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Oryza sativa Japonica Group vs Setaria italica LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Setaria italica (Setaria italica, Setaria_italica_v2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. 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)3000
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 GroupSetaria italica
Chunk size50,000,000100,100,000
Overlap0100,000
Group set size0100,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 217,639 alignment blocks

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

Uncovered: 291,343,280 out of 375,049,285
Covered: 83,706,005 out of 375,049,285

Uncovered: 3,094,989 out of 34,403,043
Matches: 24,558,920 out of 34,403,043
Mismatches: 5,969,560 out of 34,403,043
Insertions: 779,574 out of 34,403,043
Identity over aligned base-pairs: 78.4%

Setaria italica

Uncovered: 314,247,099 out of 405,732,883
Covered: 91,485,784 out of 405,732,883

Uncovered: 3,755,883 out of 39,583,990
Matches: 28,062,278 out of 39,583,990
Mismatches: 6,940,255 out of 39,583,990
Insertions: 825,574 out of 39,583,990
Identity over aligned base-pairs: 78.3%

Block size distribution

Size range All 217,639 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,764
9.6 kb
10 bp - 100 bp
32,733
2.1 Mb
13,395
937.2 kb
100 bp - 1 kb
149,816
56.8 Mb
56,211
18.9 Mb
1 kb - 10 kb
33,313
58.4 Mb
15,520
36.1 Mb
10 kb - 100 kb
13
183.6 kb
359
8.0 Mb
100 kb - 1 Mb
35
12.6 Mb
1 Mb - 10 Mb
12
40.9 Mb