BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080803.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 = 2,419,063 number of mapped reads = 2,029,573 (83.9%) number of supplementary alignments = 25,949 (1.07%) number of secondary alignments = 0 number of mapped bases = 138,249,812 bp number of sequenced bases = 138,198,320 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 160,866 duplication rate = 6.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8654 >>>>>>> ACTG content number of A's = 40,889,546 bp (29.59%) number of C's = 25,688,027 bp (18.59%) number of T's = 42,196,404 bp (30.53%) number of G's = 29,405,980 bp (21.28%) number of N's = 18,363 bp (0.01%) GC percentage = 39.87% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,157,833 number of insertions = 11,157 mapped reads with insertion percentage = 0.54% number of deletions = 29,049 mapped reads with deletion percentage = 1.41% homopolymer indels = 46.51% >>>>>>> Coverage mean coverageData = 0.0447X std coverageData = 0.4403X There is a 2.96% of reference with a coverageData >= 1X There is a 0.96% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 11266296 0.04520067374275469 0.5388089783624852 chr2 243199373 11083671 0.04557442259524246 0.43999267450591495 chr3 198022430 10374116 0.05238859052482085 0.31896996654412907 chr4 191154276 9123770 0.04772987657362161 0.3230483340600548 chr5 180915260 6898966 0.038133687561789975 0.2712671200906277 chr6 171115067 8827473 0.05158793526931208 0.36688244374448276 chr7 159138663 7825355 0.04917318552563182 0.3660390221274919 chr8 146364022 7755694 0.052989074049905514 1.1587532992566394 chr9 141213431 5311295 0.037611826030910615 0.3420335745990027 chr10 135534747 5581861 0.04118398509276739 0.3765301136447034 chr11 135006516 6277013 0.0464941484750262 0.34954612373875354 chr12 133851895 6811800 0.05089057573671258 0.31620018010720113 chr13 115169878 5126017 0.04450831318932195 0.2955493944534401 chr14 107349540 4352712 0.04054709503179986 0.2911679094782125 chr15 102531392 4200503 0.04096797008276255 0.28031284016233315 chr16 90354753 4090452 0.04527102187972336 0.31444880408765014 chr17 81195210 3006118 0.037023341647863216 0.2812182967130403 chr18 78077248 3897511 0.049918652358238856 0.6665908514277602 chr19 59128983 2222383 0.03758534118538788 0.4173415733173096 chr20 63025520 2885230 0.045778757557256175 0.30856267063108683 chr21 48129895 1417165 0.02944458948019729 0.2535901304977988 chr22 51304566 1507178 0.029377073377835416 0.23301136735688338 chrMT 16571 109034 6.579808098485306 4.773532521220737 chrX 155270560 7861497 0.050630956699067746 0.328215151708806 chrY 59373566 436702 0.007355158691327383 0.2353750125821467