BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618597.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 = 49,977,736 number of mapped reads = 46,164,498 (92.37%) number of supplementary alignments = 78,133 (0.16%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 23,337,418 number of mapped paired reads (second in pair) = 22,827,080 number of mapped paired reads (both in pair) = 45,178,386 number of mapped paired reads (singletons) = 986,112 number of mapped bases = 4,384,412,934 bp number of sequenced bases = 4,381,666,476 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,613,900 duplication rate = 22.06% >>>>>>> Insert size mean insert size = 35,666.2679 std insert size = 1,866,419.7262 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 54.009 >>>>>>> ACTG content number of A's = 1,157,350,812 bp (26.41%) number of C's = 1,000,559,714 bp (22.84%) number of T's = 1,164,200,059 bp (26.57%) number of G's = 1,059,402,690 bp (24.18%) number of N's = 153,201 bp (0%) GC percentage = 47.01% >>>>>>> Mismatches and indels general error rate = 0.0124 number of mismatches = 52,926,134 number of insertions = 754,309 mapped reads with insertion percentage = 1.6% number of deletions = 1,974,069 mapped reads with deletion percentage = 4.18% homopolymer indels = 52.6% >>>>>>> Coverage mean coverageData = 1.4163X std coverageData = 6.7212X There is a 23.95% of reference with a coverageData >= 1X There is a 16.72% of reference with a coverageData >= 2X There is a 12.51% of reference with a coverageData >= 3X There is a 9.95% of reference with a coverageData >= 4X There is a 8.12% of reference with a coverageData >= 5X There is a 6.79% of reference with a coverageData >= 6X There is a 5.77% of reference with a coverageData >= 7X There is a 4.97% of reference with a coverageData >= 8X There is a 4.32% of reference with a coverageData >= 9X There is a 3.8% of reference with a coverageData >= 10X There is a 3.36% of reference with a coverageData >= 11X There is a 2.99% of reference with a coverageData >= 12X There is a 2.68% of reference with a coverageData >= 13X There is a 2.41% of reference with a coverageData >= 14X There is a 2.18% of reference with a coverageData >= 15X There is a 1.97% of reference with a coverageData >= 16X There is a 1.8% of reference with a coverageData >= 17X There is a 1.64% of reference with a coverageData >= 18X There is a 1.5% of reference with a coverageData >= 19X There is a 1.38% of reference with a coverageData >= 20X There is a 1.27% of reference with a coverageData >= 21X There is a 1.17% of reference with a coverageData >= 22X There is a 1.09% of reference with a coverageData >= 23X There is a 1.01% of reference with a coverageData >= 24X There is a 0.93% of reference with a coverageData >= 25X There is a 0.87% of reference with a coverageData >= 26X There is a 0.81% of reference with a coverageData >= 27X There is a 0.75% of reference with a coverageData >= 28X There is a 0.7% of reference with a coverageData >= 29X There is a 0.66% of reference with a coverageData >= 30X There is a 0.62% of reference with a coverageData >= 31X There is a 0.58% of reference with a coverageData >= 32X There is a 0.54% of reference with a coverageData >= 33X There is a 0.51% of reference with a coverageData >= 34X There is a 0.48% of reference with a coverageData >= 35X There is a 0.45% of reference with a coverageData >= 36X There is a 0.43% of reference with a coverageData >= 37X There is a 0.4% of reference with a coverageData >= 38X There is a 0.38% of reference with a coverageData >= 39X There is a 0.36% of reference with a coverageData >= 40X There is a 0.34% of reference with a coverageData >= 41X There is a 0.32% of reference with a coverageData >= 42X There is a 0.3% of reference with a coverageData >= 43X There is a 0.29% of reference with a coverageData >= 44X There is a 0.27% of reference with a coverageData >= 45X There is a 0.26% of reference with a coverageData >= 46X There is a 0.25% of reference with a coverageData >= 47X There is a 0.23% of reference with a coverageData >= 48X There is a 0.22% of reference with a coverageData >= 49X There is a 0.21% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 364147175 1.460967974880191 6.238917631452546 chr2 243199373 365125990 1.5013442900611425 8.486905379602929 chr3 198022430 267673213 1.3517317861416003 5.23064201943381 chr4 191154276 189964867 0.9937777536297435 6.046477500874615 chr5 180915260 214447630 1.185348488568626 4.598293929610224 chr6 171115067 210448089 1.2298629962258087 4.674506497085715 chr7 159138663 210944797 1.3255408398146464 5.284172081119761 chr8 146364022 210293945 1.436787142949652 5.482009333438612 chr9 141213431 196024543 1.3881437594983441 6.697842201675073 chr10 135534747 210535769 1.553371173519068 5.933164858249689 chr11 135006516 238841518 1.7691110405367396 6.6134959763369645 chr12 133851895 204095630 1.5247870043229497 5.916400026061708 chr13 115169878 105179536 0.9132555996976918 3.8408286931472624 chr14 107349540 113186841 1.0543765813994173 4.585826956090709 chr15 102531392 154204589 1.5039744022981762 5.794728827368752 chr16 90354753 188317495 2.0842013147886087 17.120044458027156 chr17 81195210 170854537 2.104244043460199 7.52467434479752 chr18 78077248 94416181 1.2092662512900045 5.0336340277590175 chr19 59128983 131056759 2.2164554901950537 8.515749365367862 chr20 63025520 144333609 2.290082001703437 7.615203251684033 chr21 48129895 61078295 1.2690302981130543 8.992022629047252 chr22 51304566 114205049 2.226021149852432 8.38011031232474 chrMT 16571 77639 4.685233238790659 7.1593131913341335 chrX 155270560 217872040 1.4031767516005609 4.9228401478161565 chrY 59373566 7087198 0.1193662176194706 5.861637718197952