BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093993.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 376,678 number of mapped reads = 362,099 (96.13%) number of supplementary alignments = 23,590 (6.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 182,156 number of mapped paired reads (second in pair) = 179,943 number of mapped paired reads (both in pair) = 358,424 number of mapped paired reads (singletons) = 3,675 number of mapped bases = 46,401,867 bp number of sequenced bases = 45,566,465 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 341,280 duplication rate = 50.2% >>>>>>> Insert size mean insert size = 1,158,725.1258 std insert size = 9,614,515.7662 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 40.0336 >>>>>>> ACTG content number of A's = 12,010,000 bp (26.36%) number of C's = 10,704,735 bp (23.49%) number of T's = 11,317,215 bp (24.84%) number of G's = 11,534,037 bp (25.31%) number of N's = 478 bp (0%) GC percentage = 48.81% >>>>>>> Mismatches and indels general error rate = 0.0353 number of mismatches = 1,560,070 number of insertions = 23,947 mapped reads with insertion percentage = 6.49% number of deletions = 123,070 mapped reads with deletion percentage = 32.71% homopolymer indels = 29.23% >>>>>>> Coverage mean coverageData = 0.015X std coverageData = 2.8367X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 893672 0.0035854353999784016 1.1601759762978519 chr2 243199373 2388781 0.009822315619210088 2.997786066775366 chr3 198022430 816612 0.004123835870512245 1.2578524527243766 chr4 191154276 1065783 0.005575512210880388 1.9629944372350556 chr5 180915260 472998 0.0026144726542139123 1.1930222868361446 chr6 171115067 853894 0.004990174243393775 1.3554570555224779 chr7 159138663 933598 0.005866569332683158 1.7169367343398898 chr8 146364022 584430 0.003992989479340763 1.186088979809282 chr9 141213431 565274 0.004002976175828487 1.192001120434079 chr10 135534747 719822 0.005310977560610343 1.6687508471360986 chr11 135006516 1031342 0.007639201651570654 1.936731155783712 chr12 133851895 1059616 0.007916331703783499 1.9069454573073168 chr13 115169878 969686 0.008419614719050063 2.1838821954865315 chr14 107349540 180946 0.0016855777863603327 0.6090996446710106 chr15 102531392 653101 0.006369766246809562 1.728918076970679 chr16 90354753 285725 0.0031622575516309583 0.8610723419730729 chr17 81195210 1179538 0.014527187010169688 3.331662509924945 chr18 78077248 203229 0.0026029221726667417 0.8199211801971893 chr19 59128983 168519 0.0028500236508380333 0.6877837931352394 chr20 63025520 436235 0.006921561297709246 2.3310604753587065 chr21 48129895 109125 0.0022673018505442407 0.4346361332692596 chr22 51304566 157531 0.003070506434066707 0.7816825047848728 chrMT 16571 1230581 74.2611188220385 306.94071238171273 chrX 155270560 28800199 0.18548396424924338 9.630736775909284 chrY 59373566 641630 0.01080666099792625 1.5141325184513756