BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240202.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 = 1,824,139 number of mapped reads = 1,415,530 (77.6%) number of supplementary alignments = 5,281 (0.29%) number of secondary alignments = 0 number of mapped bases = 85,081,448 bp number of sequenced bases = 85,030,865 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 155,927 duplication rate = 8.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6231 >>>>>>> ACTG content number of A's = 22,958,239 bp (27%) number of C's = 14,378,035 bp (16.91%) number of T's = 28,219,292 bp (33.19%) number of G's = 19,456,737 bp (22.88%) number of N's = 18,562 bp (0.02%) GC percentage = 39.79% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 858,161 number of insertions = 6,074 mapped reads with insertion percentage = 0.43% number of deletions = 29,702 mapped reads with deletion percentage = 2.07% homopolymer indels = 50.66% >>>>>>> Coverage mean coverageData = 0.0275X std coverageData = 0.2828X There is a 1.99% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.14% 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 0.01% 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 6142400 0.02464346919320213 0.36682458069105833 chr2 243199373 9434576 0.038793586856821376 0.3258563687903259 chr3 198022430 6112170 0.030866048861232537 0.24072172674109948 chr4 191154276 6259339 0.032744959364654755 0.25334881914791896 chr5 180915260 4503450 0.02489259336111282 0.21397568732295122 chr6 171115067 4770345 0.02787799510372748 0.25516756513114575 chr7 159138663 4995466 0.03139064954944356 0.4812806870226895 chr8 146364022 5017686 0.03428223638183433 0.39646977397122435 chr9 141213431 3027088 0.02143626125761366 0.23821360662746188 chr10 135534747 3575275 0.026379028840478817 0.24723683144412925 chr11 135006516 3798987 0.028139286254894542 0.2573564158597942 chr12 133851895 3720456 0.027795318101398566 0.223018189709709 chr13 115169878 2040475 0.017717089185420514 0.18063563438190194 chr14 107349540 2933932 0.027330643428933186 0.2293939398008295 chr15 102531392 2228174 0.02173162732443933 0.2075503855044316 chr16 90354753 2259322 0.025005015508149306 0.21232718366527217 chr17 81195210 2246321 0.027665683726909505 0.22906884342414677 chr18 78077248 1955382 0.025044197254493396 0.3302935561600251 chr19 59128983 1380235 0.02334278267562965 0.2882134254390779 chr20 63025520 1672752 0.02654086788970563 0.22109676507005402 chr21 48129895 1282662 0.026650006196772297 0.22357879680415138 chr22 51304566 747632 0.014572426165733475 0.1554420974496369 chrMT 16571 61034 3.6831814615895238 5.215780168419946 chrX 155270560 4739130 0.030521755057752096 0.25200895642686033 chrY 59373566 177159 0.002983802589859602 0.07206891613479101