BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046487.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 = 8,513,252 number of mapped reads = 8,469,064 (99.48%) number of supplementary alignments = 77,893 (0.91%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,246,888 number of mapped paired reads (second in pair) = 4,222,176 number of mapped paired reads (both in pair) = 8,435,478 number of mapped paired reads (singletons) = 33,586 number of mapped bases = 822,488,449 bp number of sequenced bases = 822,286,425 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,793,954 duplication rate = 26.46% >>>>>>> Insert size mean insert size = 63,576.4635 std insert size = 2,669,158.6909 median insert size = 144 >>>>>>> Mapping quality mean mapping quality = 51.451 >>>>>>> ACTG content number of A's = 220,460,947 bp (26.81%) number of C's = 191,373,886 bp (23.27%) number of T's = 216,698,483 bp (26.35%) number of G's = 193,687,462 bp (23.55%) number of N's = 65,647 bp (0.01%) GC percentage = 46.83% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 3,438,152 number of insertions = 56,900 mapped reads with insertion percentage = 0.66% number of deletions = 64,421 mapped reads with deletion percentage = 0.74% homopolymer indels = 49.58% >>>>>>> Coverage mean coverageData = 0.2657X std coverageData = 57.8972X There is a 1.92% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.26% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 92411014 0.37075540124732526 40.28615743811201 chr2 243199373 50327328 0.20693855982926404 21.262200524821402 chr3 198022430 27263488 0.13767878719597573 14.985045312654588 chr4 191154276 6274715 0.03282539701073702 1.4467766814008058 chr5 180915260 6795875 0.037563857244546424 1.7700390155139327 chr6 171115067 8024453 0.046895069736904 1.7820871869635797 chr7 159138663 7792951 0.04896956436035912 2.708681584821378 chr8 146364022 34236026 0.23391012034364567 23.861847016183244 chr9 141213431 11623206 0.08230949363449713 4.146139430375843 chr10 135534747 25864507 0.19083303412961697 14.066979211275846 chr11 135006516 21253190 0.15742343873239423 25.68772190117532 chr12 133851895 29430505 0.21987365214366222 24.221603808332922 chr13 115169878 76215015 0.6617617064767578 128.32311261742248 chr14 107349540 20504322 0.1910052152994787 25.823659482101608 chr15 102531392 9747529 0.09506872782922912 7.189844591045799 chr16 90354753 329140313 3.6427559378088277 286.88735946000656 chr17 81195210 11800132 0.14533039572161954 6.679186226725244 chr18 78077248 3498501 0.04480820071936962 1.9633914979138154 chr19 59128983 14582145 0.2466158601104301 11.758802214208728 chr20 63025520 26195342 0.4156307159385595 42.09160569024695 chr21 48129895 1649456 0.03427092454699932 1.2304753671025928 chr22 51304566 3570469 0.06959359133843955 0.8574572130008213 chrMT 16571 259670 15.670146641723493 6.671662265311138 chrX 155270560 3911985 0.025194634449698643 1.282350773669469 chrY 59373566 116312 0.001958986259979736 0.09203262535414639