BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231880.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,436,695 number of mapped reads = 1,197,238 (83.33%) number of supplementary alignments = 11,298 (0.79%) number of secondary alignments = 0 number of mapped bases = 79,898,265 bp number of sequenced bases = 79,857,394 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 117,292 duplication rate = 7.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5344 >>>>>>> ACTG content number of A's = 22,219,126 bp (27.82%) number of C's = 14,372,718 bp (18%) number of T's = 25,964,660 bp (32.51%) number of G's = 17,296,764 bp (21.66%) number of N's = 4,126 bp (0.01%) GC percentage = 39.66% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 600,211 number of insertions = 6,222 mapped reads with insertion percentage = 0.51% number of deletions = 23,711 mapped reads with deletion percentage = 1.96% homopolymer indels = 46.5% >>>>>>> Coverage mean coverageData = 0.0258X std coverageData = 0.3491X There is a 1.73% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 13216976 0.053026852839817 0.7680271168401128 chr2 243199373 6419135 0.026394537620785724 0.33890382843060846 chr3 198022430 5771184 0.029144092414177526 0.2325673891526561 chr4 191154276 666175 0.0034850122840045703 0.08963564408383677 chr5 180915260 804338 0.004445937838521747 0.08971566822763734 chr6 171115067 5246924 0.030663132662654424 0.25990798720424707 chr7 159138663 5784605 0.03634946336076733 0.3855331768692339 chr8 146364022 6007951 0.04104800426979248 0.5991739443511219 chr9 141213431 2235774 0.01583258748241872 0.21783362202911002 chr10 135534747 1530817 0.01129464608806183 0.1562268275031522 chr11 135006516 5007608 0.03709160230458802 0.3430621387502466 chr12 133851895 894030 0.006679247985245184 0.11166471337561537 chr13 115169878 4916386 0.04268812371234777 0.2925319109928067 chr14 107349540 1575563 0.014676942257973346 0.1779804109632137 chr15 102531392 705290 0.006878771332783622 0.11203449210244529 chr16 90354753 3168471 0.035067009701194134 0.27212777391143067 chr17 81195210 2041982 0.025149045122243047 0.232087227954644 chr18 78077248 1821848 0.0233339166872275 0.44602799248231917 chr19 59128983 2774271 0.04691897034657268 0.44218326924483853 chr20 63025520 2700521 0.042848055835160104 0.2956231728138542 chr21 48129895 2027104 0.04211735762149491 0.2901705700145436 chr22 51304566 815435 0.015894004443970933 0.16833772000283123 chrMT 16571 79660 4.807193289481624 4.592728389377055 chrX 155270560 3490351 0.022479155095466906 0.22359909261679556 chrY 59373566 195866 0.003298875462524855 0.08337849293334754