BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231785.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 = 1,584,079 number of mapped reads = 1,311,219 (82.77%) number of supplementary alignments = 7,995 (0.5%) number of secondary alignments = 0 number of mapped bases = 79,915,234 bp number of sequenced bases = 79,885,428 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,366 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.607 >>>>>>> ACTG content number of A's = 22,988,069 bp (28.78%) number of C's = 15,911,915 bp (19.92%) number of T's = 21,284,596 bp (26.64%) number of G's = 19,694,103 bp (24.65%) number of N's = 6,745 bp (0.01%) GC percentage = 44.57% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 529,918 number of insertions = 5,877 mapped reads with insertion percentage = 0.44% number of deletions = 17,935 mapped reads with deletion percentage = 1.35% homopolymer indels = 43.25% >>>>>>> Coverage mean coverageData = 0.0258X std coverageData = 6.0662X There is a 2.23% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 6768785 0.027156542169658224 0.4650012240531009 chr2 243199373 8874080 0.03648890986244442 21.625482235014374 chr3 198022430 6402651 0.032332958443142025 0.19488083971490183 chr4 191154276 3577801 0.01871682431001439 0.16354310706198713 chr5 180915260 4306459 0.023803735516838103 0.16943428754713813 chr6 171115067 5083014 0.029705239223615534 0.2148071065194946 chr7 159138663 4597057 0.028887115885848556 0.35085773953371363 chr8 146364022 4803885 0.03282148805667557 0.2891906746888335 chr9 141213431 3790488 0.026842262617356845 0.23342519892772962 chr10 135534747 3084847 0.022760561909633402 0.2254077384381096 chr11 135006516 2944490 0.021809984341792807 0.22663505350668356 chr12 133851895 2695486 0.02013782472037471 0.1573572382286615 chr13 115169878 2347083 0.020379313070037288 0.15470970054858313 chr14 107349540 3359102 0.031291256581071514 0.23760183850921757 chr15 102531392 1742573 0.016995507093086185 0.14513207690467053 chr16 90354753 2068475 0.022892818931174546 0.1781734551266868 chr17 81195210 1993909 0.024556978176421985 0.18545318706707284 chr18 78077248 1790918 0.022937770552568657 0.4070012799451595 chr19 59128983 2028827 0.03431188728546202 0.304584542848241 chr20 63025520 1773269 0.028135729780571425 0.18501882294058875 chr21 48129895 1251151 0.025995298763897157 0.1856698409172033 chr22 51304566 871951 0.01699558281030971 0.1415750278733042 chrMT 16571 66865 4.035061251584093 2.942369142270538 chrX 155270560 3366540 0.021681766330977358 0.17821527553886063 chrY 59373566 325528 0.0054827092581907575 0.09964119186535475