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Oryza sativa Japonica Group vs Oryza sativa (circum-Aus1 var. N22) LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa (circum-Aus1 var. N22) (Oryza sativa aus subgroup, OsN22RS2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 111. 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 GroupOryza sativa (circum-Aus1 var. N22)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 112,667 alignment blocks

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

Uncovered: 65,694,717 out of 375,049,285
Covered: 309,354,568 out of 375,049,285

Uncovered: 305,090 out of 34,818,902
Matches: 34,154,018 out of 34,818,902
Mismatches: 297,599 out of 34,818,902
Insertions: 62,195 out of 34,818,902
Identity over aligned base-pairs: 99.0%

Oryza sativa (circum-Aus1 var. N22)

Uncovered: 77,775,232 out of 388,175,468
Covered: 310,400,236 out of 388,175,468

Uncovered: 305,597 out of 42,158,175
Matches: 41,281,424 out of 42,158,175
Mismatches: 479,365 out of 42,158,175
Insertions: 91,789 out of 42,158,175
Identity over aligned base-pairs: 98.6%

Block size distribution

Size range All 112,667 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,264
7.4 kb
10 bp - 100 bp
23,402
1.3 Mb
11,249
687.9 kb
100 bp - 1 kb
53,307
19.0 Mb
25,147
8.9 Mb
1 kb - 10 kb
25,628
92.2 Mb
7,330
17.2 Mb
10 kb - 100 kb
8,891
193.3 Mb
304
5.9 Mb
100 kb - 1 Mb
175
30.1 Mb
16
3.1 Mb
1 Mb - 10 Mb
2
4.5 Mb
10 Mb - 100 Mb
12
295.8 Mb