BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617660.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 27,456,926 number of mapped reads = 25,361,127 (92.37%) number of supplementary alignments = 152,583 (0.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,874,736 number of mapped paired reads (second in pair) = 12,486,391 number of mapped paired reads (both in pair) = 24,619,904 number of mapped paired reads (singletons) = 741,223 number of mapped bases = 2,444,738,103 bp number of sequenced bases = 2,443,267,496 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,402,520 duplication rate = 10.17% >>>>>>> Insert size mean insert size = 47,685.4848 std insert size = 2,040,805.973 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 52.4247 >>>>>>> ACTG content number of A's = 729,929,854 bp (29.88%) number of C's = 484,694,724 bp (19.84%) number of T's = 727,781,454 bp (29.79%) number of G's = 498,409,831 bp (20.4%) number of N's = 2,451,633 bp (0.1%) GC percentage = 40.24% >>>>>>> Mismatches and indels general error rate = 0.0156 number of mismatches = 37,326,149 number of insertions = 382,647 mapped reads with insertion percentage = 1.48% number of deletions = 890,140 mapped reads with deletion percentage = 3.44% homopolymer indels = 47.59% >>>>>>> Coverage mean coverageData = 0.7897X std coverageData = 8.9089X There is a 30.56% of reference with a coverageData >= 1X There is a 16.63% of reference with a coverageData >= 2X There is a 9.58% of reference with a coverageData >= 3X There is a 5.81% of reference with a coverageData >= 4X There is a 3.65% of reference with a coverageData >= 5X There is a 2.37% of reference with a coverageData >= 6X There is a 1.59% of reference with a coverageData >= 7X There is a 1.09% of reference with a coverageData >= 8X There is a 0.77% of reference with a coverageData >= 9X There is a 0.56% of reference with a coverageData >= 10X There is a 0.41% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% 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 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% 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 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% 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 150035259 0.6019453768983789 8.741038286401059 chr2 243199373 252261067 1.037260350996053 10.188525137877585 chr3 198022430 204877283 1.03461654823648 2.1371168360837705 chr4 191154276 136772020 0.7155059403431813 6.836827845968297 chr5 180915260 161762864 0.8941360944344883 2.0022149839664998 chr6 171115067 118654292 0.6934181430089964 4.894142521188864 chr7 159138663 191275795 1.201944212639263 11.270066924180275 chr8 146364022 108837762 0.7436100792584123 3.4743116459698635 chr9 141213431 100530107 0.711901879928121 17.053159814976798 chr10 135534747 103941906 0.7669022763586965 18.110977828779255 chr11 135006516 134330121 0.9949899084870837 10.183924823288926 chr12 133851895 104584979 0.7813485120998848 1.9733148563008174 chr13 115169878 105131394 0.9128375910930461 2.0180066589911676 chr14 107349540 69761002 0.6498491004246502 2.1172056508950026 chr15 102531392 52090837 0.5080476913841178 1.613172891343153 chr16 90354753 67884778 0.751313857279871 14.244822085430274 chr17 81195210 59781402 0.7362675950958191 10.63034748018779 chr18 78077248 45128819 0.5780021729249474 15.225215231966903 chr19 59128983 25841378 0.43703403456135886 5.157219750300085 chr20 63025520 65703246 1.0424863769469892 2.570324121922139 chr21 48129895 35614316 0.739962470310812 3.6797756782914526 chr22 51304566 15629975 0.30465075954448184 1.111265010709798 chrMT 16571 2572803 155.2593687767787 107.36051491391677 chrX 155270560 121864572 0.7848530461924011 3.698026589900225 chrY 59373566 9870126 0.16623771595595252 14.419655919191868