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Oryza sativa Japonica Group vs Triticum dicoccoides LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Triticum dicoccoides (Triticum dicoccoides, WEWSeq_v.1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. Oryza sativa Japonica Group was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterOryza sativa Japonica GroupTriticum dicoccoides
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 782,434 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 289,541,363 out of 375,049,285
Covered: 85,507,922 out of 375,049,285

Uncovered: 3,131,028 out of 34,403,043
Matches: 24,169,003 out of 34,403,043
Mismatches: 6,219,229 out of 34,403,043
Insertions: 883,783 out of 34,403,043
Identity over aligned base-pairs: 77.3%

Triticum dicoccoides

Uncovered: 9,777,863,999 out of 10,079,039,394
Covered: 301,175,395 out of 10,079,039,394

Uncovered: 19,788,334 out of 100,651,268
Matches: 62,327,755 out of 100,651,268
Mismatches: 16,476,715 out of 100,651,268
Insertions: 2,058,464 out of 100,651,268
Identity over aligned base-pairs: 77.1%

Block size distribution

Size range All 782,434 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4,275
24.2 kb
10 bp - 100 bp
167,852
11.6 Mb
99,067
7.1 Mb
100 bp - 1 kb
523,517
184.3 Mb
295,794
96.8 Mb
1 kb - 10 kb
86,785
146.0 Mb
81,918
200.5 Mb
10 kb - 100 kb
5
62.6 kb
2,452
37.3 Mb
100 kb - 1 Mb
2
228.7 kb