BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524659.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 = 1,634,225 number of mapped reads = 1,517,280 (92.84%) number of supplementary alignments = 6,711 (0.41%) number of secondary alignments = 0 number of mapped bases = 90,176,907 bp number of sequenced bases = 90,149,970 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,169 duplication rate = 2.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.835 >>>>>>> ACTG content number of A's = 23,500,893 bp (26.07%) number of C's = 16,267,341 bp (18.04%) number of T's = 28,025,534 bp (31.09%) number of G's = 22,343,652 bp (24.78%) number of N's = 12,550 bp (0.01%) GC percentage = 42.83% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 446,784 number of insertions = 6,340 mapped reads with insertion percentage = 0.42% number of deletions = 16,882 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.49% >>>>>>> Coverage mean coverageData = 0.0291X std coverageData = 0.2724X There is a 2.63% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 7271229 0.029172360617709354 0.471882585157671 chr2 243199373 7621707 0.031339336553306 0.360343040240134 chr3 198022430 5937944 0.029986219237891385 0.18768033179105828 chr4 191154276 5775734 0.030215039500345785 0.21594121752972303 chr5 180915260 5421109 0.02996490732733104 0.18754228120293379 chr6 171115067 5199737 0.03038737085612689 0.21117132813772546 chr7 159138663 4986401 0.03133368664785125 0.318763579320788 chr8 146364022 4552874 0.031106510587690737 0.2982659818915198 chr9 141213431 3769067 0.026690570247528366 0.23126911584767723 chr10 135534747 4403231 0.032487838708991724 0.2911899340516798 chr11 135006516 4109264 0.030437523474792876 0.23347349124478084 chr12 133851895 4070715 0.030412083444914993 0.19121827674436495 chr13 115169878 2857108 0.024807771351463965 0.17087181444237434 chr14 107349540 2710914 0.025253149664171828 0.17699035514597722 chr15 102531392 2598224 0.025340765879780507 0.17377007866710217 chr16 90354753 2638299 0.029199338301550113 0.19797106486994948 chr17 81195210 2473137 0.030459149006450012 0.1982079688916886 chr18 78077248 2377912 0.030455889019039197 0.41310375537157507 chr19 59128983 1878114 0.03176300191058588 0.3696156191119922 chr20 63025520 1923359 0.030517146070353725 0.19503003501359256 chr21 48129895 1190379 0.024732632389910678 0.1948533215909897 chr22 51304566 1072674 0.020907963630371614 0.1558650190891294 chrMT 16571 22067 1.331663749924567 1.2772210403678166 chrX 155270560 5022644 0.03234769037994067 0.21164418450607733 chrY 59373566 293064 0.004935933947440516 0.1743264035888368