BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013169.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 = 1,999,952 number of mapped reads = 1,418,027 (70.9%) number of supplementary alignments = 11,771 (0.59%) number of secondary alignments = 0 number of mapped bases = 87,356,439 bp number of sequenced bases = 87,264,666 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 223,091 duplication rate = 11.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7963 >>>>>>> ACTG content number of A's = 23,335,924 bp (26.74%) number of C's = 15,515,675 bp (17.78%) number of T's = 28,153,100 bp (32.26%) number of G's = 20,126,661 bp (23.06%) number of N's = 133,306 bp (0.15%) GC percentage = 40.84% >>>>>>> Mismatches and indels general error rate = 0.0116 number of mismatches = 997,230 number of insertions = 6,077 mapped reads with insertion percentage = 0.43% number of deletions = 52,166 mapped reads with deletion percentage = 3.6% homopolymer indels = 41.21% >>>>>>> Coverage mean coverageData = 0.0282X std coverageData = 0.3495X There is a 1.62% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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% 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 8618011 0.034575685169506556 0.5297793124941607 chr2 243199373 11516753 0.04735519198892014 0.47053342775392704 chr3 198022430 5127518 0.02589362225279227 0.2638292086191012 chr4 191154276 4114038 0.021522081985756888 0.25603187454334386 chr5 180915260 5016964 0.02773101616745873 0.2702868200292332 chr6 171115067 2749082 0.016065692216337676 0.24189312795681522 chr7 159138663 6568774 0.041277046546507684 0.4305620841822569 chr8 146364022 6473075 0.04422586173533821 0.39205322668037373 chr9 141213431 2561948 0.018142381938159976 0.27232987319362495 chr10 135534747 4163405 0.03071835888696498 0.4745111842932431 chr11 135006516 2054435 0.01521730254856736 0.2269343426968498 chr12 133851895 3265545 0.024396703535650356 0.25057348752907777 chr13 115169878 2489519 0.021616060060426563 0.2376770275034764 chr14 107349540 5118963 0.047685001724273805 0.37353134154045603 chr15 102531392 1528209 0.01490479130528141 0.19979533693609625 chr16 90354753 3245272 0.03591700372419811 0.3405302949503844 chr17 81195210 1565399 0.019279450105492677 0.23439107572077672 chr18 78077248 1527034 0.01955798954389376 0.5107166571869961 chr19 59128983 912301 0.015428998668893053 0.39433086931925837 chr20 63025520 1001364 0.01588823067227371 0.2167066186449166 chr21 48129895 1457309 0.03027866568169326 0.305995702845029 chr22 51304566 751354 0.014644973314850767 0.19412102290829503 chrMT 16571 21880 1.3203789753183273 1.6465184117303 chrX 155270560 5201618 0.03350034932571892 0.30737996130870715 chrY 59373566 306669 0.0051650763236959695 0.17208033641501477