BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926914.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 = 30,674,908 number of mapped reads = 28,289,177 (92.22%) number of supplementary alignments = 274,305 (0.89%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,214,940 number of mapped paired reads (second in pair) = 14,074,237 number of mapped paired reads (both in pair) = 27,967,830 number of mapped paired reads (singletons) = 321,347 number of mapped bases = 2,670,354,240 bp number of sequenced bases = 2,668,298,680 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,916,776 duplication rate = 5.41% >>>>>>> Insert size mean insert size = 112,973.8247 std insert size = 3,275,517.7464 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 53.147 >>>>>>> ACTG content number of A's = 758,176,638 bp (28.41%) number of C's = 540,389,199 bp (20.25%) number of T's = 763,505,131 bp (28.61%) number of G's = 605,966,631 bp (22.71%) number of N's = 261,081 bp (0.01%) GC percentage = 42.96% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 27,201,879 number of insertions = 425,424 mapped reads with insertion percentage = 1.48% number of deletions = 1,454,200 mapped reads with deletion percentage = 5% homopolymer indels = 52.92% >>>>>>> Coverage mean coverageData = 0.8626X std coverageData = 3.3821X There is a 32.55% of reference with a coverageData >= 1X There is a 18.5% of reference with a coverageData >= 2X There is a 11.11% of reference with a coverageData >= 3X There is a 7.11% of reference with a coverageData >= 4X There is a 4.7% of reference with a coverageData >= 5X There is a 3.2% of reference with a coverageData >= 6X There is a 2.22% of reference with a coverageData >= 7X There is a 1.56% of reference with a coverageData >= 8X There is a 1.11% of reference with a coverageData >= 9X There is a 0.8% of reference with a coverageData >= 10X There is a 0.58% of reference with a coverageData >= 11X There is a 0.43% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% 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 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% 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 225302118 0.9039179806095649 3.003798473050853 chr2 243199373 182672368 0.7511218706965992 4.179132114200272 chr3 198022430 183528805 0.9268081651154366 1.956475218933226 chr4 191154276 158292337 0.8280868223947028 2.0439848544582926 chr5 180915260 164887627 0.9114080647481037 1.8892542698063188 chr6 171115067 155605275 0.9093604539219214 2.315019401493946 chr7 159138663 139157812 0.8744437673200761 2.183603758622478 chr8 146364022 136809120 0.93471823287283 2.1046698829647346 chr9 141213431 116968884 0.8283127403086751 3.273703328183297 chr10 135534747 138434230 1.0213929126233585 10.86244969105419 chr11 135006516 131010206 0.9703991324389113 2.377878142826756 chr12 133851895 122880495 0.9180332859687941 1.97139474828156 chr13 115169878 80928958 0.7026920528647256 1.6511881023160484 chr14 107349540 82113455 0.7649166917715716 1.7970311955668166 chr15 102531392 82521701 0.8048432718049903 1.9007181029313684 chr16 90354753 86399132 0.9562212183790708 3.8446249555192784 chr17 81195210 73523616 0.9055166677935804 2.181529412243249 chr18 78077248 71605618 0.9171124730215902 3.3864444150210615 chr19 59128983 46008120 0.7780976040125703 2.194831347572622 chr20 63025520 66178401 1.0500254658747759 2.278134132248017 chr21 48129895 34998535 0.7271683223077882 2.7098825545027876 chr22 51304566 36439975 0.7102676787091425 1.875446455693694 chrMT 16571 160746 9.700440528634362 6.639734514240111 chrX 155270560 150353894 0.9683348472498585 2.0465457463449344 chrY 59373566 3572812 0.06017512911385515 1.227263596817399