BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004076.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 = 2,101,743 number of mapped reads = 1,921,272 (91.41%) number of supplementary alignments = 12,833 (0.61%) number of secondary alignments = 0 number of mapped bases = 129,537,021 bp number of sequenced bases = 129,481,471 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,395 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2902 >>>>>>> ACTG content number of A's = 36,751,497 bp (28.38%) number of C's = 23,794,264 bp (18.38%) number of T's = 41,098,042 bp (31.74%) number of G's = 27,814,424 bp (21.48%) number of N's = 23,244 bp (0.02%) GC percentage = 39.86% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,108,710 number of insertions = 9,423 mapped reads with insertion percentage = 0.49% number of deletions = 31,702 mapped reads with deletion percentage = 1.63% homopolymer indels = 46.69% >>>>>>> Coverage mean coverageData = 0.0418X std coverageData = 0.3629X There is a 3.55% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 9602760 0.03852652387172989 0.7142928653178047 chr2 243199373 13223296 0.05437224544160318 0.38980907679221133 chr3 198022430 10093130 0.05096963005655471 0.2555248354232008 chr4 191154276 8730306 0.04567151822436868 0.2679300356699016 chr5 180915260 8244413 0.04557057818118825 0.24423608744602562 chr6 171115067 6688178 0.03908585092626589 0.24257663130976237 chr7 159138663 6105553 0.03836624541705494 0.40384635870704466 chr8 146364022 11117379 0.07595704769577868 0.5061377958021515 chr9 141213431 5465753 0.03870561717319934 0.3254565515014913 chr10 135534747 5132131 0.03786579540374248 0.3509347037012452 chr11 135006516 4296460 0.03182409358671251 0.240786874998676 chr12 133851895 7490423 0.055960530106802 0.27547963511993817 chr13 115169878 3219378 0.02795329869152071 0.19267928448278382 chr14 107349540 3440053 0.03204534458182122 0.22022460952890363 chr15 102531392 3071390 0.029955606181568274 0.19908293272922598 chr16 90354753 2306253 0.02552442371238622 0.20891388425627672 chr17 81195210 2551275 0.03142149641586 0.21271182067166167 chr18 78077248 3581787 0.04587491352154215 0.5947643903997251 chr19 59128983 1803579 0.030502452578966225 0.46029692047614545 chr20 63025520 2224599 0.035296797233882404 0.2243856810814198 chr21 48129895 1549191 0.0321877078684672 0.2298036014436335 chr22 51304566 740969 0.014442554684119148 0.13295633466634701 chrMT 16571 24660 1.4881419347052078 1.7030128368534272 chrX 155270560 8479895 0.054613669197818314 0.28970500059128645 chrY 59373566 354210 0.0059657861884192705 0.15381717227379504