BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236080.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 = 7,489,976 number of mapped reads = 6,712,612 (89.62%) number of supplementary alignments = 58,584 (0.78%) number of secondary alignments = 0 number of mapped bases = 448,672,869 bp number of sequenced bases = 448,455,669 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 837,116 duplication rate = 8.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.247 >>>>>>> ACTG content number of A's = 126,155,028 bp (28.13%) number of C's = 83,181,426 bp (18.55%) number of T's = 141,670,093 bp (31.59%) number of G's = 97,444,911 bp (21.73%) number of N's = 4,211 bp (0%) GC percentage = 40.28% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 3,310,437 number of insertions = 35,721 mapped reads with insertion percentage = 0.53% number of deletions = 124,285 mapped reads with deletion percentage = 1.83% homopolymer indels = 47.06% >>>>>>> Coverage mean coverageData = 0.1449X std coverageData = 1.4537X There is a 7.44% of reference with a coverageData >= 1X There is a 3.47% of reference with a coverageData >= 2X There is a 1.66% of reference with a coverageData >= 3X There is a 0.79% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.19% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% of reference with a coverageData >= 16X There is a 0.01% 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% 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 41437750 0.16624933504177708 1.9794109059424971 chr2 243199373 34068048 0.1400827953614831 1.58111177357531 chr3 198022430 26831717 0.13549837258334826 0.6017789208400494 chr4 191154276 22143428 0.11584061033507825 0.8642083638268023 chr5 180915260 24648712 0.13624451580259178 0.6213128066229142 chr6 171115067 49841756 0.2912762556438119 1.396106878644421 chr7 159138663 23288294 0.14633963589351004 1.54085287208256 chr8 146364022 31075367 0.2123156126442057 4.104811726325574 chr9 141213431 19149961 0.1356100539756732 1.197622393041862 chr10 135534747 20167919 0.1488025723765139 1.2565510396293562 chr11 135006516 16727099 0.12389845687151871 1.013021575002071 chr12 133851895 13679118 0.10219592333750672 0.5860852426486652 chr13 115169878 15358257 0.1333530717120322 0.6127680858414553 chr14 107349540 14661178 0.1365742042304047 0.715882274295421 chr15 102531392 12254231 0.11951686952616423 0.6036636447549378 chr16 90354753 10070474 0.11145483403623493 0.6647777262600628 chr17 81195210 11368323 0.14001223717507474 0.8208649769738233 chr18 78077248 14268517 0.1827487182949891 2.1256092030660745 chr19 59128983 6627102 0.11207874148621835 1.2904637812259387 chr20 63025520 7538265 0.11960654985472552 0.6277738285177361 chr21 48129895 7522242 0.156290430303245 0.8435080913955241 chr22 51304566 4377191 0.08531776684359829 0.4582981802333304 chrMT 16571 588756 35.529298171504436 26.543230517603842 chrX 155270560 19817080 0.1276293458334922 0.722102606361709 chrY 59373566 1162084 0.019572413757327628 0.6220058128244177