BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716795.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 = 866,612 number of mapped reads = 619,490 (71.48%) number of supplementary alignments = 608 (0.07%) number of secondary alignments = 0 number of mapped bases = 32,276,869 bp number of sequenced bases = 32,268,637 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,869 duplication rate = 5.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4527 >>>>>>> ACTG content number of A's = 6,887,878 bp (21.35%) number of C's = 5,285,904 bp (16.38%) number of T's = 10,593,827 bp (32.83%) number of G's = 9,500,570 bp (29.44%) number of N's = 458 bp (0%) GC percentage = 45.82% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 226,894 number of insertions = 1,827 mapped reads with insertion percentage = 0.29% number of deletions = 4,913 mapped reads with deletion percentage = 0.79% homopolymer indels = 41.74% >>>>>>> Coverage mean coverageData = 0.0104X std coverageData = 0.1244X There is a 0.94% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 3082483 0.012367002287228002 0.13847865666888493 chr2 243199373 2691750 0.011068079521734622 0.17827907015637326 chr3 198022430 2138003 0.010796771860642252 0.11468424733226704 chr4 191154276 2052590 0.010737871226066635 0.11803555860121838 chr5 180915260 2727332 0.015075190451043212 0.13501605272745118 chr6 171115067 1335820 0.007806559781202669 0.11255811852963855 chr7 159138663 1756425 0.01103707274454103 0.12789084832766764 chr8 146364022 1960193 0.013392587694809315 0.13176558941112915 chr9 141213431 1393855 0.009870555443129201 0.1147616769102578 chr10 135534747 1657363 0.012228325478779254 0.13431108307555326 chr11 135006516 1252092 0.009274307915626829 0.11345999116844349 chr12 133851895 1501615 0.011218481441745745 0.11745838692788257 chr13 115169878 504253 0.004378341010311741 0.07318495323656948 chr14 107349540 1309869 0.012201906035181892 0.12302442992825248 chr15 102531392 600021 0.005852071139344329 0.08511468463437184 chr16 90354753 846183 0.009365118844384424 0.1149930922877273 chr17 81195210 1197872 0.014752988507573292 0.13655174335449458 chr18 78077248 802955 0.01028410991125097 0.12539967996811374 chr19 59128983 850161 0.014378075807595068 0.14955651161070968 chr20 63025520 777404 0.01233474947925856 0.12570560520944293 chr21 48129895 410326 0.008525387391765555 0.10548102473970196 chr22 51304566 362782 0.0070711445059295506 0.09487602336131709 chrMT 16571 9020 0.5443244221833323 0.9205409680630546 chrX 155270560 963314 0.006204099476423606 0.0880828132504524 chrY 59373566 93188 0.0015695200116496288 0.054743361511685795