BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068162.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,843,764 number of mapped reads = 1,588,886 (86.18%) number of supplementary alignments = 9,405 (0.51%) number of secondary alignments = 0 number of mapped bases = 106,423,296 bp number of sequenced bases = 106,379,172 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 183,608 duplication rate = 9.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7661 >>>>>>> ACTG content number of A's = 30,236,116 bp (28.42%) number of C's = 19,606,095 bp (18.43%) number of T's = 33,749,677 bp (31.73%) number of G's = 22,671,428 bp (21.31%) number of N's = 115,856 bp (0.11%) GC percentage = 39.74% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 901,453 number of insertions = 7,258 mapped reads with insertion percentage = 0.45% number of deletions = 25,262 mapped reads with deletion percentage = 1.57% homopolymer indels = 48.79% >>>>>>> Coverage mean coverageData = 0.0344X std coverageData = 0.3916X There is a 1.67% of reference with a coverageData >= 1X There is a 0.79% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 8058559 0.03233114913683605 0.5193212689304816 chr2 243199373 9637683 0.03962873292440602 0.44030123632950635 chr3 198022430 6582370 0.0332405273483413 0.33339049140282345 chr4 191154276 7882831 0.041238057368907614 0.3776303455681223 chr5 180915260 7076883 0.03911711483044603 0.3659879898350935 chr6 171115067 5852307 0.03420100346861916 0.3802442347536074 chr7 159138663 5473911 0.03439711567766533 0.43195013654606274 chr8 146364022 5389751 0.036824288690290294 0.4455995328021033 chr9 141213431 5060534 0.035836067179757146 0.39962855388288304 chr10 135534747 5832085 0.043030183248875656 0.4258831128550905 chr11 135006516 5490842 0.04067094065296819 0.4417094911553641 chr12 133851895 4796278 0.03583272392221268 0.33998218547111003 chr13 115169878 2979373 0.025869377060553977 0.30216346798170707 chr14 107349540 3800412 0.03540221970210585 0.3609310181447527 chr15 102531392 2463234 0.024024193487980735 0.27272927979668227 chr16 90354753 3004004 0.03324677341545054 0.3354296894340367 chr17 81195210 2088597 0.025723155343769663 0.2934101257773216 chr18 78077248 2729349 0.03495703383397939 0.5120372007099768 chr19 59128983 2042839 0.03454886075074215 0.4239669053700416 chr20 63025520 2101861 0.03334936387672803 0.3312373841443873 chr21 48129895 1701492 0.03535208211029756 0.33974780541470384 chr22 51304566 792957 0.015455875798656985 0.20999945723176602 chrMT 16571 13727 0.8283748717639249 1.3961014784956869 chrX 155270560 5324306 0.03429050555366066 0.3435810564861691 chrY 59373566 247111 0.004161969991831045 0.11264499371452974