BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926958.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 9,796,144 number of mapped reads = 9,467,647 (96.65%) number of supplementary alignments = 206,377 (2.11%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,747,866 number of mapped paired reads (second in pair) = 4,719,781 number of mapped paired reads (both in pair) = 9,309,660 number of mapped paired reads (singletons) = 157,987 number of mapped bases = 871,902,360 bp number of sequenced bases = 871,235,284 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 548,541 duplication rate = 4.82% >>>>>>> Insert size mean insert size = 235,080.1089 std insert size = 4,822,102.7645 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 52.5836 >>>>>>> ACTG content number of A's = 247,505,798 bp (28.41%) number of C's = 172,783,956 bp (19.83%) number of T's = 249,665,271 bp (28.66%) number of G's = 201,232,931 bp (23.1%) number of N's = 47,328 bp (0.01%) GC percentage = 42.93% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 8,655,519 number of insertions = 148,536 mapped reads with insertion percentage = 1.54% number of deletions = 457,537 mapped reads with deletion percentage = 4.71% homopolymer indels = 52.81% >>>>>>> Coverage mean coverageData = 0.2817X std coverageData = 1.2627X There is a 16.79% of reference with a coverageData >= 1X There is a 6.44% of reference with a coverageData >= 2X There is a 2.52% of reference with a coverageData >= 3X There is a 1.1% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.24% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 75705026 0.3037305411568062 1.5365196449389946 chr2 243199373 74578144 0.30665434322480756 2.4236814339322965 chr3 198022430 58224397 0.29402930264011 0.7914204118778563 chr4 191154276 51368573 0.2687283490325898 1.1041114440518522 chr5 180915260 52355245 0.2893909833808381 0.7768359259136527 chr6 171115067 50879288 0.29733961416734855 0.8132168833969455 chr7 159138663 45070356 0.2832143688425986 0.7909423746200399 chr8 146364022 43686791 0.29848039431438966 0.8279881416571798 chr9 141213431 37158780 0.26313913440712305 0.8848794219612405 chr10 135534747 42616833 0.31443474048761827 2.306679236653258 chr11 135006516 41829310 0.3098317861931938 0.9077632053457036 chr12 133851895 40261313 0.30079001122845517 0.9254447633270102 chr13 115169878 26255880 0.22797523498288327 0.6861712054262072 chr14 107349540 27299852 0.25430804826923337 0.7496936616044961 chr15 102531392 26135162 0.2548991239678088 0.7462609955195745 chr16 90354753 26499638 0.2932843831690846 0.9784019317885715 chr17 81195210 26743536 0.32937332140652137 0.8989894757589295 chr18 78077248 22852854 0.29269543414235094 0.9748945213071107 chr19 59128983 18805773 0.318046616834252 1.1031254973265037 chr20 63025520 21783446 0.345628976960444 0.9140252472912677 chr21 48129895 11072779 0.23006031905949514 0.9394690808312453 chr22 51304566 327317 0.006379880496406499 0.12752752617787969 chrMT 16571 1713373 103.39587230704242 107.81984672160955 chrX 155270560 47369780 0.3050789537952333 0.8093029996490368 chrY 59373566 1308914 0.02204539979963474 0.7793498130139389