BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238497.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 = 3,631,495 number of mapped reads = 2,821,536 (77.7%) number of supplementary alignments = 23,743 (0.65%) number of secondary alignments = 0 number of mapped bases = 173,575,245 bp number of sequenced bases = 173,501,838 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,020,279 duplication rate = 20.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6116 >>>>>>> ACTG content number of A's = 42,660,948 bp (24.59%) number of C's = 30,897,145 bp (17.81%) number of T's = 57,978,634 bp (33.42%) number of G's = 41,953,542 bp (24.18%) number of N's = 11,569 bp (0.01%) GC percentage = 41.99% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 1,038,302 number of insertions = 12,593 mapped reads with insertion percentage = 0.44% number of deletions = 43,214 mapped reads with deletion percentage = 1.52% homopolymer indels = 41.49% >>>>>>> Coverage mean coverageData = 0.0561X std coverageData = 1.005X There is a 1.84% of reference with a coverageData >= 1X There is a 0.98% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.36% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.2% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 12414487 0.04980724601685145 0.8118495029903875 chr2 243199373 11006926 0.045258858459310256 2.301682132571424 chr3 198022430 15928828 0.08043951384699198 0.7452429871711186 chr4 191154276 8658702 0.04529693073672074 0.5479991174585644 chr5 180915260 8177978 0.04520336206022643 0.5458634166603226 chr6 171115067 7615147 0.04450307698503253 0.8804360797105527 chr7 159138663 6760260 0.0424803116512296 0.6846311345907116 chr8 146364022 17657709 0.12064241443160123 1.1986627245101975 chr9 141213431 6210964 0.04398281350447466 0.6542094546850252 chr10 135534747 5414938 0.03995239685657878 0.573533065456387 chr11 135006516 5421551 0.04015769875877695 0.5528523278752975 chr12 133851895 6465140 0.04830069832033383 0.5749297980447036 chr13 115169878 7605246 0.06603502697120162 0.8090909088186565 chr14 107349540 4114792 0.038330783718309364 0.5060454361537724 chr15 102531392 10177069 0.09925807893059718 0.8902978074395373 chr16 90354753 5245530 0.05805483193562601 0.6681172948636946 chr17 81195210 7405008 0.09120005970795568 0.8352031473835635 chr18 78077248 6163864 0.07894571284069848 2.2687417135312318 chr19 59128983 2795186 0.047272688589959345 0.7052258322808668 chr20 63025520 2662050 0.04223765230338441 0.5475235699545736 chr21 48129895 4262460 0.08856158942378745 0.7869256351100081 chr22 51304566 2801718 0.054609525397797926 0.6063421922862635 chrMT 16571 46874 2.828676603705268 4.361575353657296 chrX 155270560 8022817 0.051669917336551116 0.5897104944227562 chrY 59373566 540001 0.009094973342177223 0.37765941586339474