BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238313.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 = 2,483,314 number of mapped reads = 2,250,655 (90.63%) number of supplementary alignments = 21,494 (0.87%) number of secondary alignments = 0 number of mapped bases = 147,410,651 bp number of sequenced bases = 147,337,710 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,054 duplication rate = 3.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2724 >>>>>>> ACTG content number of A's = 40,377,537 bp (27.4%) number of C's = 28,049,676 bp (19.04%) number of T's = 45,304,532 bp (30.75%) number of G's = 33,571,524 bp (22.79%) number of N's = 34,441 bp (0.02%) GC percentage = 41.82% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,248,147 number of insertions = 11,645 mapped reads with insertion percentage = 0.51% number of deletions = 43,567 mapped reads with deletion percentage = 1.91% homopolymer indels = 45.15% >>>>>>> Coverage mean coverageData = 0.0476X std coverageData = 0.4239X There is a 3.96% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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% 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 12115169 0.04860637438492079 0.7198827685390523 chr2 243199373 10520647 0.0432593508372244 0.5325935030808508 chr3 198022430 9933851 0.05016528178146284 0.25895089211268046 chr4 191154276 7118716 0.037240684064007025 0.25298091173718534 chr5 180915260 7935217 0.043861512843084656 0.24441370603305948 chr6 171115067 7520448 0.04394965406523787 0.2862306902224277 chr7 159138663 7880613 0.0495204172979636 0.5547140839749408 chr8 146364022 7422616 0.05071339184707564 0.5457946195909203 chr9 141213431 7202817 0.05100660007333155 0.4291842846001835 chr10 135534747 6364436 0.04695796569421419 0.4067757988572342 chr11 135006516 6256583 0.04634282244569588 0.3556429268572117 chr12 133851895 7500510 0.056035889518037826 0.2864820163686178 chr13 115169878 6005525 0.05214492803404724 0.2657009884704159 chr14 107349540 6652267 0.061968286030848384 0.3322385597306049 chr15 102531392 4025231 0.03925852289218896 0.23313260161716817 chr16 90354753 5368413 0.059414837866913324 0.3221138428421794 chr17 81195210 4285086 0.05277510828532866 0.3193165371017847 chr18 78077248 3847658 0.04928014368539219 0.8202708281772718 chr19 59128983 3937546 0.0665924864630261 0.5202445496181881 chr20 63025520 3413396 0.05415895021572214 0.2836429532484851 chr21 48129895 1894065 0.03935319202337757 0.26532593852590036 chr22 51304566 1709260 0.03331594306830312 0.21073570137123632 chrMT 16571 5441 0.3283446985697906 0.6894897870366601 chrX 155270560 8101653 0.052177650418727156 0.30390517070504003 chrY 59373566 393487 0.006627309533673621 0.1712202708478628