BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818920.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,035,484 number of mapped reads = 2,842,240 (93.63%) number of supplementary alignments = 44,016 (1.45%) number of secondary alignments = 0 number of mapped bases = 263,307,229 bp number of sequenced bases = 263,132,031 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 927,545 duplication rate = 27.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2892 >>>>>>> ACTG content number of A's = 74,025,173 bp (28.13%) number of C's = 53,825,433 bp (20.46%) number of T's = 77,272,386 bp (29.37%) number of G's = 58,004,946 bp (22.04%) number of N's = 4,093 bp (0%) GC percentage = 42.5% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,611,453 number of insertions = 41,920 mapped reads with insertion percentage = 1.42% number of deletions = 89,185 mapped reads with deletion percentage = 3.06% homopolymer indels = 41.09% >>>>>>> Coverage mean coverageData = 0.0851X std coverageData = 1.0334X There is a 4.93% of reference with a coverageData >= 1X There is a 1.81% of reference with a coverageData >= 2X There is a 0.78% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 24947872 0.10009151391442271 1.5237204955519474 chr2 243199373 19936235 0.08197486183486172 1.6442235085219368 chr3 198022430 16586522 0.08376082446821807 0.45286561479518694 chr4 191154276 13430312 0.07025901947388297 0.5718930498390505 chr5 180915260 11677800 0.06454845213167756 0.43194659112791645 chr6 171115067 12878685 0.07526330220821524 0.48194083929180515 chr7 159138663 23806947 0.1495987621813814 2.2951279767676107 chr8 146364022 23037433 0.15739819584897716 0.8178076075852513 chr9 141213431 9695087 0.06865555869115594 0.8267399154812727 chr10 135534747 12224458 0.0901942732072979 1.3028945639258915 chr11 135006516 11569218 0.0856937749582398 0.571739137733321 chr12 133851895 10179945 0.07605379811768821 0.4376475946706517 chr13 115169878 8064814 0.07002537590601599 0.40618187667691674 chr14 107349540 7763029 0.07231543796088925 0.46858105262569677 chr15 102531392 7315973 0.07135349337693572 0.41291951806088484 chr16 90354753 6493631 0.07186817277891291 1.141543999970274 chr17 81195210 6428802 0.07917710909301177 0.5983955975862136 chr18 78077248 5067712 0.06490638604475403 0.9163489099321716 chr19 59128983 4507220 0.07622691565657404 1.232636658770073 chr20 63025520 10843111 0.17204318187299367 0.7204566493005912 chr21 48129895 2526246 0.05248808458859094 0.43519716529126234 chr22 51304566 2334249 0.04549788024714993 0.38112509065089545 chrMT 16571 367744 22.192022207470885 13.688620480652085 chrX 155270560 10651617 0.06860036442194838 0.4900921910778008 chrY 59373566 972567 0.016380471403721987 1.2825911888682249