BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716235.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 = 1,659,650 number of mapped reads = 1,559,494 (93.97%) number of supplementary alignments = 24,172 (1.46%) number of secondary alignments = 0 number of mapped bases = 123,999,863 bp number of sequenced bases = 123,947,351 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,053 duplication rate = 2.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2568 >>>>>>> ACTG content number of A's = 31,500,865 bp (25.41%) number of C's = 23,699,393 bp (19.12%) number of T's = 37,546,299 bp (30.29%) number of G's = 31,193,638 bp (25.17%) number of N's = 7,156 bp (0.01%) GC percentage = 44.29% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 974,365 number of insertions = 11,206 mapped reads with insertion percentage = 0.71% number of deletions = 29,973 mapped reads with deletion percentage = 1.89% homopolymer indels = 44.13% >>>>>>> Coverage mean coverageData = 0.0401X std coverageData = 0.4339X There is a 3.45% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 9822305 0.03940734414459092 0.6869513639927827 chr2 243199373 11208278 0.04608678822539563 0.6315705121660329 chr3 198022430 8244794 0.041635657132376366 0.23039668154098122 chr4 191154276 7987587 0.041786075452479025 0.25748190002288673 chr5 180915260 7604698 0.04203458569498228 0.23572226166171234 chr6 171115067 7313846 0.04274226769288528 0.2759406621545036 chr7 159138663 7251048 0.04556433906950695 0.6066623790828912 chr8 146364022 6447964 0.04405429634886639 0.581734680359902 chr9 141213431 5480886 0.038812781200677715 0.4726430007040145 chr10 135534747 6052636 0.044657448617216954 0.41983638822683916 chr11 135006516 5788808 0.04287798968162396 0.4231289781678272 chr12 133851895 5775851 0.04315105886248379 0.24085712193666875 chr13 115169878 3876239 0.03365670839731201 0.20484432786533138 chr14 107349540 3837503 0.0357477358542943 0.27024648879763746 chr15 102531392 3691351 0.036002154345080965 0.21505382405457457 chr16 90354753 3800883 0.042066220910370926 0.268338414172022 chr17 81195210 3521320 0.04336856817046227 0.26124752027324777 chr18 78077248 3505425 0.0448968821237142 0.8842540223607762 chr19 59128983 2769336 0.04683550873858257 0.5001001351231213 chr20 63025520 2669847 0.04236136409505229 0.24790470661031244 chr21 48129895 1677265 0.03484871512809243 0.23535172566180934 chr22 51304566 1456128 0.02838203523639592 0.18913909586907862 chrMT 16571 32875 1.9838875143322672 1.8719054126687595 chrX 155270560 3883718 0.025012584484785782 0.2631825841848144 chrY 59373566 299272 0.0050404922621625926 0.16909885005004027