BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046414.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 6,791,526 number of mapped reads = 6,759,371 (99.53%) number of supplementary alignments = 40,951 (0.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,381,975 number of mapped paired reads (second in pair) = 3,377,396 number of mapped paired reads (both in pair) = 6,737,016 number of mapped paired reads (singletons) = 22,355 number of mapped bases = 661,524,902 bp number of sequenced bases = 661,316,778 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,777,652 duplication rate = 39.26% >>>>>>> Insert size mean insert size = 18,016.8945 std insert size = 1,335,864.5251 median insert size = 147 >>>>>>> Mapping quality mean mapping quality = 53.3733 >>>>>>> ACTG content number of A's = 196,447,119 bp (29.71%) number of C's = 134,575,045 bp (20.35%) number of T's = 198,485,118 bp (30.01%) number of G's = 131,751,291 bp (19.92%) number of N's = 58,205 bp (0.01%) GC percentage = 40.27% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 2,585,549 number of insertions = 61,680 mapped reads with insertion percentage = 0.89% number of deletions = 72,356 mapped reads with deletion percentage = 1.04% homopolymer indels = 48.75% >>>>>>> Coverage mean coverageData = 0.2137X std coverageData = 14.8169X There is a 2.4% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 93995624 0.3771128979453977 19.422112125998126 chr2 243199373 72787442 0.299291240360229 20.84917632355181 chr3 198022430 36074948 0.18217606965029165 9.861305299194143 chr4 191154276 19607523 0.10257433634390685 5.605963509877471 chr5 180915260 33870927 0.1872198453574342 11.598371016510367 chr6 171115067 50493797 0.2950867967693342 14.595279644236186 chr7 159138663 31014137 0.19488750511872782 11.76155803556027 chr8 146364022 70466615 0.4814476538503431 25.57839049347314 chr9 141213431 9290523 0.06579064706670855 3.248813463625876 chr10 135534747 25196021 0.1859008229085343 14.927801937257364 chr11 135006516 41415486 0.30676657117794226 22.571995201577373 chr12 133851895 16714111 0.12487018581246086 6.875235592326798 chr13 115169878 25628117 0.22252447814523169 16.081268808659345 chr14 107349540 23920938 0.22283223570403748 11.617268028297326 chr15 102531392 6702808 0.06537322735265312 2.698332311263776 chr16 90354753 22064046 0.2441935290332762 15.365854515195476 chr17 81195210 22225862 0.27373365990432197 13.313357999446998 chr18 78077248 3671081 0.04701857575717833 2.719346696833014 chr19 59128983 4929395 0.08336681522156401 3.6904786832112904 chr20 63025520 10653677 0.16903751051954827 9.22168545448364 chr21 48129895 5388390 0.11195515801561587 12.996542643249828 chr22 51304566 3048947 0.05942837524441782 7.714184290977617 chrMT 16571 39794 2.4014241747631404 2.2837664583943216 chrX 155270560 32118711 0.2068564124454758 21.311138545473284 chrY 59373566 205982 0.0034692543142852495 0.7490218971034017