BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083639.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 = 2,062,558 number of mapped reads = 1,696,412 (82.25%) number of supplementary alignments = 12,511 (0.61%) number of secondary alignments = 0 number of mapped bases = 100,252,700 bp number of sequenced bases = 100,222,388 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,913 duplication rate = 3.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4223 >>>>>>> ACTG content number of A's = 29,576,717 bp (29.51%) number of C's = 19,520,897 bp (19.48%) number of T's = 29,554,356 bp (29.49%) number of G's = 21,557,568 bp (21.51%) number of N's = 12,850 bp (0.01%) GC percentage = 40.99% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 809,428 number of insertions = 6,689 mapped reads with insertion percentage = 0.39% number of deletions = 19,117 mapped reads with deletion percentage = 1.12% homopolymer indels = 45.72% >>>>>>> Coverage mean coverageData = 0.0324X std coverageData = 0.244X There is a 2.84% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7710426 0.03093443045022544 0.3233229424890503 chr2 243199373 8335333 0.034273661552573165 0.24119234386480576 chr3 198022430 6862747 0.03465641240742273 0.20632526354887135 chr4 191154276 6724690 0.035179385681123866 0.2129396932435839 chr5 180915260 5917834 0.03271052978062768 0.20144767840654762 chr6 171115067 6378158 0.037274087617310755 0.23834076386646913 chr7 159138663 5013796 0.0315058321182452 0.24268697617073617 chr8 146364022 5532855 0.037802015306739795 0.4050159150339016 chr9 141213431 4424632 0.03133294027818076 0.22426944906303084 chr10 135534747 4470205 0.03298198505509439 0.2498016751216924 chr11 135006516 4825129 0.035739971247017444 0.22870703267143155 chr12 133851895 4562306 0.034084732233338945 0.2069971089243242 chr13 115169878 4005137 0.03477590729061986 0.2071131704165609 chr14 107349540 2985133 0.02780759936186033 0.18978191846308434 chr15 102531392 2772677 0.02704222527282181 0.1835290589196245 chr16 90354753 2467816 0.027312520017624308 0.1911441129607819 chr17 81195210 2518020 0.031011927920378553 0.20255269982271748 chr18 78077248 2556299 0.03274063911678854 0.36958822989681334 chr19 59128983 1439422 0.024343763869573064 0.248113939386916 chr20 63025520 1980439 0.03142281095023095 0.20322962176380027 chr21 48129895 1479844 0.03074687779809202 0.201550677060575 chr22 51304566 1123121 0.021891248431962176 0.1631144915710243 chrMT 16571 69957 4.221652284110796 2.9606290566425453 chrX 155270560 5835296 0.037581470692190456 0.2253738468824888 chrY 59373566 261428 0.004403104236656427 0.10931117760255352