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Oryza meridionalis vs Oryza longistaminata LastZ results

Oryza meridionalis (Oryza meridionalis, Oryza_meridionalis_v1.3) and Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 80. Oryza meridionalis 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
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 meridionalisOryza longistaminata
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}

Statistics over 304,216 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza meridionalis

Uncovered: 130,998,641 out of 335,668,232
Covered: 204,669,591 out of 335,668,232

Uncovered: 1,628,944 out of 35,224,824
Matches: 31,274,950 out of 35,224,824
Mismatches: 1,869,053 out of 35,224,824
Insertions: 451,877 out of 35,224,824
Identity over aligned base-pairs: 93.1%

Oryza longistaminata

Uncovered: 149,025,185 out of 326,442,508
Covered: 177,417,323 out of 326,442,508

Uncovered: 7,610,771 out of 34,512,301
Matches: 25,997,819 out of 34,512,301
Mismatches: 765,319 out of 34,512,301
Insertions: 138,392 out of 34,512,301
Identity over aligned base-pairs: 96.6%

Block size distribution

Size range All 304,216 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,697
22.3 kb
10 bp - 100 bp
62,504
3.7 Mb
30,068
1.9 Mb
100 bp - 1 kb
183,119
67.9 Mb
71,507
24.7 Mb
1 kb - 10 kb
54,375
131.9 Mb
12,605
29.4 Mb
10 kb - 100 kb
521
6.5 Mb
2,697
95.8 Mb
100 kb - 1 Mb
350
58.2 Mb