BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063543.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 = 2,599,950 number of mapped reads = 2,366,911 (91.04%) number of supplementary alignments = 16,684 (0.64%) number of secondary alignments = 0 number of mapped bases = 158,013,402 bp number of sequenced bases = 157,938,349 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,071 duplication rate = 3.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5573 >>>>>>> ACTG content number of A's = 44,815,747 bp (28.38%) number of C's = 29,260,443 bp (18.53%) number of T's = 49,332,256 bp (31.24%) number of G's = 34,526,494 bp (21.86%) number of N's = 3,409 bp (0%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,270,267 number of insertions = 12,545 mapped reads with insertion percentage = 0.53% number of deletions = 45,441 mapped reads with deletion percentage = 1.9% homopolymer indels = 45.58% >>>>>>> Coverage mean coverageData = 0.051X std coverageData = 0.5609X There is a 4.21% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 17075031 0.06850547024314134 1.167340568128435 chr2 243199373 13864178 0.05700745782761537 0.5768571753335566 chr3 198022430 12104159 0.061125191727018 0.2896428677598421 chr4 191154276 8382646 0.043852777847355084 0.25937908887640954 chr5 180915260 7727378 0.0427126932244411 0.24175646368645934 chr6 171115067 7071605 0.041326606265478655 0.2640897466321372 chr7 159138663 12539031 0.0787931151589479 0.9917932352352898 chr8 146364022 4644397 0.03173182136249303 0.870754803061578 chr9 141213431 6126931 0.043387735547619405 0.43434376130035535 chr10 135534747 6689505 0.049356383865164846 0.41090368283446127 chr11 135006516 10326791 0.07649105617983654 0.4354348346595917 chr12 133851895 4707992 0.035173144168037365 0.23536979800409732 chr13 115169878 4004972 0.03477447462434578 0.21637470086740346 chr14 107349540 3907440 0.03639922444008609 0.27520165520883666 chr15 102531392 3164178 0.03086057780235735 0.20978700139328588 chr16 90354753 3701305 0.04096414274963488 0.2780005513986121 chr17 81195210 3602325 0.0443662255445857 0.277157708544082 chr18 78077248 4340177 0.05558824255690979 0.7861317166587464 chr19 59128983 3862962 0.06533110843458952 0.7584860841583457 chr20 63025520 2094475 0.033232173252993394 0.2314522087185739 chr21 48129895 3483633 0.07237981715937672 0.3350917160093243 chr22 51304566 1290487 0.025153453203365955 0.1798138212077042 chrMT 16571 62221 3.7548126244644258 3.1134242444330997 chrX 155270560 12789965 0.08237211870685596 0.3933597787550471 chrY 59373566 449618 0.007572696576789745 0.19154075057187833