads with deletion percentage = 3.97% homopolymer indels = 51.43% >>>>>>> Coverage mean coverageData = 1.3672X std coverageData = 6.758X There is a 19.09% of reference with a coverageData >= 1X There is a 13.67% of reference with a coverageData >= 2X There is a 10.76% of reference with a coverageData >= 3X There is a 8.89% of reference with a coverageData >= 4X There is a 7.52% of reference with a coverageData >= 5X There is a 6.48% of reference with a coverageData >= 6X There is a 5.65% of reference with a coverageData >= 7X There is a 4.98% of reference with a coverageData >= 8X There is a 4.41% of reference with a coverageData >= 9X There is a 3.94% of reference with a coverageData >= 10X There is a 3.54% of reference with a coverageData >= 11X There is a 3.19% of reference with a coverageData >= 12X There is a 2.88% of reference with a coverageData >= 13X There is a 2.62% of reference with a coverageData >= 14X There is a 2.39% of reference with a coverageData >= 15X There is a 2.18% of reference with a coverageData >= 16X There is a 2% of reference with a coverageData >= 17X There is a 1.84% of reference with a coverageData >= 18X There is a 1.69% of reference with a coverageData >= 19X There is a 1.56% of reference with a coverageData >= 20X There is a 1.44% of reference with a coverageData >= 21X There is a 1.34% of reference with a coverageData >= 22X There is a 1.24% of reference with a coverageData >= 23X There is a 1.16% of reference with a coverageData >= 24X There is a 1.08% of reference with a coverageData >= 25X There is a 1% of reference with a coverageData >= 26X There is a 0.94% of reference with a coverageData >= 27X There is a 0.88% of reference with a coverageData >= 28X There is a 0.82% of reference with a coverageData >= 29X There is a 0.77% of reference with a coverageData >= 30X There is a 0.72% of reference with a coverageData >= 31X There is a 0.68% of reference with a coverageData >= 32X There is a 0.64% of reference with a coverageData >= 33X There is a 0.6% of reference with a coverageData >= 34X There is a 0.57% of reference with a coverageData >= 35X There is a 0.54% of reference with a coverageData >= 36X There is a 0.51% of reference with a coverageData >= 37X There is a 0.48% of reference with a coverageData >= 38X There is a 0.45% of reference with a coverageData >= 39X There is a 0.43% of reference with a coverageData >= 40X There is a 0.41% of reference with a coverageData >= 41X There is a 0.39% of reference with a coverageData >= 42X There is a 0.37% of reference with a coverageData >= 43X There is a 0.35% of reference with a coverageData >= 44X There is a 0.33% of reference with a coverageData >= 45X There is a 0.32% of reference with a coverageData >= 46X There is a 0.3% of reference with a coverageData >= 47X There is a 0.29% of reference with a coverageData >= 48X There is a 0.27% of reference with a coverageData >= 49X There is a 0.26% of reference with a coverageData >= 50X There is a 0.25% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 389085437 1.5610209332236729 8.031738239840124 chr2 243199373 341362852 1.4036337667696208 6.988179734174073 chr3 198022430 257986655 1.3028153174365147 6.010405393429198 chr4 191154276 187891859 0.9829330681569477 5.6030927646111435 chr5 180915260 227708026 1.2586446604891153 5.7952436728563965 chr6 171115067 213145861 1.2456288317381192 5.939604850812277 chr7 159138663 200773364 1.2616253034625533 6.039312500195124 chr8 146364022 197016221 1.3460700130254688 6.05873745959297 chr9 141213431 186919768 1.3236684830637675 7.420780536994793 chr10 135534747 216138395 1.5947083665563635 7.074262765802398 chr11 135006516 227932048 1.6883040519318342 7.444431829603437 chr12 133851895 192029606 1.4346424157835045 6.652487553230548 chr13 115169878 100440276 0.8721054302063252 4.628862579093359 chr14 107349540 130157362 1.212463155408025 5.772528940745195 chr15 102531392 143552988 1.4000881603167936 6.969100194961627 chr16 90354753 158020736 1.74889234659299 9.651506776871262 chr17 81195210 159706060 1.9669394290623794 7.810905874573701 chr18 78077248 103004693 1.3192664398212397 6.233300700340236 chr19 59128983 106641095 1.8035333873406887 8.088626237728807 chr20 63025520 136405076 2.1642832300312635 8.64572577371017 chr21 48129895 55972302 1.162942532910159 8.711803977445223 chr22 51304566 91134705 1.776346865501211 8.022419093652902 chrMT 16571 52411 3.1628145555488505 13.941726467235938 chrX 155270560 203574335 1.3110942280365319 5.8386971356111035 chrY 59373566 5875723 0.09896193535015228 2.7868518028050877