Skip to main content

Table 3 Summary of mutations generated by Galaxy's Filter pileup

From: Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis

1Chr. Position 2Ref.
base
3Con.
base
4Con. Qual. SNP Qual. Max.
Mapping
Qual.
Coverage 5QA
coverage
Total
number of
deviants
6% deviant reads
II 14,208,479 G A 225 225 60 3,801 3,407 3,379 99.2
II 14,427,587 G A 225 225 60 7,847 4,268 4,211 98.7
III 2,849,685 A C 225 225 60 341 319 316 99.1
III 2,954,586 G A 225 225 60 7,820 2,236 2,208 98.7
III 3,007,742 C G 225 225 60 1,438 1,177 1,175 99.8
III 3,113,098 G A 225 225 60 4,170 3,790 3,776 99.6
III 3,114,003 G T 225 225 60 937 568 567 99.8
III 3,147,629 G A 225 225 60 2,539 1,558 1,537 98.7
V 4,851,838 C T 225 225 60 750 669 668 99.9
V 4,979,060 C T 202 202 60 172 66 65 98.5
V 4,984,678 C T 152 152 60 134 18 16 88.9
V 5,016,518 C T 225 225 60 563 509 504 99
V 5,020,510 C T 225 225 60 2,961 1,333 1,319 98.9
V 5,355,232 C T 225 225 60 7,841 6,875 6,821 99.2
  1. 1. Chromosome
  2. 2. Reference base
  3. 3. Consensus base
  4. 4. Consensus Quality
  5. 5. Quality adjusted coverage
  6. 6. The percentage of total number of deviants/quality adjusted coverage