BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716428.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 = 1,540,215 number of mapped reads = 1,424,863 (92.51%) number of supplementary alignments = 6,069 (0.39%) number of secondary alignments = 0 number of mapped bases = 83,582,108 bp number of sequenced bases = 83,557,301 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,252 duplication rate = 3.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1121 >>>>>>> ACTG content number of A's = 21,216,048 bp (25.39%) number of C's = 15,060,201 bp (18.02%) number of T's = 26,097,824 bp (31.23%) number of G's = 21,181,506 bp (25.35%) number of N's = 1,722 bp (0%) GC percentage = 43.37% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 399,906 number of insertions = 5,483 mapped reads with insertion percentage = 0.38% number of deletions = 14,913 mapped reads with deletion percentage = 1.04% homopolymer indels = 44.7% >>>>>>> Coverage mean coverageData = 0.027X std coverageData = 0.2605X There is a 2.4% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% 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 7405438 0.029710810630237106 0.39856598609220834 chr2 243199373 6448102 0.02651364565812429 0.3723101346639238 chr3 198022430 4597930 0.02321923834587829 0.1674524864568834 chr4 191154276 5014797 0.026234291510172654 0.22113165633435872 chr5 180915260 4661995 0.025768942874138976 0.1762352281953269 chr6 171115067 4358083 0.025468727426556773 0.1976775590618407 chr7 159138663 4640003 0.0291569811667954 0.2979960445384034 chr8 146364022 4306600 0.029423897629705747 0.3765818556144145 chr9 141213431 2741720 0.019415433649508877 0.18042105254322893 chr10 135534747 3729269 0.027515224564517025 0.28937249424834977 chr11 135006516 2952665 0.021870536974674615 0.19819765359518296 chr12 133851895 4175715 0.031196532555627994 0.19525520615961614 chr13 115169878 2465143 0.02140440749620313 0.16220352554371303 chr14 107349540 2764573 0.02575300276088747 0.18015567109092745 chr15 102531392 3118109 0.030411261752888327 0.19138288697950587 chr16 90354753 2828209 0.0313011646437681 0.20180443049660063 chr17 81195210 3720879 0.04582633630727724 0.24736328617091657 chr18 78077248 1496457 0.019166364572685758 0.27159546016430164 chr19 59128983 2543480 0.04301579142668495 0.32977882125131264 chr20 63025520 2809637 0.044579354521787365 0.24301337542824936 chr21 48129895 1064950 0.022126580579492225 0.20455640723045107 chr22 51304566 1041096 0.02029246285798422 0.15767973253268552 chrMT 16571 14731 0.8889626455856617 1.113272424608305 chrX 155270560 4360463 0.028082999121018175 0.1958509313423777 chrY 59373566 322064 0.005424366796496609 0.2605068189687074