BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3212690.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,836,015 number of mapped reads = 1,864,418 (65.74%) number of supplementary alignments = 11,588 (0.41%) number of secondary alignments = 0 number of mapped bases = 116,531,113 bp number of sequenced bases = 116,494,030 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,768 duplication rate = 3.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3423 >>>>>>> ACTG content number of A's = 32,985,351 bp (28.32%) number of C's = 22,047,676 bp (18.93%) number of T's = 35,714,234 bp (30.66%) number of G's = 25,745,490 bp (22.1%) number of N's = 1,279 bp (0%) GC percentage = 41.03% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 954,176 number of insertions = 8,479 mapped reads with insertion percentage = 0.45% number of deletions = 23,319 mapped reads with deletion percentage = 1.24% homopolymer indels = 46.75% >>>>>>> Coverage mean coverageData = 0.0376X std coverageData = 0.2864X There is a 3.28% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% 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 9730326 0.03903832199479254 0.3944705362530813 chr2 243199373 10780817 0.04432913155577913 0.3510311736160679 chr3 198022430 8752710 0.044200598891751805 0.23306042241293903 chr4 191154276 8123117 0.042495083918499425 0.23794826534577715 chr5 180915260 7487926 0.04138913433836372 0.2263802908264143 chr6 171115067 5720102 0.033428394707054054 0.2535368864940285 chr7 159138663 6870707 0.043174341611755276 0.3849246705071779 chr8 146364022 4824488 0.03296225352429848 0.306358719231682 chr9 141213431 5182430 0.03669927119042947 0.27100436800269156 chr10 135534747 5507044 0.04063197166701466 0.30093073367669604 chr11 135006516 5440680 0.040299388216195435 0.2547824421137956 chr12 133851895 5213486 0.03894966148966363 0.22142663986967603 chr13 115169878 3916303 0.03400457713430937 0.20576470704793348 chr14 107349540 3845467 0.035821923410198124 0.22221690207698283 chr15 102531392 3630811 0.03541170103298705 0.21293156163879084 chr16 90354753 1614862 0.0178724632228257 0.17050182858864005 chr17 81195210 2618248 0.032246335713646164 0.22049034742016382 chr18 78077248 3557682 0.0455661808162091 0.4997321620054762 chr19 59128983 1559213 0.02636969081643092 0.28222286239741623 chr20 63025520 1199913 0.019038525981221573 0.17137899770333956 chr21 48129895 1680738 0.03492087402226828 0.21600827395762182 chr22 51304566 1296770 0.025275917936816775 0.1766589354466973 chrMT 16571 261188 15.761752459115321 8.887686681765846 chrX 155270560 7411902 0.047735398133425935 0.2588757348174576 chrY 59373566 304183 0.005123205838773437 0.10920474523977355