BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124844.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 91,527,834 number of mapped reads = 86,997,022 (95.05%) number of supplementary alignments = 2,751,586 (3.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 44,745,367 number of mapped paired reads (second in pair) = 42,251,655 number of mapped paired reads (both in pair) = 84,117,912 number of mapped paired reads (singletons) = 2,879,110 number of mapped bases = 11,329,565,031 bp number of sequenced bases = 11,316,545,947 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,112,575 duplication rate = 22.82% >>>>>>> Insert size mean insert size = 155,548.9339 std insert size = 3,747,372.6186 median insert size = 251 >>>>>>> Mapping quality mean mapping quality = 53.1923 >>>>>>> ACTG content number of A's = 3,262,382,396 bp (28.83%) number of C's = 2,173,429,507 bp (19.21%) number of T's = 3,384,750,824 bp (29.91%) number of G's = 2,495,790,082 bp (22.05%) number of N's = 193,138 bp (0%) GC percentage = 41.26% >>>>>>> Mismatches and indels general error rate = 0.0155 number of mismatches = 164,872,041 number of insertions = 3,001,063 mapped reads with insertion percentage = 3.13% number of deletions = 5,599,773 mapped reads with deletion percentage = 6.08% homopolymer indels = 42.51% >>>>>>> Coverage mean coverageData = 3.6598X std coverageData = 62.617X There is a 46.49% of reference with a coverageData >= 1X There is a 37.09% of reference with a coverageData >= 2X There is a 30.2% of reference with a coverageData >= 3X There is a 25.33% of reference with a coverageData >= 4X There is a 21.46% of reference with a coverageData >= 5X There is a 18.41% of reference with a coverageData >= 6X There is a 15.91% of reference with a coverageData >= 7X There is a 13.85% of reference with a coverageData >= 8X There is a 12.12% of reference with a coverageData >= 9X There is a 10.67% of reference with a coverageData >= 10X There is a 9.43% of reference with a coverageData >= 11X There is a 8.36% of reference with a coverageData >= 12X There is a 7.45% of reference with a coverageData >= 13X There is a 6.65% of reference with a coverageData >= 14X There is a 5.96% of reference with a coverageData >= 15X There is a 5.35% of reference with a coverageData >= 16X There is a 4.82% of reference with a coverageData >= 17X There is a 4.35% of reference with a coverageData >= 18X There is a 3.93% of reference with a coverageData >= 19X There is a 3.56% of reference with a coverageData >= 20X There is a 3.24% of reference with a coverageData >= 21X There is a 2.94% of reference with a coverageData >= 22X There is a 2.68% of reference with a coverageData >= 23X There is a 2.45% of reference with a coverageData >= 24X There is a 2.24% of reference with a coverageData >= 25X There is a 2.05% of reference with a coverageData >= 26X There is a 1.88% of reference with a coverageData >= 27X There is a 1.72% of reference with a coverageData >= 28X There is a 1.58% of reference with a coverageData >= 29X There is a 1.46% of reference with a coverageData >= 30X There is a 1.34% of reference with a coverageData >= 31X There is a 1.24% of reference with a coverageData >= 32X There is a 1.15% of reference with a coverageData >= 33X There is a 1.06% of reference with a coverageData >= 34X There is a 0.98% of reference with a coverageData >= 35X There is a 0.91% of reference with a coverageData >= 36X There is a 0.84% of reference with a coverageData >= 37X There is a 0.78% of reference with a coverageData >= 38X There is a 0.73% of reference with a coverageData >= 39X There is a 0.68% of reference with a coverageData >= 40X There is a 0.63% of reference with a coverageData >= 41X There is a 0.59% of reference with a coverageData >= 42X There is a 0.55% of reference with a coverageData >= 43X There is a 0.51% of reference with a coverageData >= 44X There is a 0.48% of reference with a coverageData >= 45X There is a 0.45% of reference with a coverageData >= 46X There is a 0.42% of reference with a coverageData >= 47X There is a 0.39% of reference with a coverageData >= 48X There is a 0.37% of reference with a coverageData >= 49X There is a 0.35% of reference with a coverageData >= 50X There is a 0.33% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 940288688 3.7724627695110136 24.476772554577988 chr2 243199373 989526718 4.068788113199617 76.27455183133269 chr3 198022430 741271884 3.7433733340207977 8.671750404928504 chr4 191154276 753039030 3.9394307349943873 116.4761670582276 chr5 180915260 622719996 3.4420534564082654 9.799722805693683 chr6 171115067 596175839 3.484063966149749 15.114122567140214 chr7 159138663 664667735 4.176657780516857 32.44360945689089 chr8 146364022 635283272 4.340433279429831 13.097738575247611 chr9 141213431 454966792 3.2218379567592264 55.8138890782605 chr10 135534747 661059296 4.87741564899221 184.47142610673268 chr11 135006516 460604449 3.4117201350488893 17.152918885745404 chr12 133851895 563187966 4.207545705647275 19.056974915658408 chr13 115169878 277861807 2.412625695409697 6.020564913081818 chr14 107349540 325691550 3.0339352176078256 9.900985654991267 chr15 102531392 310968256 3.0329077752109326 10.389151308627175 chr16 90354753 422244209 4.673182040572896 84.24650919359584 chr17 81195210 282086857 3.4741810138800058 31.505552264961175 chr18 78077248 239721640 3.070313646300648 48.16118256347875 chr19 59128983 194628203 3.2915871899910742 16.409629787001606 chr20 63025520 258858547 4.107202082584959 35.499388207059454 chr21 48129895 140483667 2.9188442443101112 50.84927137564277 chr22 51304566 112964875 2.201848369597357 10.052744775814816 chrMT 16571 5919076 357.1948584877195 206.1688718106514 chrX 155270560 396720296 2.5550258593773347 10.52343911231001 chrY 59373566 278624383 4.692734524316764 153.6098382820147