BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068146.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 = 4,789,609 number of mapped reads = 4,346,209 (90.74%) number of supplementary alignments = 35,620 (0.74%) number of secondary alignments = 0 number of mapped bases = 280,688,888 bp number of sequenced bases = 280,574,930 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 596,891 duplication rate = 11.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4919 >>>>>>> ACTG content number of A's = 74,176,902 bp (26.44%) number of C's = 50,202,790 bp (17.89%) number of T's = 91,584,419 bp (32.64%) number of G's = 64,578,211 bp (23.02%) number of N's = 32,608 bp (0.01%) GC percentage = 40.91% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 1,583,039 number of insertions = 18,494 mapped reads with insertion percentage = 0.42% number of deletions = 64,317 mapped reads with deletion percentage = 1.47% homopolymer indels = 45.09% >>>>>>> Coverage mean coverageData = 0.0907X std coverageData = 0.8631X There is a 6.42% of reference with a coverageData >= 1X There is a 1.71% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 23785395 0.09542762583528328 1.8949694625716273 chr2 243199373 21929465 0.09017073000430803 1.2176119038126916 chr3 198022430 17933858 0.09056478096950936 0.40483936837085205 chr4 191154276 19067042 0.09974687670601728 0.4616231759641952 chr5 180915260 18439654 0.1019242600099074 0.4305747896600123 chr6 171115067 16252852 0.0949820041270825 0.5215143932057491 chr7 159138663 14918577 0.09374577314376456 0.8311033545152728 chr8 146364022 12607160 0.086135648827688 1.000758756921734 chr9 141213431 10578923 0.07491442510167465 0.650450680159689 chr10 135534747 13445411 0.09920268637827612 0.7100296220496255 chr11 135006516 13461197 0.09970775780926011 0.6485103823961271 chr12 133851895 13141149 0.0981767871123528 0.44178092911571487 chr13 115169878 9739208 0.08456384750186155 0.40487732492406237 chr14 107349540 8898507 0.08289282841826802 0.42248542204584033 chr15 102531392 8463864 0.08254900118785084 0.41530883691683057 chr16 90354753 7708156 0.08530991169883448 0.4613710945080245 chr17 81195210 6837282 0.08420794773484791 0.4528111708184463 chr18 78077248 7887574 0.10102269485727776 1.4457353043307855 chr19 59128983 5357744 0.09061113058548631 1.2341827521105135 chr20 63025520 5759774 0.09138796474824801 0.44429947966781974 chr21 48129895 3978303 0.08265762890195376 0.42121050345103067 chr22 51304566 3019021 0.05884507433509914 0.31728965898577677 chrMT 16571 247860 14.957455796270594 9.158619110308283 chrX 155270560 16313463 0.10506475277734556 0.522497147284464 chrY 59373566 917449 0.015452145825298753 0.42693899326344786