BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230339.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 = 2,205,680 number of mapped reads = 1,411,631 (64%) number of supplementary alignments = 8,468 (0.38%) number of secondary alignments = 0 number of mapped bases = 88,081,738 bp number of sequenced bases = 88,038,167 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,900 duplication rate = 6.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3516 >>>>>>> ACTG content number of A's = 22,954,509 bp (26.07%) number of C's = 14,700,435 bp (16.7%) number of T's = 30,465,636 bp (34.61%) number of G's = 19,768,458 bp (22.45%) number of N's = 149,129 bp (0.17%) GC percentage = 39.15% >>>>>>> Mismatches and indels general error rate = 0.0123 number of mismatches = 1,071,843 number of insertions = 7,989 mapped reads with insertion percentage = 0.56% number of deletions = 27,054 mapped reads with deletion percentage = 1.89% homopolymer indels = 48.03% >>>>>>> Coverage mean coverageData = 0.0285X std coverageData = 0.2889X There is a 2.23% of reference with a coverageData >= 1X There is a 0.43% 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% 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 6314267 0.025333004085073073 0.3770866771612729 chr2 243199373 9999115 0.04111488807168923 0.36821614947033376 chr3 198022430 8967075 0.045283127774969734 0.2643162531879995 chr4 191154276 4590629 0.02401530897483036 0.21204700207079177 chr5 180915260 4638976 0.02564170650944536 0.1985485894505172 chr6 171115067 4160292 0.024312832720919893 0.22387595223453569 chr7 159138663 4022999 0.0252798341029169 0.3453262814952223 chr8 146364022 5602981 0.03828113578349193 0.4122667574453344 chr9 141213431 4860106 0.03441674043030652 0.33560342690803086 chr10 135534747 3296357 0.02432112113655991 0.2647457569106652 chr11 135006516 3012658 0.02231490811895331 0.24348317424711857 chr12 133851895 6218287 0.046456473402935385 0.26915799847078564 chr13 115169878 1861627 0.01616418313823342 0.15408511815930806 chr14 107349540 2049158 0.019088651893617803 0.18113675241049765 chr15 102531392 1844198 0.017986666951717578 0.165655480869864 chr16 90354753 1673204 0.018518162514372653 0.18391282745114562 chr17 81195210 1792880 0.022081105523343064 0.22855195562483058 chr18 78077248 3945344 0.05053128921757078 0.6080364567677797 chr19 59128983 1183211 0.020010677335681556 0.27233069210918437 chr20 63025520 1337361 0.021219356857349214 0.18428712003931136 chr21 48129895 940276 0.01953621548519896 0.18976407191905423 chr22 51304566 1448883 0.028240819735225905 0.2056974579759397 chrMT 16571 81078 4.892764468046588 4.2867339463754295 chrX 155270560 3971864 0.025580277420265633 0.21661754160963903 chrY 59373566 268912 0.0045291535967369725 0.1265874178372964