BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708617.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,449,917 number of mapped reads = 2,514,845 (72.9%) number of supplementary alignments = 844 (0.02%) number of secondary alignments = 0 number of mapped bases = 122,421,763 bp number of sequenced bases = 122,398,017 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,710 duplication rate = 2.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1136 >>>>>>> ACTG content number of A's = 36,083,715 bp (29.48%) number of C's = 23,011,961 bp (18.8%) number of T's = 38,698,717 bp (31.62%) number of G's = 24,592,956 bp (20.09%) number of N's = 10,668 bp (0.01%) GC percentage = 38.89% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 769,039 number of insertions = 5,692 mapped reads with insertion percentage = 0.23% number of deletions = 15,576 mapped reads with deletion percentage = 0.62% homopolymer indels = 48.45% >>>>>>> Coverage mean coverageData = 0.0395X std coverageData = 0.4182X There is a 3.31% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 9646724 0.03870290858773828 0.754404333815111 chr2 243199373 10528684 0.043292397797423596 0.4182356042551007 chr3 198022430 8532578 0.043088947045039294 0.24180051554582302 chr4 191154276 8476338 0.04434291598059779 0.24968570341446797 chr5 180915260 7763366 0.0429116150843218 0.24419031438413688 chr6 171115067 7407805 0.0432913660373344 0.33091430563464264 chr7 159138663 7086072 0.0445276582473236 0.6515901142428804 chr8 146364022 6507580 0.044461609561398906 0.7699537481539648 chr9 141213431 5151674 0.03648147321057584 0.31211146012184576 chr10 135534747 5470024 0.04035883137775732 0.31874370864972884 chr11 135006516 5481642 0.04060279579394523 0.348353650781825 chr12 133851895 5487595 0.04099751445431535 0.24437616604093448 chr13 115169878 4214976 0.03659790279538196 0.22550518658011323 chr14 107349540 3500972 0.032612827218449186 0.22850133822463845 chr15 102531392 3330667 0.03248436342305779 0.20988007208582052 chr16 90354753 3119669 0.034526894229902884 0.2283740217626773 chr17 81195210 2922233 0.0359902142010594 0.26899733233960516 chr18 78077248 3498075 0.04480274458444027 0.6487362318056111 chr19 59128983 2075491 0.03510107725005181 0.5630247802562283 chr20 63025520 2217688 0.03518714323975431 0.22512651261993694 chr21 48129895 1547322 0.03214887545464207 0.2207634766175841 chr22 51304566 1148323 0.022382471766742944 0.17195984827363314 chrMT 16571 12321 0.743527849858186 1.0646812465019875 chrX 155270560 7016424 0.04518837312108619 0.2763023052741649 chrY 59373566 277520 0.00467413394034645 0.08512127380571494