BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085042.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 = 2,701,068 number of mapped reads = 2,475,088 (91.63%) number of supplementary alignments = 17,788 (0.66%) number of secondary alignments = 0 number of mapped bases = 165,885,470 bp number of sequenced bases = 165,826,375 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,084 duplication rate = 2.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1199 >>>>>>> ACTG content number of A's = 47,591,248 bp (28.7%) number of C's = 31,460,866 bp (18.97%) number of T's = 51,391,401 bp (30.99%) number of G's = 35,365,004 bp (21.33%) number of N's = 17,856 bp (0.01%) GC percentage = 40.3% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,453,362 number of insertions = 12,085 mapped reads with insertion percentage = 0.48% number of deletions = 34,925 mapped reads with deletion percentage = 1.4% homopolymer indels = 46.63% >>>>>>> Coverage mean coverageData = 0.0536X std coverageData = 0.3893X There is a 4.49% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% 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 17928146 0.07192818990007652 0.6200155522120817 chr2 243199373 14711023 0.06048955973254092 0.4870150967486276 chr3 198022430 11468642 0.05791587346948525 0.2811655805858291 chr4 191154276 12924498 0.06761291596741471 0.30364474078887316 chr5 180915260 8662766 0.0478830033464286 0.25145642556377756 chr6 171115067 12072531 0.0705521215148167 0.35853624027094083 chr7 159138663 9717537 0.06106333191953485 0.3253559122770493 chr8 146364022 9485366 0.06480667769569765 0.6905363864316361 chr9 141213431 4416209 0.03127329297735142 0.3187096220059291 chr10 135534747 9245318 0.06821363675840263 0.4961270042238241 chr11 135006516 7609831 0.05636639790037986 0.37929535532146347 chr12 133851895 7486149 0.05592859929252402 0.27680998235494064 chr13 115169878 4426252 0.038432375520967385 0.22475709258153018 chr14 107349540 5800043 0.054029509581503564 0.28000683313152525 chr15 102531392 2974996 0.02901546484417182 0.20225695514651798 chr16 90354753 3415882 0.037805227578896705 0.23785956237425268 chr17 81195210 2654025 0.03268696515471787 0.23277563693612943 chr18 78077248 5492238 0.07034364223493123 0.5533291957480485 chr19 59128983 2221421 0.03756907166828829 0.43784623320932287 chr20 63025520 3880645 0.061572597893678624 0.29051904495596903 chr21 48129895 1713788 0.03560755742350986 0.22523487759811572 chr22 51304566 1046201 0.02039196667212817 0.1604699735587064 chrMT 16571 114189 6.890893730010259 5.413115065582619 chrX 155270560 6114268 0.03937815384964156 0.2554206882502105 chrY 59373566 303506 0.005111803458124783 0.10332527671225022