BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472772.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 = 15,546,032 number of mapped reads = 15,370,975 (98.87%) number of supplementary alignments = 57,469 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,728,103 number of mapped paired reads (second in pair) = 7,642,872 number of mapped paired reads (both in pair) = 15,254,398 number of mapped paired reads (singletons) = 116,577 number of mapped bases = 1,515,391,364 bp number of sequenced bases = 1,515,170,599 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,646,264 duplication rate = 47.22% >>>>>>> Insert size mean insert size = 26,926.1519 std insert size = 1,587,116.732 median insert size = 260 >>>>>>> Mapping quality mean mapping quality = 55.0517 >>>>>>> ACTG content number of A's = 418,654,636 bp (27.63%) number of C's = 341,330,312 bp (22.53%) number of T's = 415,518,673 bp (27.42%) number of G's = 339,374,367 bp (22.4%) number of N's = 292,611 bp (0.02%) GC percentage = 44.93% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 9,951,421 number of insertions = 98,030 mapped reads with insertion percentage = 0.63% number of deletions = 86,264 mapped reads with deletion percentage = 0.55% homopolymer indels = 44.43% >>>>>>> Coverage mean coverageData = 0.4895X std coverageData = 16.641X There is a 4.33% of reference with a coverageData >= 1X There is a 1.86% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% 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 0.21% 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 0.2% 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 0.19% 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 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 187788188 0.7534111138683983 23.192305133050827 chr2 243199373 104671920 0.4303955175081804 15.190217104714266 chr3 198022430 151408653 0.7646035502139833 21.376317710763963 chr4 191154276 77527761 0.4055769121272495 19.047734058056182 chr5 180915260 87189666 0.48193649336158817 16.040108726207 chr6 171115067 95458649 0.5578623243036804 15.255238497628214 chr7 159138663 64013175 0.40224778688759 15.361898610643912 chr8 146364022 55220704 0.37728331898395084 11.918088265339623 chr9 141213431 86524792 0.6127235305259313 14.50985845950816 chr10 135534747 41215953 0.30409879320466804 13.856203221160248 chr11 135006516 80822296 0.5986547790034075 22.111036725498032 chr12 133851895 75636451 0.5650756830898808 16.567346471281734 chr13 115169878 39723544 0.3449126168215616 16.48096562231403 chr14 107349540 30956042 0.28836678759871726 12.761319776003578 chr15 102531392 42457080 0.4140885944472499 14.958484900621915 chr16 90354753 48134626 0.5327293186225632 15.7733441361207 chr17 81195210 57646119 0.7099694550947032 17.2625697753096 chr18 78077248 23586490 0.30209171819170677 10.288459609383066 chr19 59128983 38510328 0.651293596576826 17.217333544944214 chr20 63025520 27755248 0.4403811027659907 12.067685329486025 chr21 48129895 9602431 0.1995107406737538 10.322283078261892 chr22 51304566 12518757 0.24400863268193324 6.863606319767853 chrMT 16571 5430 0.3276808882988353 1.092442759732026 chrX 155270560 74471669 0.47962517170028884 16.62345154993434 chrY 59373566 2545392 0.042870795397399575 1.573687503565418