BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081236.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,013,671 number of mapped reads = 2,650,067 (87.93%) number of supplementary alignments = 33,736 (1.12%) number of secondary alignments = 0 number of mapped bases = 169,216,528 bp number of sequenced bases = 169,154,106 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 166,058 duplication rate = 5.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1073 >>>>>>> ACTG content number of A's = 49,187,153 bp (29.08%) number of C's = 32,820,366 bp (19.4%) number of T's = 51,533,587 bp (30.47%) number of G's = 35,591,944 bp (21.04%) number of N's = 21,056 bp (0.01%) GC percentage = 40.44% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,532,914 number of insertions = 12,544 mapped reads with insertion percentage = 0.47% number of deletions = 38,316 mapped reads with deletion percentage = 1.43% homopolymer indels = 47.97% >>>>>>> Coverage mean coverageData = 0.0547X std coverageData = 0.4273X There is a 4.11% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% 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 17856877 0.07164225681106728 0.798077736909657 chr2 243199373 10597085 0.04357365263437583 0.4193863514389049 chr3 198022430 11570673 0.0584311231813487 0.309190358525338 chr4 191154276 7310277 0.038242811790409545 0.2548736528765278 chr5 180915260 10201120 0.05638617770551804 0.30344247413765274 chr6 171115067 11882750 0.069443037415285 0.39357241243450125 chr7 159138663 10692552 0.06719015856002258 0.5968881810903859 chr8 146364022 9877757 0.06748760293017911 0.49490334651549883 chr9 141213431 4847599 0.03432817236768364 0.3080436637316619 chr10 135534747 5557625 0.041005167479303294 0.3971968004406282 chr11 135006516 9905963 0.0733739621871288 0.49579820010338654 chr12 133851895 4634898 0.034627062993766354 0.24038053979246352 chr13 115169878 4520608 0.039251652241916936 0.25504261159805747 chr14 107349540 6059488 0.05644633409700684 0.3129880357600339 chr15 102531392 3138957 0.030614594601427046 0.22779464180334652 chr16 90354753 5638541 0.062404475833163976 0.32649217612613585 chr17 81195210 2715324 0.03344192348292467 0.27087968173694327 chr18 78077248 4984407 0.06383942989384052 0.4800896309846204 chr19 59128983 5088557 0.08605859160472962 0.6248503192618079 chr20 63025520 3925276 0.06228073961150975 0.3205717852247704 chr21 48129895 3239004 0.06729713414084947 0.33995895454639286 chr22 51304566 1315894 0.025648672283866508 0.19673017314453398 chrMT 16571 51450 3.104821676422666 3.097893613615229 chrX 155270560 13158900 0.08474819695375607 0.39852945678749896 chrY 59373566 444946 0.007494008360555605 0.12520916351218278