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Oryza sativa Japonica Group vs Oryza sativa (circum-Basmati var. ARC 10497) LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa (circum-Basmati var. ARC 10497) (Oryza sativa aromatic subgroup, Os117425RS1) 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-Basmati var. ARC 10497)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 82,152 alignment blocks

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

Uncovered: 47,257,764 out of 375,049,285
Covered: 327,791,521 out of 375,049,285

Uncovered: 246,027 out of 34,818,902
Matches: 34,304,439 out of 34,818,902
Mismatches: 224,945 out of 34,818,902
Insertions: 43,491 out of 34,818,902
Identity over aligned base-pairs: 99.2%

Oryza sativa (circum-Basmati var. ARC 10497)

Uncovered: 52,142,964 out of 380,354,188
Covered: 328,211,224 out of 380,354,188

Uncovered: 172,480 out of 42,075,030
Matches: 41,509,721 out of 42,075,030
Mismatches: 330,984 out of 42,075,030
Insertions: 61,845 out of 42,075,030
Identity over aligned base-pairs: 99.1%

Block size distribution

Size range All 82,152 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
897
5.2 kb
10 bp - 100 bp
17,047
975.5 kb
8,253
502.8 kb
100 bp - 1 kb
39,582
14.1 Mb
18,570
6.6 Mb
1 kb - 10 kb
17,638
61.6 Mb
5,626
13.2 Mb
10 kb - 100 kb
6,397
170.5 Mb
243
5.0 Mb
100 kb - 1 Mb
591
99.8 Mb
10
1.9 Mb
1 Mb - 10 Mb
1
3.1 Mb
10 Mb - 100 Mb
12
316.7 Mb