BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472629.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,346,632 number of mapped reads = 16,236,459 (99.33%) number of supplementary alignments = 70,438 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,136,087 number of mapped paired reads (second in pair) = 8,100,372 number of mapped paired reads (both in pair) = 16,165,964 number of mapped paired reads (singletons) = 70,495 number of mapped bases = 1,597,693,194 bp number of sequenced bases = 1,597,486,046 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,940,381 duplication rate = 50.15% >>>>>>> Insert size mean insert size = 20,974.0655 std insert size = 1,445,650.0655 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 54.8036 >>>>>>> ACTG content number of A's = 424,564,745 bp (26.58%) number of C's = 375,489,953 bp (23.51%) number of T's = 425,979,612 bp (26.67%) number of G's = 371,154,941 bp (23.23%) number of N's = 296,795 bp (0.02%) GC percentage = 46.74% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 9,269,634 number of insertions = 91,807 mapped reads with insertion percentage = 0.56% number of deletions = 86,343 mapped reads with deletion percentage = 0.52% homopolymer indels = 47.37% >>>>>>> Coverage mean coverageData = 0.5161X std coverageData = 20.0203X There is a 3.24% of reference with a coverageData >= 1X There is a 1.49% of reference with a coverageData >= 2X There is a 0.71% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 252398449 1.012629168133547 32.447867415241305 chr2 243199373 122866528 0.5052090656500171 23.487014441168313 chr3 198022430 134439453 0.6789102274929159 18.136836223859657 chr4 191154276 26221224 0.13717309677132203 7.043380743421889 chr5 180915260 67074788 0.3707525169518591 15.227644287791748 chr6 171115067 138022814 0.8066081872264351 23.365499795269923 chr7 159138663 96394875 0.6057288227939932 31.442115549834224 chr8 146364022 68424903 0.46749810551120274 14.347196438543032 chr9 141213431 62658077 0.4437118803522308 15.364391820080902 chr10 135534747 29215458 0.21555695972192282 8.619899414778427 chr11 135006516 36025229 0.26684066863854183 12.871727134712433 chr12 133851895 68281657 0.5101284296348587 13.482168583407374 chr13 115169878 59664495 0.5180564227045548 20.56654470694666 chr14 107349540 17785482 0.16567823206322077 7.049930976546181 chr15 102531392 28666174 0.27958436378197227 16.9578621988488 chr16 90354753 86503359 0.9573747492840803 32.09453500918435 chr17 81195210 66082336 0.8138698822258111 23.818595239565724 chr18 78077248 16936226 0.21691627758191478 7.776988491851191 chr19 59128983 50393651 0.8522664934047657 24.37622399962906 chr20 63025520 62777058 0.9960577556519962 25.92776235587135 chr21 48129895 7487138 0.15556107072329994 6.6576140143843014 chr22 51304566 31065935 0.6055198868654302 17.001094318730484 chrMT 16571 1206 0.07277774425200652 0.2881848579764573 chrX 155270560 65746734 0.42343335401121757 14.812579315238734 chrY 59373566 2559945 0.04311590447506555 2.908648733850576