BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081951.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 = 3,005,636 number of mapped reads = 2,798,514 (93.11%) number of supplementary alignments = 18,873 (0.63%) number of secondary alignments = 0 number of mapped bases = 192,865,391 bp number of sequenced bases = 192,796,195 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 129,883 duplication rate = 3.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9601 >>>>>>> ACTG content number of A's = 55,274,598 bp (28.67%) number of C's = 35,774,696 bp (18.56%) number of T's = 60,968,889 bp (31.62%) number of G's = 40,752,601 bp (21.14%) number of N's = 25,411 bp (0.01%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,431,698 number of insertions = 13,504 mapped reads with insertion percentage = 0.48% number of deletions = 39,223 mapped reads with deletion percentage = 1.39% homopolymer indels = 48.22% >>>>>>> Coverage mean coverageData = 0.0623X std coverageData = 0.5199X There is a 5.19% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.13% 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 17851578 0.07162099708469734 0.9605439727229645 chr2 243199373 17059870 0.07014767262578428 0.6346559472428597 chr3 198022430 12439889 0.06282060572633111 0.29109315433079735 chr4 191154276 9842609 0.051490394073109826 0.2745673471349118 chr5 180915260 9731526 0.05379052049009022 0.26919371220486255 chr6 171115067 17083448 0.09983602437534037 0.5049531056033781 chr7 159138663 13054609 0.08203291867545727 0.7516780132737678 chr8 146364022 11273848 0.07702608773623343 0.760813754275025 chr9 141213431 9483619 0.06715805240933492 0.5121991300228985 chr10 135534747 7662172 0.056532897796311966 0.49529415529723525 chr11 135006516 8293928 0.06143353851157821 0.37058413620087116 chr12 133851895 8224342 0.061443597791424616 0.29527819059243676 chr13 115169878 5376094 0.04667968824278862 0.24685673630417598 chr14 107349540 4708883 0.043864957409225976 0.2758422236935018 chr15 102531392 3922386 0.038255464238698716 0.22520001682040666 chr16 90354753 4184943 0.04631679973714277 0.2972506198305696 chr17 81195210 5080171 0.06256737312459688 0.3210210574401557 chr18 78077248 5029116 0.06441205509702391 0.788195848339248 chr19 59128983 3839280 0.0649305941893166 0.6925642698405036 chr20 63025520 4796873 0.07611001067504083 0.3233462311168722 chr21 48129895 2068820 0.042984095435903195 0.2654559392059871 chr22 51304566 1504200 0.029319027861964567 0.1923766786700249 chrMT 16571 20600 1.2431355983344397 1.3827969993319509 chrX 155270560 9947351 0.06406463015268316 0.3407796494438679 chrY 59373566 385236 0.006488341966861145 0.1473514439792735