BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525091.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 3,702,324 number of mapped reads = 3,357,502 (90.69%) number of supplementary alignments = 11,817 (0.32%) number of secondary alignments = 0 number of mapped bases = 197,079,425 bp number of sequenced bases = 197,017,362 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 304,267 duplication rate = 6.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7938 >>>>>>> ACTG content number of A's = 50,973,030 bp (25.87%) number of C's = 36,864,380 bp (18.71%) number of T's = 63,117,356 bp (32.04%) number of G's = 46,043,696 bp (23.37%) number of N's = 18,900 bp (0.01%) GC percentage = 42.08% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 943,542 number of insertions = 16,702 mapped reads with insertion percentage = 0.49% number of deletions = 38,506 mapped reads with deletion percentage = 1.14% homopolymer indels = 42.93% >>>>>>> Coverage mean coverageData = 0.0637X std coverageData = 0.5313X There is a 4.98% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.06% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 16203704 0.06500968356664596 0.9912871191506335 chr2 243199373 17042832 0.07007761487937718 0.71669324472705 chr3 198022430 13466967 0.06800728079137297 0.32684587632606266 chr4 191154276 13229422 0.06920808823549414 0.4316255666880517 chr5 180915260 12311615 0.06805183266464089 0.32409820618098556 chr6 171115067 11573373 0.0676350318116639 0.36963813919427446 chr7 159138663 11048079 0.0694242291076682 0.6339629476990312 chr8 146364022 10108067 0.0690611453680878 0.5569183161160742 chr9 141213431 8492362 0.06013848640218932 0.42356749635232965 chr10 135534747 9865127 0.07278670022529352 0.6445250847261932 chr11 135006516 9141562 0.0677120058412588 0.42508671087638933 chr12 133851895 9111906 0.06807453865333771 0.33328332938890876 chr13 115169878 6281156 0.05453818402065165 0.2896641689903553 chr14 107349540 6027102 0.05614464673067067 0.3044944600222951 chr15 102531392 5912285 0.05766316914921042 0.2991338817835629 chr16 90354753 5960498 0.06596773055203858 0.3654268394993448 chr17 81195210 5319426 0.0655140370965233 0.3549563741122457 chr18 78077248 5338709 0.06837726913735484 0.7981487903131154 chr19 59128983 4134296 0.06991995786567139 0.7182260081629107 chr20 63025520 4331619 0.06872801684143186 0.34701667462891683 chr21 48129895 2712228 0.056352252586464195 0.38126947787134086 chr22 51304566 2455919 0.04786940406044951 0.27298967416011927 chrMT 16571 35845 2.163116287490194 2.0428408363838813 chrX 155270560 6324224 0.040730348367391735 0.31483385035181066 chrY 59373566 651102 0.01096619327193519 0.38694397600351893