BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971279.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,524,774 number of mapped reads = 7,610,356 (72.31%) number of secondary alignments = 0 number of mapped bases = 300,559,646 bp number of sequenced bases = 300,530,128 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 880,092 duplication rate = 10.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8514 >>>>>>> ACTG content number of A's = 87,264,832 bp (29.04%) number of C's = 61,529,410 bp (20.47%) number of T's = 88,425,472 bp (29.42%) number of G's = 63,307,939 bp (21.07%) number of N's = 2,475 bp (0%) GC percentage = 41.54% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 797,558 number of insertions = 9,414 mapped reads with insertion percentage = 0.12% number of deletions = 22,794 mapped reads with deletion percentage = 0.3% homopolymer indels = 40.21% >>>>>>> Coverage mean coverageData = 0.0971X std coverageData = 1.4228X There is a 4.48% of reference with a coverageData >= 1X There is a 2.22% of reference with a coverageData >= 2X There is a 1.24% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.22% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% 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% 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 24857421 0.09972862214052418 1.458477621813027 chr2 243199373 25890955 0.1064597933811285 0.6818808737207326 chr3 198022430 20822948 0.10515449184216151 0.5999690695056872 chr4 191154276 18863872 0.09868401792905747 0.6087376362605401 chr5 180915260 18662758 0.10315745614825417 0.6023865221599265 chr6 171115067 17662249 0.10321854942206814 0.6044524948698714 chr7 159138663 16165804 0.10158313319497977 0.8339271743643133 chr8 146364022 16012147 0.1093994738679701 5.582304959094497 chr9 141213431 12652510 0.08959848868766598 0.6337213361366126 chr10 135534747 14139302 0.10432234030731617 0.7280661522511911 chr11 135006516 14075588 0.1042585826005613 0.650473268536527 chr12 133851895 13853301 0.10349723476085265 0.6169919850054094 chr13 115169878 9283780 0.08060944546628764 0.5277689813043115 chr14 107349540 9239738 0.08607151926314728 0.5879412760695069 chr15 102531392 9089940 0.08865518962231586 0.5537150552750971 chr16 90354753 8251510 0.09132347470420289 0.5782128519320052 chr17 81195210 7718245 0.09505788580385469 0.593926080667069 chr18 78077248 7828530 0.10026646943293903 0.9221113301143474 chr19 59128983 5382583 0.09103121222294656 1.290352968357586 chr20 63025520 6585079 0.10448273969020803 0.6222863461890346 chr21 48129895 3624005 0.07529634128642915 0.5604042410447587 chr22 51304566 3449762 0.06724083778430169 0.5132330877347517 chrMT 16571 34322 2.0712087381570212 3.3317013316230644 chrX 155270560 15538197 0.10007175217246592 0.6373207808158426 chrY 59373566 875100 0.014738882283068529 0.25774120630999264