BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080699.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 = 2,203,422 number of mapped reads = 1,914,986 (86.91%) number of supplementary alignments = 18,668 (0.85%) number of secondary alignments = 0 number of mapped bases = 129,640,682 bp number of sequenced bases = 129,592,449 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 129,427 duplication rate = 5.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0422 >>>>>>> ACTG content number of A's = 37,334,672 bp (28.81%) number of C's = 23,554,568 bp (18.18%) number of T's = 41,392,987 bp (31.94%) number of G's = 27,308,429 bp (21.07%) number of N's = 1,793 bp (0%) GC percentage = 39.25% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,066,039 number of insertions = 10,133 mapped reads with insertion percentage = 0.52% number of deletions = 27,397 mapped reads with deletion percentage = 1.42% homopolymer indels = 47.73% >>>>>>> Coverage mean coverageData = 0.0419X std coverageData = 0.3846X There is a 3.17% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% 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 10043432 0.04029451144276186 0.5812467749353228 chr2 243199373 11028585 0.0453479170770724 0.3864205347709267 chr3 198022430 9595510 0.048456682407139434 0.2786411174117341 chr4 191154276 9112572 0.04767129561883303 0.2877463666024198 chr5 180915260 8295634 0.045853699682381684 0.27051780558472255 chr6 171115067 7507878 0.043876194724570924 0.28399258715140424 chr7 159138663 6901333 0.0433667901306925 0.44549207487024794 chr8 146364022 6685685 0.0456784728148561 0.8735872368872496 chr9 141213431 5456438 0.038639653192761816 0.31295786562944344 chr10 135534747 5721551 0.04221464330471654 0.31603990064698023 chr11 135006516 5650889 0.04185641676732107 0.3138159244512234 chr12 133851895 5829043 0.04354845331102709 0.26627197556256316 chr13 115169878 4308336 0.037408531421731644 0.24771832966241952 chr14 107349540 3891662 0.03625224663282209 0.2487619678884058 chr15 102531392 3836955 0.03742224625215271 0.24358426860379162 chr16 90354753 3166330 0.0350433142128118 0.24689834151822718 chr17 81195210 3011916 0.03709474980112743 0.2534346822067864 chr18 78077248 3473973 0.04449405030259263 0.5018442942241631 chr19 59128983 2084269 0.0352495323655406 0.41274117297012586 chr20 63025520 2276815 0.03612528702658859 0.24382213391862997 chr21 48129895 1688966 0.03509182806237163 0.24905846522129288 chr22 51304566 1299138 0.02532207367274094 0.19619430991680156 chrMT 16571 76504 4.616740088105727 3.207264222387089 chrX 155270560 8350020 0.053777226024044736 0.3084391740659325 chrY 59373566 347248 0.005848528619621735 0.15285650483399593