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Oryza sativa Japonica Group vs Aegilops umbellulata LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Aegilops umbellulata (Aegilops umbellulata, TA1851) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 113. 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 GroupAegilops umbellulata
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 306,945 alignment blocks

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

Uncovered: 295,757,045 out of 375,049,285
Covered: 79,292,240 out of 375,049,285

Uncovered: 3,611,375 out of 34,818,902
Matches: 24,253,911 out of 34,818,902
Mismatches: 6,092,095 out of 34,818,902
Insertions: 861,521 out of 34,818,902
Identity over aligned base-pairs: 77.7%

Aegilops umbellulata

Uncovered: 4,113,964,095 out of 4,246,573,824
Covered: 132,609,729 out of 4,246,573,824

Uncovered: 6,260,270 out of 43,535,509
Matches: 29,022,575 out of 43,535,509
Mismatches: 7,399,088 out of 43,535,509
Insertions: 853,576 out of 43,535,509
Identity over aligned base-pairs: 77.9%

Block size distribution

Size range All 306,945 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,401
13.4 kb
10 bp - 100 bp
43,960
2.8 Mb
19,814
1.4 Mb
100 bp - 1 kb
215,521
80.8 Mb
99,187
35.3 Mb
1 kb - 10 kb
45,056
77.0 Mb
41,441
103.1 Mb
10 kb - 100 kb
7
79.3 kb
1,311
20.7 Mb
100 kb - 1 Mb
2
236.2 kb