BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068948.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 = 2,431,235 number of mapped reads = 1,991,245 (81.9%) number of supplementary alignments = 8,064 (0.33%) number of secondary alignments = 0 number of mapped bases = 128,903,682 bp number of sequenced bases = 128,846,502 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,954 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8753 >>>>>>> ACTG content number of A's = 34,334,141 bp (26.65%) number of C's = 21,936,385 bp (17.03%) number of T's = 42,944,109 bp (33.33%) number of G's = 29,322,541 bp (22.76%) number of N's = 309,326 bp (0.24%) GC percentage = 39.78% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,215,704 number of insertions = 11,435 mapped reads with insertion percentage = 0.57% number of deletions = 34,865 mapped reads with deletion percentage = 1.73% homopolymer indels = 48.48% >>>>>>> Coverage mean coverageData = 0.0416X std coverageData = 0.3977X There is a 3.62% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.06% 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% 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 15185712 0.060925473080365965 0.7368710026749412 chr2 243199373 11781200 0.048442559101499 0.3972092355420453 chr3 198022430 9810668 0.049543215887210355 0.2567721894235372 chr4 191154276 5958299 0.03117010576315855 0.21121527089302916 chr5 180915260 6821108 0.03770333138288058 0.2178282154751426 chr6 171115067 7463001 0.043613932605946384 0.29291111702783923 chr7 159138663 8542460 0.05367935006466656 0.680852609710013 chr8 146364022 7314001 0.04997130374020468 0.502931407729348 chr9 141213431 5127135 0.03630770078803623 0.3860152863044411 chr10 135534747 7844224 0.05787611054455283 0.46850789849146257 chr11 135006516 6177513 0.04575714701059318 0.3614205006027555 chr12 133851895 5450648 0.04072148548961522 0.23347735384908683 chr13 115169878 2956495 0.025670731369533968 0.17640966357157362 chr14 107349540 3214112 0.029940622009186065 0.2237919458748418 chr15 102531392 2088719 0.020371507294078287 0.15820778741263603 chr16 90354753 2408465 0.026655653632299787 0.21360193919640494 chr17 81195210 2103180 0.025902759534706544 0.20694659675186056 chr18 78077248 2787523 0.03570211644754692 0.5885112231950368 chr19 59128983 2089209 0.0353330785344304 0.4662889433277529 chr20 63025520 1696202 0.026912939393439354 0.1994264879257659 chr21 48129895 1472407 0.030592358449982076 0.21554189097945997 chr22 51304566 870510 0.016967495641615992 0.14325785982701492 chrMT 16571 185528 11.195944722708346 7.564371873501661 chrX 155270560 9242479 0.059524993018637916 0.3152852469946307 chrY 59373566 312884 0.0052697525360023015 0.10928421441830957