BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238651.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,096,524 number of mapped reads = 2,511,252 (81.1%) number of supplementary alignments = 19,973 (0.65%) number of secondary alignments = 0 number of mapped bases = 149,254,891 bp number of sequenced bases = 149,161,417 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,182,725 duplication rate = 24.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2459 >>>>>>> ACTG content number of A's = 36,452,166 bp (24.44%) number of C's = 24,337,424 bp (16.32%) number of T's = 52,665,246 bp (35.31%) number of G's = 35,703,418 bp (23.94%) number of N's = 3,163 bp (0%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 1,026,240 number of insertions = 9,839 mapped reads with insertion percentage = 0.39% number of deletions = 56,212 mapped reads with deletion percentage = 2.21% homopolymer indels = 41.04% >>>>>>> Coverage mean coverageData = 0.0482X std coverageData = 1.0486X There is a 1.28% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.33% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.18% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 15838412 0.06354412252397157 0.8810389301120026 chr2 243199373 22117916 0.09094561275863158 2.2832447197601775 chr3 198022430 4786615 0.024172084950174585 0.48135202402645044 chr4 191154276 14372520 0.07518806432559218 0.8492871885602988 chr5 180915260 6422714 0.0355012285862453 0.5497274074067834 chr6 171115067 9561012 0.05587475239687689 1.0328464202469543 chr7 159138663 8940591 0.05618113682405387 0.8729123386979603 chr8 146364022 10379315 0.0709143876901661 1.5135428190150517 chr9 141213431 5536445 0.03920622111362764 0.620316463293309 chr10 135534747 3915277 0.028887625399854105 0.49106076383190206 chr11 135006516 6469485 0.047919798182185516 0.6681830858499216 chr12 133851895 2099925 0.015688421893466656 0.3433943652849252 chr13 115169878 2171611 0.01885572024310037 0.6230268946708777 chr14 107349540 2234820 0.020818160934830274 0.4584117816733983 chr15 102531392 6310477 0.06154677974136936 0.923395940018609 chr16 90354753 3527269 0.03903800168652998 0.6116536593791481 chr17 81195210 6848892 0.08435093646534075 0.9373339817203744 chr18 78077248 4956120 0.06347713484983487 2.587426014541864 chr19 59128983 1929200 0.03262697753485799 0.5919579371809235 chr20 63025520 1953760 0.030999506231761356 0.5272946511928316 chr21 48129895 1399590 0.029079431816753393 0.4928758856675977 chr22 51304566 1942494 0.03786201017663808 0.5813006154171224 chrMT 16571 11773 0.7104580290869591 2.4444241889595224 chrX 155270560 4981811 0.03208471071399498 0.5186968359166886 chrY 59373566 546847 0.009210277179578535 0.3847019898078949