BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084358.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,203,424 number of mapped reads = 2,931,561 (91.51%) number of supplementary alignments = 16,968 (0.53%) number of secondary alignments = 0 number of mapped bases = 201,128,395 bp number of sequenced bases = 201,052,137 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,023 duplication rate = 2.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5716 >>>>>>> ACTG content number of A's = 55,993,219 bp (27.85%) number of C's = 39,885,939 bp (19.84%) number of T's = 59,820,904 bp (29.75%) number of G's = 45,087,185 bp (22.43%) number of N's = 264,890 bp (0.13%) GC percentage = 42.26% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 2,082,221 number of insertions = 14,996 mapped reads with insertion percentage = 0.51% number of deletions = 42,823 mapped reads with deletion percentage = 1.45% homopolymer indels = 47.1% >>>>>>> Coverage mean coverageData = 0.065X std coverageData = 0.5082X There is a 5.29% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 20086206 0.08058638297234172 0.8876900354689337 chr2 243199373 20139149 0.08280921431487408 0.5718070381838933 chr3 198022430 11587037 0.05851376028463038 0.29559752073709933 chr4 191154276 8874217 0.0464243708573906 0.2800990328174094 chr5 180915260 11710296 0.06472807213719838 0.3000662103485501 chr6 171115067 8775517 0.05128430332788871 0.2984713608745918 chr7 159138663 11897752 0.07476342816830125 0.9163952520891485 chr8 146364022 5959568 0.040717438060017236 0.33479344923794224 chr9 141213431 7842238 0.055534646700850995 0.45189050788417046 chr10 135534747 15026132 0.11086553324956588 0.7361267236745725 chr11 135006516 11113286 0.08231666388606014 0.4871627136788667 chr12 133851895 10943129 0.08175550297588241 0.34028925224349416 chr13 115169878 4901571 0.04255948764658759 0.23905573515881842 chr14 107349540 5840437 0.054405794379743036 0.30183568004810246 chr15 102531392 5636021 0.05496873581897727 0.27735967823510915 chr16 90354753 4641275 0.05136724794101313 0.3210041220929923 chr17 81195210 5139806 0.06330183763303279 0.33536705941919276 chr18 78077248 5357514 0.06861812035178289 0.7930986259840191 chr19 59128983 4171189 0.07054389892009473 0.6451109669313555 chr20 63025520 4173411 0.06621779558502651 0.3152871786676544 chr21 48129895 2111854 0.04387821747793134 0.2818079867134466 chr22 51304566 1760725 0.03431907015839487 0.21651525213224554 chrMT 16571 53750 3.243618369440589 2.727506325547503 chrX 155270560 12885615 0.0829881401857506 0.42133366133737876 chrY 59373566 500700 0.008433045776633999 0.18496988570103506