BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234097.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 = 4,412,854 number of mapped reads = 4,137,120 (93.75%) number of supplementary alignments = 36,406 (0.82%) number of secondary alignments = 0 number of mapped bases = 260,293,446 bp number of sequenced bases = 260,199,401 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 737,216 duplication rate = 14.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7258 >>>>>>> ACTG content number of A's = 65,964,827 bp (25.35%) number of C's = 47,073,447 bp (18.09%) number of T's = 85,242,546 bp (32.76%) number of G's = 61,893,646 bp (23.79%) number of N's = 24,935 bp (0.01%) GC percentage = 41.88% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,408,971 number of insertions = 16,113 mapped reads with insertion percentage = 0.39% number of deletions = 54,506 mapped reads with deletion percentage = 1.31% homopolymer indels = 43.72% >>>>>>> Coverage mean coverageData = 0.0841X std coverageData = 0.8832X There is a 5.12% of reference with a coverageData >= 1X There is a 1.84% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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% 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 26307009 0.10554440704883941 1.4824382068095414 chr2 243199373 15058109 0.06191672624090194 1.7818717717880064 chr3 198022430 23715731 0.11976285211730812 0.5288807470597273 chr4 191154276 12188785 0.06376412421974803 0.39460498019999923 chr5 180915260 10928096 0.06040450098018266 0.3830038259964156 chr6 171115067 18457778 0.10786763739513365 0.758795381698158 chr7 159138663 19778846 0.12428686798757382 1.2083310249974464 chr8 146364022 14015996 0.09576121104406382 0.71711578476912 chr9 141213431 8432928 0.05971760575663656 0.4950616736608447 chr10 135534747 6662593 0.0491578222372747 0.4914574940066199 chr11 135006516 8964511 0.06640058025051176 0.49932289560614496 chr12 133851895 6509222 0.04863003246984288 0.34737866527344935 chr13 115169878 10442684 0.09067200713714396 0.5290472782881273 chr14 107349540 14587677 0.13588951568865595 0.5897947077607378 chr15 102531392 5897348 0.05751748693707387 0.4324195357886056 chr16 90354753 7057061 0.07810392664124709 0.47081804790155996 chr17 81195210 9101702 0.11209653869975827 0.5476816640218718 chr18 78077248 4495514 0.05757777220836472 1.5266224008227496 chr19 59128983 8213612 0.1389100840783952 0.9990032565508529 chr20 63025520 8916612 0.1414762147142935 0.5954590687274457 chr21 48129895 5224322 0.10854629955041456 0.5170716473926603 chr22 51304566 2801593 0.05460708896748098 0.34449904196841236 chrMT 16571 218357 13.177056303180255 11.714221840477045 chrX 155270560 11759198 0.07573359689048587 0.46074843860944603 chrY 59373566 558162 0.009400850203270594 0.2516067728873432