BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153331.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 43,075,792 number of mapped reads = 42,790,107 (99.34%) number of supplementary alignments = 226,684 (0.53%) number of secondary alignments = 0 number of mapped bases = 4,141,833,538 bp number of sequenced bases = 4,141,319,157 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,700,719 duplication rate = 60% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.6801 >>>>>>> ACTG content number of A's = 1,093,404,919 bp (26.4%) number of C's = 971,007,131 bp (23.45%) number of T's = 1,125,611,813 bp (27.18%) number of G's = 949,963,360 bp (22.94%) number of N's = 1,331,934 bp (0.03%) GC percentage = 46.39% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 10,827,144 number of insertions = 295,828 mapped reads with insertion percentage = 0.69% number of deletions = 255,218 mapped reads with deletion percentage = 0.59% homopolymer indels = 49.57% >>>>>>> Coverage mean coverageData = 1.3379X std coverageData = 14.3429X There is a 8.9% of reference with a coverageData >= 1X There is a 6.4% of reference with a coverageData >= 2X There is a 4.41% of reference with a coverageData >= 3X There is a 3.74% of reference with a coverageData >= 4X There is a 2.98% of reference with a coverageData >= 5X There is a 2.74% of reference with a coverageData >= 6X There is a 2.4% of reference with a coverageData >= 7X There is a 2.25% of reference with a coverageData >= 8X There is a 2.08% of reference with a coverageData >= 9X There is a 1.98% of reference with a coverageData >= 10X There is a 1.87% of reference with a coverageData >= 11X There is a 1.79% of reference with a coverageData >= 12X There is a 1.72% of reference with a coverageData >= 13X There is a 1.65% of reference with a coverageData >= 14X There is a 1.59% of reference with a coverageData >= 15X There is a 1.54% of reference with a coverageData >= 16X There is a 1.49% of reference with a coverageData >= 17X There is a 1.44% of reference with a coverageData >= 18X There is a 1.4% of reference with a coverageData >= 19X There is a 1.35% of reference with a coverageData >= 20X There is a 1.32% of reference with a coverageData >= 21X There is a 1.28% of reference with a coverageData >= 22X There is a 1.24% of reference with a coverageData >= 23X There is a 1.21% of reference with a coverageData >= 24X There is a 1.18% of reference with a coverageData >= 25X There is a 1.15% of reference with a coverageData >= 26X There is a 1.12% of reference with a coverageData >= 27X There is a 1.09% of reference with a coverageData >= 28X There is a 1.06% of reference with a coverageData >= 29X There is a 1.04% of reference with a coverageData >= 30X There is a 1.01% of reference with a coverageData >= 31X There is a 0.99% of reference with a coverageData >= 32X There is a 0.97% of reference with a coverageData >= 33X There is a 0.94% of reference with a coverageData >= 34X There is a 0.92% of reference with a coverageData >= 35X There is a 0.9% of reference with a coverageData >= 36X There is a 0.88% of reference with a coverageData >= 37X There is a 0.86% of reference with a coverageData >= 38X There is a 0.85% of reference with a coverageData >= 39X There is a 0.83% of reference with a coverageData >= 40X There is a 0.81% of reference with a coverageData >= 41X There is a 0.79% of reference with a coverageData >= 42X There is a 0.78% of reference with a coverageData >= 43X There is a 0.76% of reference with a coverageData >= 44X There is a 0.75% of reference with a coverageData >= 45X There is a 0.73% of reference with a coverageData >= 46X There is a 0.72% of reference with a coverageData >= 47X There is a 0.7% of reference with a coverageData >= 48X There is a 0.69% of reference with a coverageData >= 49X There is a 0.68% of reference with a coverageData >= 50X There is a 0.66% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 429090985 1.721524236443126 16.167865099675698 chr2 243199373 328321375 1.350009134275194 13.035318099265837 chr3 198022430 220100083 1.1114906680015997 10.89734521801093 chr4 191154276 170549656 0.8922094737760404 9.987186415470866 chr5 180915260 267123541 1.4765119371356512 16.008537220979257 chr6 171115067 141234285 0.8253760903474385 8.969603480754012 chr7 159138663 206290064 1.2962912978601562 14.034811266581219 chr8 146364022 225611319 1.541439733051337 24.936656386185277 chr9 141213431 116126473 0.8223472241815298 8.927585568453791 chr10 135534747 219147427 1.6169095516148342 15.508204015891506 chr11 135006516 198506407 1.4703468608878107 13.117250848210196 chr12 133851895 142428230 1.0640733177516837 9.86744959325854 chr13 115169878 57628342 0.5003768606926892 8.087650730935675 chr14 107349540 131078656 1.2210453440228994 12.21114854572179 chr15 102531392 206700898 2.0159767069191843 18.224935774532295 chr16 90354753 151630930 1.6781732555895537 15.89564652310741 chr17 81195210 173432392 2.1359928990885053 16.03250853787979 chr18 78077248 47983183 0.6145603774354342 7.4222485837882815 chr19 59128983 200327348 3.3879721557193028 22.805389732046976 chr20 63025520 106210785 1.6852028352959245 15.644692525838162 chr21 48129895 44220963 0.9187836998190002 10.207413069165712 chr22 51304566 60113295 1.1716948351146756 11.611015227511999 chrMT 16571 76118 4.593446382234023 13.400265782331454 chrX 155270560 295328910 1.9020277250239839 19.734678931949762 chrY 59373566 2571873 0.043316801958635937 1.5909306857460968