BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548997.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 = 11,798,132 number of mapped reads = 10,171,850 (86.22%) number of secondary alignments = 0 number of mapped bases = 403,598,906 bp number of sequenced bases = 403,553,279 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 981,467 duplication rate = 8.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1279 >>>>>>> ACTG content number of A's = 120,939,127 bp (29.97%) number of C's = 79,986,441 bp (19.82%) number of T's = 121,525,958 bp (30.11%) number of G's = 81,097,485 bp (20.1%) number of N's = 4,268 bp (0%) GC percentage = 39.92% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 1,194,322 number of insertions = 12,594 mapped reads with insertion percentage = 0.12% number of deletions = 35,247 mapped reads with deletion percentage = 0.35% homopolymer indels = 43.18% >>>>>>> Coverage mean coverageData = 0.1304X std coverageData = 1.0733X There is a 9.3% of reference with a coverageData >= 1X There is a 2.49% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.08% 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 0.01% 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 32238870 0.12934318827634936 1.5768399274143599 chr2 243199373 35604152 0.14639902875078548 0.722390712373827 chr3 198022430 28632492 0.14459216564507363 0.49885469230808754 chr4 191154276 28233298 0.14769901354443152 0.5697544966759615 chr5 180915260 25982753 0.14361836033068742 0.5043037035215471 chr6 171115067 24660208 0.14411476693633296 0.5963220757440009 chr7 159138663 22189278 0.13943360828662987 1.0256833737809157 chr8 146364022 21636961 0.1478297788236511 3.42681740618531 chr9 141213431 17189265 0.12172542567852487 0.6901684213798693 chr10 135534747 19143109 0.14124133791314783 0.7905894511607295 chr11 135006516 18656553 0.13819001891730914 0.6790429833239493 chr12 133851895 18781491 0.14031546583632604 0.5133079771313527 chr13 115169878 13787874 0.11971770952123437 0.4465826853399503 chr14 107349540 12543941 0.11685137169660904 0.5511073299533451 chr15 102531392 11433253 0.11150978034122466 0.4313408334267621 chr16 90354753 10674573 0.11814069150296941 0.5139766733019611 chr17 81195210 9648307 0.11882852449054569 0.5082274041698337 chr18 78077248 11216055 0.14365330857972863 1.4187992781039749 chr19 59128983 6578553 0.11125767206244694 1.1787312686687244 chr20 63025520 8148163 0.12928355053635415 0.5050608769536048 chr21 48129895 5303341 0.11018808580405172 0.5566106365995898 chr22 51304566 3981282 0.0776009293207938 0.39674643561083023 chrMT 16571 37821 2.28236075070907 3.0489857634981123 chrX 155270560 13622000 0.08773073272872849 0.521021984809703 chrY 59373566 3675313 0.061901503440099925 0.6375671389789691