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Oryza longistaminata vs Oryza sativa Japonica Group LastZ results

Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) and Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 80. Oryza longistaminata 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 longistaminataOryza sativa Japonica Group
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}

Statistics over 350,224 alignment blocks

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

Uncovered: 63,545,502 out of 326,442,508
Covered: 262,897,006 out of 326,442,508

Uncovered: 941,072 out of 34,512,301
Matches: 32,369,355 out of 34,512,301
Mismatches: 1,041,484 out of 34,512,301
Insertions: 160,390 out of 34,512,301
Identity over aligned base-pairs: 96.4%

Oryza sativa Japonica Group

Uncovered: 162,259,490 out of 375,049,285
Covered: 212,789,795 out of 375,049,285

Uncovered: 5,823,255 out of 34,818,902
Matches: 28,017,923 out of 34,818,902
Mismatches: 781,259 out of 34,818,902
Insertions: 196,465 out of 34,818,902
Identity over aligned base-pairs: 96.6%

Block size distribution

Size range All 350,224 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4,358
26.2 kb
10 bp - 100 bp
66,997
4.0 Mb
31,668
2.0 Mb
100 bp - 1 kb
210,803
76.2 Mb
98,069
33.3 Mb
1 kb - 10 kb
66,849
172.7 Mb
16,429
38.3 Mb
10 kb - 100 kb
1,217
15.7 Mb
3,063
109.5 Mb
100 kb - 1 Mb
504
85.5 Mb