BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716860.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 = 2,017,782 number of mapped reads = 1,894,901 (93.91%) number of supplementary alignments = 43,922 (2.18%) number of secondary alignments = 0 number of mapped bases = 146,487,120 bp number of sequenced bases = 146,426,559 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,205 duplication rate = 3.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1271 >>>>>>> ACTG content number of A's = 35,473,081 bp (24.23%) number of C's = 30,028,622 bp (20.51%) number of T's = 43,805,562 bp (29.92%) number of G's = 37,113,713 bp (25.35%) number of N's = 5,581 bp (0%) GC percentage = 45.85% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 992,786 number of insertions = 12,925 mapped reads with insertion percentage = 0.67% number of deletions = 29,178 mapped reads with deletion percentage = 1.51% homopolymer indels = 38.83% >>>>>>> Coverage mean coverageData = 0.0473X std coverageData = 0.3975X There is a 3.91% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 15621916 0.06267553491872745 0.7964204103649588 chr2 243199373 13344852 0.054872065809149925 0.40569095769820557 chr3 198022430 9102381 0.04596641400673651 0.2512271822981916 chr4 191154276 6898032 0.036086202957866347 0.3367077859558061 chr5 180915260 7343985 0.04059350770078765 0.23707841939392157 chr6 171115067 9713443 0.05676556232187315 0.29760016441533726 chr7 159138663 8957710 0.05628870967704435 0.5062465681314056 chr8 146364022 8840719 0.06040226880346319 0.4057646161443024 chr9 141213431 4350193 0.030805802034510443 0.27580404219792654 chr10 135534747 7608764 0.05613884386414946 0.5338514142922565 chr11 135006516 6058959 0.044879011617483706 0.3247492340344585 chr12 133851895 6580609 0.04916336074285687 0.2617225445701856 chr13 115169878 2676139 0.02323644903053557 0.1741494771128244 chr14 107349540 2813558 0.026209315848023197 0.2081261306738817 chr15 102531392 2935518 0.02863043154627219 0.1949661352022422 chr16 90354753 4460892 0.04937086154172764 0.2794986241277448 chr17 81195210 3689444 0.04543918292717021 0.2843923260786751 chr18 78077248 3971506 0.050866367626072065 0.4252546930445751 chr19 59128983 3597945 0.06084909324417097 0.5709838103357362 chr20 63025520 3846218 0.061026358846384764 0.30728637333913333 chr21 48129895 2248392 0.04671508217501825 0.3128897094119998 chr22 51304566 2262860 0.044106405655980015 0.26791398909679853 chrMT 16571 68043 4.106149296964577 3.56050643439407 chrX 155270560 8992153 0.05791280072667993 0.2991168182087017 chrY 59373566 502889 0.008469914035481715 0.3043379373618325