BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926926.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 11,515,182 number of mapped reads = 11,078,941 (96.21%) number of supplementary alignments = 323,098 (2.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,556,772 number of mapped paired reads (second in pair) = 5,522,169 number of mapped paired reads (both in pair) = 10,868,852 number of mapped paired reads (singletons) = 210,089 number of mapped bases = 990,215,143 bp number of sequenced bases = 989,410,629 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 794,654 duplication rate = 5.93% >>>>>>> Insert size mean insert size = 278,883.6284 std insert size = 5,279,488.8781 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 52.6386 >>>>>>> ACTG content number of A's = 279,006,343 bp (28.2%) number of C's = 191,655,072 bp (19.37%) number of T's = 286,378,794 bp (28.94%) number of G's = 232,322,088 bp (23.48%) number of N's = 48,332 bp (0%) GC percentage = 42.85% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 9,681,550 number of insertions = 177,186 mapped reads with insertion percentage = 1.57% number of deletions = 540,578 mapped reads with deletion percentage = 4.75% homopolymer indels = 51.74% >>>>>>> Coverage mean coverageData = 0.3199X std coverageData = 1.3613X There is a 18.23% of reference with a coverageData >= 1X There is a 7.28% of reference with a coverageData >= 2X There is a 3% of reference with a coverageData >= 3X There is a 1.42% of reference with a coverageData >= 4X There is a 0.71% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 87549328 0.351250190064722 1.2957699149677184 chr2 243199373 84607192 0.3478923113835495 2.981916592004305 chr3 198022430 63187090 0.3190905696895044 0.8670824377654629 chr4 191154276 55592776 0.2908267456177648 1.1613767288328642 chr5 180915260 59596434 0.3294162913620443 0.8838628029165867 chr6 171115067 54564864 0.318878196739975 1.0958338029137407 chr7 159138663 49182269 0.3090529232358827 0.9556394440700119 chr8 146364022 44523502 0.30419703825848676 0.8896584153737714 chr9 141213431 43842293 0.31046829391178804 1.2498137782273604 chr10 135534747 49234041 0.36325770394509976 1.8613396684463999 chr11 135006516 48914805 0.3623144011804586 1.0254727229705385 chr12 133851895 45947579 0.34327178558062255 0.9577528865434917 chr13 115169878 27886081 0.242129986453576 0.7479124896224112 chr14 107349540 30970731 0.2885036209749944 0.8615064691982025 chr15 102531392 32426897 0.3162631109114368 0.8849437584154273 chr16 90354753 31293988 0.3463457865907729 1.7133027022544185 chr17 81195210 30033233 0.3698892212976603 1.0093278348867625 chr18 78077248 26140743 0.33480615249144025 1.289146250812819 chr19 59128983 20320265 0.3436599780517111 1.107553315102604 chr20 63025520 24802182 0.39352601930138775 1.0164318302685413 chr21 48129895 12090249 0.25120040257723397 1.171621505071474 chr22 51304566 14575686 0.2841011460851262 0.8955560748365116 chrMT 16571 319704 19.292981715044355 14.952470008278333 chrX 155270560 50747839 0.32683490675888593 0.9102760277320026 chrY 59373566 1865372 0.031417550362395276 1.2533205663619125