BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716358.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 = 2,121,296 number of mapped reads = 1,908,346 (89.96%) number of supplementary alignments = 8,896 (0.42%) number of secondary alignments = 0 number of mapped bases = 109,641,967 bp number of sequenced bases = 109,610,473 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,460 duplication rate = 2.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4428 >>>>>>> ACTG content number of A's = 28,393,322 bp (25.9%) number of C's = 21,211,239 bp (19.35%) number of T's = 34,196,837 bp (31.2%) number of G's = 25,807,273 bp (23.54%) number of N's = 1,802 bp (0%) GC percentage = 42.9% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 585,794 number of insertions = 6,000 mapped reads with insertion percentage = 0.31% number of deletions = 18,518 mapped reads with deletion percentage = 0.96% homopolymer indels = 44.28% >>>>>>> Coverage mean coverageData = 0.0354X std coverageData = 0.3233X There is a 3.14% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 7967537 0.03196596649602731 0.5482445258905665 chr2 243199373 8520239 0.03503396778905347 0.35949707514465973 chr3 198022430 6728416 0.03397804986031128 0.2004606485802743 chr4 191154276 6981547 0.036523101371794583 0.23607707167312492 chr5 180915260 5955138 0.032916725764316396 0.201849265253624 chr6 171115067 5753957 0.03362624402911288 0.2266495625805789 chr7 159138663 7121522 0.04475041995294381 0.4532754609203894 chr8 146364022 4775037 0.03262439043933898 0.3139804776332322 chr9 141213431 5044738 0.035724208131448915 0.35427286842085953 chr10 135534747 4321292 0.03188327787264767 0.3198993320756468 chr11 135006516 4228338 0.03131951053384712 0.27094795730750404 chr12 133851895 8094683 0.06047492267479665 0.3070910563357791 chr13 115169878 4046635 0.03513622719996282 0.20342609267970635 chr14 107349540 3875851 0.03610496141855848 0.23209382182456326 chr15 102531392 2817866 0.0274829585850156 0.18195816826750338 chr16 90354753 3146043 0.034818788116215645 0.22829608174472701 chr17 81195210 3380663 0.04163623691594615 0.233764243911502 chr18 78077248 3440479 0.04406506489572993 0.5968817632584461 chr19 59128983 1934317 0.032713517159596674 0.44792744451903826 chr20 63025520 2958057 0.04693427360853191 0.24595455711673453 chr21 48129895 1312986 0.0272800512031036 0.20758440838534245 chr22 51304566 1064537 0.020749361762459895 0.15557609031002156 chrMT 16571 13679 0.8254782451270292 1.0534357204045062 chrX 155270560 5855537 0.037711830240066115 0.2548340080934265 chrY 59373566 302873 0.00510114214800573 0.12301605586565512