BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082983.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 = 3,376,140 number of mapped reads = 2,635,856 (78.07%) number of supplementary alignments = 18,058 (0.53%) number of secondary alignments = 0 number of mapped bases = 179,545,757 bp number of sequenced bases = 179,474,012 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,785 duplication rate = 2.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2847 >>>>>>> ACTG content number of A's = 51,263,123 bp (28.56%) number of C's = 32,771,271 bp (18.26%) number of T's = 57,471,012 bp (32.02%) number of G's = 37,950,626 bp (21.15%) number of N's = 17,980 bp (0.01%) GC percentage = 39.41% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,736,257 number of insertions = 15,921 mapped reads with insertion percentage = 0.6% number of deletions = 41,486 mapped reads with deletion percentage = 1.56% homopolymer indels = 47.99% >>>>>>> Coverage mean coverageData = 0.058X std coverageData = 0.422X There is a 4.76% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% 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 17234043 0.06914343053933655 0.7253328367113535 chr2 243199373 17995833 0.07399621462017503 0.5041677195466956 chr3 198022430 11046762 0.055785407743961124 0.2782098314421095 chr4 191154276 11859324 0.06204058966486316 0.3082986467684445 chr5 180915260 9239072 0.05106850577447143 0.26504819177735806 chr6 171115067 13039852 0.07620516549837192 0.4397387977181354 chr7 159138663 11972575 0.0752336030371199 0.41494969235766765 chr8 146364022 13386805 0.09146240187359705 0.5889169129697017 chr9 141213431 5411853 0.03832392543454312 0.391025776753452 chr10 135534747 6515561 0.048072993414744046 0.3754131290566467 chr11 135006516 7963259 0.05898425673024552 0.3554137217924577 chr12 133851895 5701803 0.04259785040772116 0.24702357293098656 chr13 115169878 4215730 0.036604449646113195 0.22126966746642746 chr14 107349540 3862561 0.0359811602359917 0.27367377647449526 chr15 102531392 3988515 0.03890042768560091 0.23132261207791285 chr16 90354753 7154079 0.07917767203679922 0.3758302268208273 chr17 81195210 4113846 0.05066611688054012 0.2994538617786686 chr18 78077248 4789280 0.06134027674745913 0.8228450731205499 chr19 59128983 2621092 0.044328379535971386 0.4859750787319171 chr20 63025520 3457189 0.05485379573226845 0.29213347994547306 chr21 48129895 4037643 0.08389054245807102 0.35585763308203366 chr22 51304566 2199970 0.042880588834919686 0.24008879059592042 chrMT 16571 9099 0.5490917868565567 0.8488365833168807 chrX 155270560 7422385 0.04780291254182377 0.2886731936128876 chrY 59373566 307626 0.00518119460771482 0.1075310572669438