BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6003991.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 = 3,315,451 number of mapped reads = 2,764,987 (83.4%) number of supplementary alignments = 17,890 (0.54%) number of secondary alignments = 0 number of mapped bases = 185,559,388 bp number of sequenced bases = 185,476,482 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 130,488 duplication rate = 3.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3037 >>>>>>> ACTG content number of A's = 52,405,027 bp (28.25%) number of C's = 33,199,206 bp (17.9%) number of T's = 60,047,906 bp (32.37%) number of G's = 39,804,220 bp (21.46%) number of N's = 20,123 bp (0.01%) GC percentage = 39.36% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 1,770,070 number of insertions = 16,925 mapped reads with insertion percentage = 0.61% number of deletions = 49,811 mapped reads with deletion percentage = 1.78% homopolymer indels = 46.8% >>>>>>> Coverage mean coverageData = 0.0599X std coverageData = 0.6063X There is a 5.06% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% 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 0.01% 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 9152434 0.03671980420060819 1.1389244705350097 chr2 243199373 17161937 0.0705673570959412 0.6817911795161996 chr3 198022430 13448911 0.06791609920148944 0.2982103744324601 chr4 191154276 9963627 0.05212348480240118 0.27747141878075704 chr5 180915260 10697797 0.05913153484122898 0.2862777818898325 chr6 171115067 12753363 0.07453091784138448 0.37951961930611583 chr7 159138663 10105464 0.06350099849714082 0.8793634318643602 chr8 146364022 10961463 0.07489178590623863 0.9626402580722291 chr9 141213431 6749687 0.047797769321248205 0.5693611046194066 chr10 135534747 11017900 0.08129206896295015 0.5425995826172664 chr11 135006516 7496297 0.05552544589773726 0.47617385830468334 chr12 133851895 8962413 0.06695768483516801 0.31336930045838324 chr13 115169878 7226724 0.06274838634456138 0.2834404204635643 chr14 107349540 5709984 0.05319057724886385 0.3133456540060851 chr15 102531392 4624173 0.04510007042526059 0.2446695235526372 chr16 90354753 4534713 0.050187874455259705 0.35423636069180825 chr17 81195210 3665794 0.04514790958727738 0.2879983767782841 chr18 78077248 6901744 0.08839635331409222 1.2689179194394795 chr19 59128983 3305519 0.05590353211385354 0.7551555432258948 chr20 63025520 4041042 0.06411755111262867 0.3087654616312144 chr21 48129895 2478028 0.051486254021539 0.30046655006495965 chr22 51304566 2008479 0.03914815301234592 0.22184903264231123 chrMT 16571 31899 1.924989439382053 1.7914148929992044 chrX 155270560 12080536 0.07780313280250938 0.38539826406539957 chrY 59373566 479460 0.008075310820980501 0.1630415915444703