BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084781.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 = 2,192,524 number of mapped reads = 1,953,282 (89.09%) number of supplementary alignments = 19,226 (0.88%) number of secondary alignments = 0 number of mapped bases = 130,787,257 bp number of sequenced bases = 130,737,184 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,998 duplication rate = 3.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6138 >>>>>>> ACTG content number of A's = 36,523,279 bp (27.94%) number of C's = 24,950,104 bp (19.08%) number of T's = 40,327,042 bp (30.85%) number of G's = 28,881,414 bp (22.09%) number of N's = 55,345 bp (0.04%) GC percentage = 41.18% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,153,497 number of insertions = 10,386 mapped reads with insertion percentage = 0.53% number of deletions = 30,514 mapped reads with deletion percentage = 1.55% homopolymer indels = 46.46% >>>>>>> Coverage mean coverageData = 0.0422X std coverageData = 0.3375X There is a 3.54% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 11694497 0.046918627336138115 0.5596418689952269 chr2 243199373 10587252 0.04353322078671642 0.40461870051084514 chr3 198022430 7926264 0.04002710198031607 0.23071739773375227 chr4 191154276 8495426 0.04444277249649388 0.2607476842723989 chr5 180915260 9157504 0.05061764275716708 0.26139540610200224 chr6 171115067 4758116 0.027806528574131933 0.21455640467470033 chr7 159138663 6850660 0.043048369710131346 0.35705471417936263 chr8 146364022 7457172 0.05094948811942323 0.38296287716197575 chr9 141213431 5113669 0.03621234158668661 0.3248559005810474 chr10 135534747 6650008 0.049064967819654394 0.3268858376064938 chr11 135006516 4625423 0.03426073894092638 0.28746786642721534 chr12 133851895 5962927 0.044548693165681365 0.2488403262307985 chr13 115169878 4672332 0.04056904531929781 0.233829185146888 chr14 107349540 4510262 0.04201473057080636 0.25559078361769627 chr15 102531392 3872152 0.037765526483830435 0.22897499063216523 chr16 90354753 4041812 0.0447326993412289 0.2723504958135218 chr17 81195210 3831005 0.04718264784338879 0.29415997525211757 chr18 78077248 3864360 0.04949406003654227 0.6690563575656849 chr19 59128983 2558995 0.0432781838984107 0.42547229359123356 chr20 63025520 2834340 0.04497130686109373 0.2541167973407749 chr21 48129895 1942667 0.04036300099969053 0.24791795620583854 chr22 51304566 2071501 0.04037654270382094 0.23010387915315214 chrMT 16571 9618 0.5804115623679923 0.8950666530123353 chrX 155270560 6962306 0.04483983312741321 0.27120068692380916 chrY 59373566 336989 0.005675741288640133 0.13035615535506892