BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927018.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 31,836,442 number of mapped reads = 31,237,002 (98.12%) number of supplementary alignments = 356,509 (1.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,676,016 number of mapped paired reads (second in pair) = 15,560,986 number of mapped paired reads (both in pair) = 30,900,382 number of mapped paired reads (singletons) = 336,620 number of mapped bases = 2,954,535,411 bp number of sequenced bases = 2,952,280,480 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,269,094 duplication rate = 5.4% >>>>>>> Insert size mean insert size = 120,653.0257 std insert size = 3,416,780.2356 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 53.3855 >>>>>>> ACTG content number of A's = 855,405,583 bp (28.97%) number of C's = 582,047,824 bp (19.72%) number of T's = 863,039,539 bp (29.23%) number of G's = 651,629,561 bp (22.07%) number of N's = 157,973 bp (0.01%) GC percentage = 41.79% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 27,220,327 number of insertions = 490,545 mapped reads with insertion percentage = 1.54% number of deletions = 1,576,590 mapped reads with deletion percentage = 4.92% homopolymer indels = 53.04% >>>>>>> Coverage mean coverageData = 0.9544X std coverageData = 4.4004X There is a 36.17% of reference with a coverageData >= 1X There is a 20.88% of reference with a coverageData >= 2X There is a 12.55% of reference with a coverageData >= 3X There is a 7.92% of reference with a coverageData >= 4X There is a 5.13% of reference with a coverageData >= 5X There is a 3.39% of reference with a coverageData >= 6X There is a 2.28% of reference with a coverageData >= 7X There is a 1.55% of reference with a coverageData >= 8X There is a 1.07% of reference with a coverageData >= 9X There is a 0.75% of reference with a coverageData >= 10X There is a 0.53% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 234894241 0.9424018285595365 5.931467582530032 chr2 243199373 261434798 1.074981381633743 7.0429030559891945 chr3 198022430 199417531 1.0070451665500721 2.288312323018214 chr4 191154276 184981430 0.9677075180886877 2.9082256453597437 chr5 180915260 183818672 1.0160484637945963 1.919392722620978 chr6 171115067 172211259 1.0064061687799823 1.9933181908334587 chr7 159138663 153907981 0.9671312935436689 2.704206863071215 chr8 146364022 149612363 1.0221935756862435 2.261973288791177 chr9 141213431 126929311 0.8988472987388856 4.898772712432465 chr10 135534747 148428246 1.095130579319265 9.977684989690244 chr11 135006516 140076696 1.0375550762305428 5.479297595804686 chr12 133851895 131825853 0.9848635538555506 1.9425386789700798 chr13 115169878 93714706 0.8137084767946008 1.731075865709021 chr14 107349540 90159137 0.8398651452069567 1.8388221865797678 chr15 102531392 83141724 0.8108904246613564 1.779665379518422 chr16 90354753 91426427 1.0118607374201998 5.849058817513033 chr17 81195210 70404403 0.8671004484131515 2.3976262018402146 chr18 78077248 78848167 1.0098737983183015 5.141478864787422 chr19 59128983 41909638 0.70878333895917 3.4243274653791635 chr20 63025520 65344420 1.0367930324097285 2.1513437553859656 chr21 48129895 38785204 0.805844351000558 2.315590096666028 chr22 51304566 34282720 0.6682196668421286 1.7125782797355682 chrMT 16571 4902953 295.87550540100176 217.44275823296513 chrX 155270560 169178975 1.089575351566968 2.593730147228838 chrY 59373566 4898556 0.08250398839106278 2.4911973461149834