BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085044.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 = 2,512,243 number of mapped reads = 2,319,399 (92.32%) number of supplementary alignments = 14,809 (0.59%) number of secondary alignments = 0 number of mapped bases = 157,237,327 bp number of sequenced bases = 157,179,504 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,663 duplication rate = 2.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9105 >>>>>>> ACTG content number of A's = 45,058,865 bp (28.67%) number of C's = 29,549,234 bp (18.8%) number of T's = 48,819,804 bp (31.06%) number of G's = 33,733,656 bp (21.46%) number of N's = 17,945 bp (0.01%) GC percentage = 40.26% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,379,974 number of insertions = 11,382 mapped reads with insertion percentage = 0.49% number of deletions = 33,543 mapped reads with deletion percentage = 1.43% homopolymer indels = 47.21% >>>>>>> Coverage mean coverageData = 0.0508X std coverageData = 0.3991X There is a 4.34% of reference with a coverageData >= 1X There is a 0.55% 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 12059275 0.0483821261973907 0.59112035363298 chr2 243199373 16418426 0.06751014937855124 0.47075308096932406 chr3 198022430 9873239 0.04985919524369032 0.25767450133557945 chr4 191154276 9303119 0.0486681187293974 0.25593284690867557 chr5 180915260 7965720 0.04403011664134911 0.23614087809874348 chr6 171115067 11234070 0.06565213804346054 0.3732820277674091 chr7 159138663 13893449 0.08730404502644339 0.43593425564442206 chr8 146364022 9199798 0.0628555971220851 0.790969412641117 chr9 141213431 5061804 0.035845060658571494 0.33507344051287674 chr10 135534747 11680066 0.08617765007522388 0.5162007317943742 chr11 135006516 6329356 0.04688185568761733 0.37644309749169547 chr12 133851895 6669104 0.0498245019243097 0.2592085742298914 chr13 115169878 3038135 0.026379597276294763 0.18098328956956483 chr14 107349540 5218289 0.04861025953161979 0.2663498585880442 chr15 102531392 2616308 0.02551714113078656 0.18630783234971127 chr16 90354753 4065962 0.04499997913778814 0.2574814492285873 chr17 81195210 2430104 0.029929154687819638 0.22888000702374642 chr18 78077248 3914595 0.05013746129986549 0.645358125828998 chr19 59128983 2218974 0.03752768756398195 0.4294106864625353 chr20 63025520 3435013 0.054501938262468914 0.2653119194467843 chr21 48129895 1743477 0.03622440896661005 0.22837029120455218 chr22 51304566 965138 0.018811931865869404 0.15012194796573353 chrMT 16571 66125 3.990404924265283 3.051667602889247 chrX 155270560 7535860 0.04853373363244133 0.27549991075791286 chrY 59373566 301921 0.005085108076547062 0.1085823742731915