BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006164.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 9,329,604 number of mapped reads = 7,421,148 (79.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,738,137 number of mapped paired reads (second in pair) = 3,683,011 number of mapped paired reads (both in pair) = 6,862,098 number of mapped paired reads (singletons) = 559,050 number of mapped bases = 287,098,544 bp number of sequenced bases = 287,061,682 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 473,246 duplication rate = 5.63% >>>>>>> Insert size mean insert size = 58,262.5504 std insert size = 2,316,335.7336 median insert size = 89 >>>>>>> Mapping quality mean mapping quality = 47.4054 >>>>>>> ACTG content number of A's = 77,956,250 bp (27.16%) number of C's = 63,856,659 bp (22.24%) number of T's = 79,240,968 bp (27.6%) number of G's = 65,968,190 bp (22.98%) number of N's = 39,615 bp (0.01%) GC percentage = 45.23% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 1,054,604 number of insertions = 8,434 mapped reads with insertion percentage = 0.11% number of deletions = 27,049 mapped reads with deletion percentage = 0.36% homopolymer indels = 40.61% >>>>>>> Coverage mean coverageData = 0.0927X std coverageData = 0.5738X There is a 6.75% of reference with a coverageData >= 1X There is a 1.7% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% 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 24315591 0.09755478603200751 0.6288655504264165 chr2 243199373 24322208 0.10000933678393982 0.5003998219309415 chr3 198022430 18481456 0.0933301141693898 0.39722464178660893 chr4 191154276 17460863 0.09134434952425548 0.46203608997193324 chr5 180915260 16924395 0.09354874210168894 0.4107059668224061 chr6 171115067 16102090 0.09410094787269668 0.4316183326944299 chr7 159138663 15371230 0.09659016677801296 0.5533832709056727 chr8 146364022 14253497 0.09738388440842381 1.2039921842673396 chr9 141213431 11765991 0.08332062266796704 0.42458664292432413 chr10 135534747 13564238 0.1000794135838834 0.5664701643591235 chr11 135006516 13253144 0.0981666988577055 0.4825308189056049 chr12 133851895 13141083 0.09817629403005464 0.4168422699756932 chr13 115169878 8865230 0.07697524868438256 0.38709098909708545 chr14 107349540 8846890 0.08241199729407317 1.2050281497527948 chr15 102531392 8445098 0.08236597431545647 0.3762469637855109 chr16 90354753 9090404 0.10060792264021794 0.46768345483414125 chr17 81195210 8392843 0.10336623305734415 0.4544243301298168 chr18 78077248 7313572 0.09367097569832379 0.5884879662391556 chr19 59128983 6399450 0.10822864989915351 0.5575250314103056 chr20 63025520 6629909 0.10519403885917958 0.45780310331597773 chr21 48129895 3805140 0.07905980264448946 0.4562528121450651 chr22 51304566 4021022 0.07837551924715629 0.45405378022126497 chrMT 16571 44026 2.6568100899161187 2.3791949061617084 chrX 155270560 15467064 0.09961362926751859 0.4385455100482089 chrY 59373566 822110 0.013846397570258791 0.33866648589757814