BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926927.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 11,408,376 number of mapped reads = 10,486,669 (91.92%) number of supplementary alignments = 319,232 (2.8%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,258,282 number of mapped paired reads (second in pair) = 5,228,387 number of mapped paired reads (both in pair) = 10,289,024 number of mapped paired reads (singletons) = 197,645 number of mapped bases = 943,598,219 bp number of sequenced bases = 942,871,820 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 638,780 duplication rate = 4.99% >>>>>>> Insert size mean insert size = 320,639.2958 std insert size = 5,558,799.1948 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 52.5779 >>>>>>> ACTG content number of A's = 268,052,339 bp (28.43%) number of C's = 182,126,584 bp (19.32%) number of T's = 273,416,176 bp (29%) number of G's = 219,096,552 bp (23.24%) number of N's = 180,169 bp (0.02%) GC percentage = 42.55% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 9,012,815 number of insertions = 160,006 mapped reads with insertion percentage = 1.5% number of deletions = 498,802 mapped reads with deletion percentage = 4.63% homopolymer indels = 51.92% >>>>>>> Coverage mean coverageData = 0.3048X std coverageData = 1.288X There is a 18.45% of reference with a coverageData >= 1X There is a 6.84% of reference with a coverageData >= 2X There is a 2.58% of reference with a coverageData >= 3X There is a 1.12% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 79474025 0.3188518635626589 1.224964852199409 chr2 243199373 82698035 0.34004213900666597 1.9740217463900844 chr3 198022430 67689382 0.3418268425450592 0.8494369898212593 chr4 191154276 51028129 0.26694735826887805 1.2561114171281664 chr5 180915260 56878620 0.3143937111772661 0.7956964976304992 chr6 171115067 57400077 0.33544724030643075 1.4739102851166768 chr7 159138663 49657645 0.31204010429571094 0.9839068749487225 chr8 146364022 48887743 0.3340147553474583 0.9137130035790951 chr9 141213431 42714600 0.3024825591837649 1.419060446055533 chr10 135534747 47509592 0.3505344057638592 2.7984728476946295 chr11 135006516 44062533 0.32637338037817376 1.1129932520736607 chr12 133851895 41568242 0.3105540044838364 0.8317654975168456 chr13 115169878 30270990 0.2628377360962386 0.733026503613188 chr14 107349540 28334915 0.2639500364882793 0.7494433426250047 chr15 102531392 27114525 0.26445095956563236 0.7527398741012274 chr16 90354753 29375212 0.32510975930618724 1.5631891374494165 chr17 81195210 24667434 0.30380405445099534 0.9245199986237179 chr18 78077248 22665503 0.2902958746701728 1.413135399279747 chr19 59128983 13705969 0.23179781394176863 0.9706269846173429 chr20 63025520 18012266 0.28579321519282985 0.8210969281691427 chr21 48129895 9608346 0.19963363726432398 0.9855841926554411 chr22 51304566 11766798 0.22935186704434846 0.715719401846881 chrMT 16571 57635 3.4780640878643414 3.4661754459314498 chrX 155270560 56793885 0.36577368562334034 0.9317944928449039 chrY 59373566 1656118 0.027893187348726874 1.0051170375733516