BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231807.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 = 5,749,840 number of mapped reads = 4,990,011 (86.79%) number of supplementary alignments = 33,603 (0.58%) number of secondary alignments = 0 number of mapped bases = 321,215,151 bp number of sequenced bases = 321,090,139 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 462,975 duplication rate = 6.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4492 >>>>>>> ACTG content number of A's = 82,750,179 bp (25.77%) number of C's = 58,037,974 bp (18.08%) number of T's = 104,300,583 bp (32.48%) number of G's = 75,877,988 bp (23.63%) number of N's = 123,415 bp (0.04%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 2,088,311 number of insertions = 21,871 mapped reads with insertion percentage = 0.43% number of deletions = 72,011 mapped reads with deletion percentage = 1.43% homopolymer indels = 44.3% >>>>>>> Coverage mean coverageData = 0.1038X std coverageData = 1.3536X There is a 8.09% of reference with a coverageData >= 1X There is a 1.47% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 27294495 0.10950622666653256 3.179545057237784 chr2 243199373 17718901 0.07285751102656009 1.8218010610693558 chr3 198022430 25800972 0.1302931794140694 0.45315505120911703 chr4 191154276 16003747 0.08372162702758477 0.44945996703490176 chr5 180915260 23648072 0.1307135285326401 0.48308501544663673 chr6 171115067 25248696 0.14755390301194224 0.8650304546067387 chr7 159138663 21054837 0.13230497606983163 2.0005502251542064 chr8 146364022 18741144 0.12804474585974415 1.5943072966521643 chr9 141213431 8231896 0.05829400179363959 0.877266281884696 chr10 135534747 16009916 0.11812407042748971 0.9329051499206433 chr11 135006516 12132396 0.08986526250332984 0.9021896592111269 chr12 133851895 10180022 0.0760543733803694 0.3954529706469102 chr13 115169878 8907082 0.07733864231409536 0.39025153426515097 chr14 107349540 12353841 0.11508052107163198 0.4799262059096487 chr15 102531392 10649096 0.10386181043947984 0.4598571024692812 chr16 90354753 9335693 0.10332265531177978 0.5388890639996047 chr17 81195210 7057528 0.08692049691108626 0.4814473716078675 chr18 78077248 8557420 0.10960196752836371 2.0389253836253958 chr19 59128983 9017371 0.15250340091254402 1.7256208777671371 chr20 63025520 6540659 0.10377794582258107 0.5026172544121237 chr21 48129895 8270367 0.1718343038147081 0.5670287360557361 chr22 51304566 2345256 0.04571242255513866 0.25534083824676124 chrMT 16571 443368 26.755657473900186 15.572468076676092 chrX 155270560 14765118 0.09509283665879739 0.6095814571752185 chrY 59373566 907258 0.015280503785135627 0.3774535411104333