BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013313.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 = 1,454,104 number of mapped reads = 1,179,884 (81.14%) number of supplementary alignments = 10,243 (0.7%) number of secondary alignments = 0 number of mapped bases = 75,610,077 bp number of sequenced bases = 75,576,418 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,695 duplication rate = 4.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3339 >>>>>>> ACTG content number of A's = 20,025,183 bp (26.5%) number of C's = 14,151,725 bp (18.73%) number of T's = 23,744,542 bp (31.42%) number of G's = 17,645,895 bp (23.35%) number of N's = 9,073 bp (0.01%) GC percentage = 42.07% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 577,351 number of insertions = 4,825 mapped reads with insertion percentage = 0.41% number of deletions = 19,545 mapped reads with deletion percentage = 1.64% homopolymer indels = 45.11% >>>>>>> Coverage mean coverageData = 0.0244X std coverageData = 0.2375X There is a 1.99% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.07% 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 5534634 0.022205096130934014 0.3256979510927688 chr2 243199373 7403850 0.03044354065830589 0.31108250109240765 chr3 198022430 4678668 0.023626959834802553 0.18266294214259296 chr4 191154276 4500753 0.023545133774564374 0.18429045475357494 chr5 180915260 4079757 0.022550651614463037 0.1783600676936721 chr6 171115067 4037963 0.023597939508155644 0.21819833396835323 chr7 159138663 4907531 0.030838081126771815 0.367281726226693 chr8 146364022 4006524 0.027373694335893557 0.2388534094491004 chr9 141213431 2746167 0.01944692498831786 0.1942966479379251 chr10 135534747 4095936 0.030220560340884394 0.26356871653407665 chr11 135006516 3237508 0.02398038328757406 0.20309844803394472 chr12 133851895 3845862 0.028732219293570702 0.2025189442633137 chr13 115169878 1757902 0.015263557021394083 0.14703234333937953 chr14 107349540 2349603 0.021887406317716872 0.18153443849650427 chr15 102531392 2117566 0.02065285527382677 0.17123906477811796 chr16 90354753 2499972 0.02766840611030169 0.20581106520689318 chr17 81195210 1986036 0.024460014328431444 0.19542532050925243 chr18 78077248 1768413 0.022649530372791826 0.28637646930561445 chr19 59128983 1569568 0.02654481643968069 0.2827959518443456 chr20 63025520 1952328 0.030976785276821198 0.2129677669672618 chr21 48129895 1237132 0.025704024494547516 0.19405539928429466 chr22 51304566 758647 0.014787124405262487 0.14341123745250267 chrMT 16571 158272 9.551143564057691 6.619027965239575 chrX 155270560 4216656 0.02715682869952939 0.20714027311916178 chrY 59373566 162829 0.002742449392377746 0.06799017865943718