BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618569.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 239,646,346 number of mapped reads = 214,744,217 (89.61%) number of supplementary alignments = 1,514,671 (0.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 107,980,563 number of mapped paired reads (second in pair) = 106,763,654 number of mapped paired reads (both in pair) = 209,963,100 number of mapped paired reads (singletons) = 4,781,117 number of mapped bases = 20,130,264,994 bp number of sequenced bases = 20,116,874,321 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,366,664 duplication rate = 29.2% >>>>>>> Insert size mean insert size = 85,585.9401 std insert size = 2,916,222.9349 median insert size = 185 >>>>>>> Mapping quality mean mapping quality = 52.5731 >>>>>>> ACTG content number of A's = 5,318,410,520 bp (26.44%) number of C's = 4,549,854,397 bp (22.62%) number of T's = 5,352,658,107 bp (26.61%) number of G's = 4,891,984,819 bp (24.32%) number of N's = 3,966,478 bp (0.02%) GC percentage = 46.93% >>>>>>> Mismatches and indels general error rate = 0.0141 number of mismatches = 277,766,558 number of insertions = 3,264,724 mapped reads with insertion percentage = 1.49% number of deletions = 9,631,280 mapped reads with deletion percentage = 4.38% homopolymer indels = 51.92% >>>>>>> Coverage mean coverageData = 6.5027X std coverageData = 25.683X There is a 41.03% of reference with a coverageData >= 1X There is a 33.49% of reference with a coverageData >= 2X There is a 28.63% of reference with a coverageData >= 3X There is a 25.22% of reference with a coverageData >= 4X There is a 22.58% of reference with a coverageData >= 5X There is a 20.46% of reference with a coverageData >= 6X There is a 18.71% of reference with a coverageData >= 7X There is a 17.23% of reference with a coverageData >= 8X There is a 15.95% of reference with a coverageData >= 9X There is a 14.84% of reference with a coverageData >= 10X There is a 13.87% of reference with a coverageData >= 11X There is a 13% of reference with a coverageData >= 12X There is a 12.23% of reference with a coverageData >= 13X There is a 11.53% of reference with a coverageData >= 14X There is a 10.9% of reference with a coverageData >= 15X There is a 10.33% of reference with a coverageData >= 16X There is a 9.8% of reference with a coverageData >= 17X There is a 9.32% of reference with a coverageData >= 18X There is a 8.87% of reference with a coverageData >= 19X There is a 8.46% of reference with a coverageData >= 20X There is a 8.08% of reference with a coverageData >= 21X There is a 7.72% of reference with a coverageData >= 22X There is a 7.39% of reference with a coverageData >= 23X There is a 7.08% of reference with a coverageData >= 24X There is a 6.79% of reference with a coverageData >= 25X There is a 6.52% of reference with a coverageData >= 26X There is a 6.27% of reference with a coverageData >= 27X There is a 6.03% of reference with a coverageData >= 28X There is a 5.8% of reference with a coverageData >= 29X There is a 5.59% of reference with a coverageData >= 30X There is a 5.39% of reference with a coverageData >= 31X There is a 5.2% of reference with a coverageData >= 32X There is a 5.01% of reference with a coverageData >= 33X There is a 4.84% of reference with a coverageData >= 34X There is a 4.68% of reference with a coverageData >= 35X There is a 4.52% of reference with a coverageData >= 36X There is a 4.38% of reference with a coverageData >= 37X There is a 4.24% of reference with a coverageData >= 38X There is a 4.1% of reference with a coverageData >= 39X There is a 3.97% of reference with a coverageData >= 40X There is a 3.85% of reference with a coverageData >= 41X There is a 3.73% of reference with a coverageData >= 42X There is a 3.62% of reference with a coverageData >= 43X There is a 3.52% of reference with a coverageData >= 44X There is a 3.41% of reference with a coverageData >= 45X There is a 3.31% of reference with a coverageData >= 46X There is a 3.22% of reference with a coverageData >= 47X There is a 3.13% of reference with a coverageData >= 48X There is a 3.04% of reference with a coverageData >= 49X There is a 2.96% of reference with a coverageData >= 50X There is a 2.88% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1860718004 7.465249219980881 30.30592211006713 chr2 243199373 1704627619 7.009177688134911 30.0278878589922 chr3 198022430 1303350413 6.581832234863495 21.16747064899043 chr4 191154276 1033816300 5.408282365600861 21.596774621583663 chr5 180915260 1164908857 6.438975114647598 21.271180963159217 chr6 171115067 1108730392 6.479443402841902 21.034129255368917 chr7 159138663 1030918838 6.478116747782404 21.423623610970342 chr8 146364022 999879950 6.831459919842869 21.57443369012738 chr9 141213431 923034156 6.536447344020697 28.08610882226577 chr10 135534747 1048218510 7.733946705194351 25.33387590027472 chr11 135006516 1076713580 7.975271208391156 29.036076997866648 chr12 133851895 921700800 6.885974980032969 21.97514143396824 chr13 115169878 542058159 4.706596624162439 16.460876413183176 chr14 107349540 665347121 6.197950368487839 23.341896850158193 chr15 102531392 693888363 6.767569906785231 23.26987688469242 chr16 90354753 778845988 8.619867379859917 43.54327991582206 chr17 81195210 734011290 9.040081182128848 29.746549700329147 chr18 78077248 528555955 6.769654009833953 28.06926393098192 chr19 59128983 485245091 8.206552292637944 29.611489791208534 chr20 63025520 610650321 9.688937449464914 29.863844299090033 chr21 48129895 284230114 5.905479619267817 44.78395433903847 chr22 51304566 397243289 7.742844740173808 28.580845824557514 chrMT 16571 23289 1.4054070363888722 4.529833252078642 chrX 155270560 46606277 0.3001617112735344 5.290134390521066 chrY 59373566 186942318 3.1485782410306973 22.34735587814498