BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714223.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 213,536 number of mapped reads = 29,680 (13.9%) number of supplementary alignments = 729 (0.34%) number of secondary alignments = 0 number of mapped bases = 3,112,087 bp number of sequenced bases = 3,084,434 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,504 duplication rate = 41.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 33.0132 >>>>>>> ACTG content number of A's = 322,534 bp (10.46%) number of C's = 227,660 bp (7.38%) number of T's = 276,732 bp (8.97%) number of G's = 2,257,411 bp (73.19%) number of N's = 97 bp (0%) GC percentage = 80.57% >>>>>>> Mismatches and indels general error rate = 0.034 number of mismatches = 88,110 number of insertions = 2,840 mapped reads with insertion percentage = 7.36% number of deletions = 4,269 mapped reads with deletion percentage = 13.84% homopolymer indels = 41.58% >>>>>>> Coverage mean coverageData = 0.001X std coverageData = 2.5589X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 33147 1.329866295498618E-4 0.04471923023949123 chr2 243199373 2116856 0.008704200072094758 9.122891131375852 chr3 198022430 35232 1.77919238744823E-4 0.052606839572389534 chr4 191154276 33030 1.7279236798239345E-4 0.04410680019750183 chr5 180915260 51305 2.835858069684116E-4 0.07213794654881243 chr6 171115067 30737 1.7962766540014855E-4 0.055904329596792306 chr7 159138663 49703 3.1232510731851504E-4 0.12369259262503027 chr8 146364022 54810 3.744772742033558E-4 0.13995542236798503 chr9 141213431 10272 7.274095620550427E-5 0.021058791174114022 chr10 135534747 25833 1.906005697564773E-4 0.059037747493352964 chr11 135006516 53232 3.9429207994671903E-4 0.13478999535875472 chr12 133851895 29777 2.2246229685429555E-4 0.07133880957844198 chr13 115169878 22858 1.9847203450193808E-4 0.06445139465755141 chr14 107349540 29865 2.782033346393473E-4 0.08370193407685318 chr15 102531392 20041 1.9546208833290784E-4 0.05276619478304592 chr16 90354753 15253 1.6881237005871732E-4 0.0529677209765717 chr17 81195210 14978 1.844690099329751E-4 0.07072628233072069 chr18 78077248 9914 1.269768114777816E-4 0.03558574516450069 chr19 59128983 12848 2.1728768783322384E-4 0.05652614648401589 chr20 63025520 11193 1.7759472670753054E-4 0.07357491386413995 chr21 48129895 5756 1.1959303048552256E-4 0.030784948504859813 chr22 51304566 3570 6.958444985189037E-5 0.03588368555540898 chrMT 16571 1631 0.09842495926618793 0.6845120188443735 chrX 155270560 436161 0.002809038622646817 0.31630870836898367 chrY 59373566 4085 6.88016616687635E-5 0.02190675369838004