BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237295.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 = 2,586,837 number of mapped reads = 2,271,152 (87.8%) number of supplementary alignments = 18,224 (0.7%) number of secondary alignments = 0 number of mapped bases = 150,792,914 bp number of sequenced bases = 150,733,108 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 156,737 duplication rate = 5.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5421 >>>>>>> ACTG content number of A's = 41,284,442 bp (27.39%) number of C's = 27,995,623 bp (18.57%) number of T's = 47,546,930 bp (31.54%) number of G's = 33,903,790 bp (22.49%) number of N's = 2,323 bp (0%) GC percentage = 41.07% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,148,764 number of insertions = 11,092 mapped reads with insertion percentage = 0.48% number of deletions = 34,287 mapped reads with deletion percentage = 1.49% homopolymer indels = 47.13% >>>>>>> Coverage mean coverageData = 0.0487X std coverageData = 0.4297X There is a 3.6% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 16131080 0.06471831418225434 0.559026447635413 chr2 243199373 13729837 0.0564550674232207 0.4938646038302253 chr3 198022430 7286187 0.03679475602839537 0.24278750114878975 chr4 191154276 2963314 0.015502211417964828 0.27364153408555225 chr5 180915260 8130665 0.04494184183246897 0.27146278073230135 chr6 171115067 20476269 0.11966374065703986 0.6390579957916153 chr7 159138663 10464302 0.06575587479957652 0.7798627513759494 chr8 146364022 10734282 0.07333962167287258 0.5864782703102068 chr9 141213431 7445121 0.05272247085335672 0.3914680869771141 chr10 135534747 5581047 0.04117797925280371 0.45517968126103275 chr11 135006516 4533049 0.03357652011403657 0.29492120600536553 chr12 133851895 4032190 0.030124265330722436 0.23780497367488296 chr13 115169878 9172622 0.07964427990450768 0.3759137572538638 chr14 107349540 4408122 0.04106325933022163 0.2924359510304054 chr15 102531392 6931689 0.06760552904616764 0.3406065877949865 chr16 90354753 1905044 0.021084048561341315 0.22294426084337945 chr17 81195210 2939288 0.03620026353771361 0.2524909931072245 chr18 78077248 1688557 0.02162674842228046 0.6022258221326391 chr19 59128983 2760606 0.046687865407730754 0.4213024895250665 chr20 63025520 1240569 0.01968359800918739 0.19278776288483873 chr21 48129895 2233079 0.04639692232862756 0.32539521187409437 chr22 51304566 1284203 0.0250309689784726 0.19628302232489184 chrMT 16571 36527 2.204272524289421 2.324683355028731 chrX 155270560 4375808 0.02818182661284921 0.2322585805098727 chrY 59373566 309457 0.0052120332472535 0.23410893877208638