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Oryza barthii vs Oryza sativa Indica Group LastZ results

Oryza barthii (Oryza barthii, O.barthii_v1) and Oryza sativa Indica Group (Oryza sativa Indica Group, ASM465v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. Oryza barthii 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 barthiiOryza sativa Indica Group
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 215,912 alignment blocks

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

Uncovered: 38,573,540 out of 308,272,304
Covered: 269,698,764 out of 308,272,304

Uncovered: 398,964 out of 39,538,509
Matches: 37,603,112 out of 39,538,509
Mismatches: 1,393,496 out of 39,538,509
Insertions: 142,937 out of 39,538,509
Identity over aligned base-pairs: 96.1%

Oryza sativa Indica Group

Uncovered: 128,346,754 out of 427,004,890
Covered: 298,658,136 out of 427,004,890

Uncovered: 3,550,966 out of 45,465,969
Matches: 40,025,984 out of 45,465,969
Mismatches: 1,616,381 out of 45,465,969
Insertions: 272,638 out of 45,465,969
Identity over aligned base-pairs: 95.5%

Block size distribution

Size range All 215,912 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,484
14.7 kb
10 bp - 100 bp
39,168
2.3 Mb
17,095
1.1 Mb
100 bp - 1 kb
110,067
41.9 Mb
52,096
19.5 Mb
1 kb - 10 kb
57,827
183.4 Mb
17,434
42.7 Mb
10 kb - 100 kb
6,357
94.3 Mb
1,459
25.4 Mb
100 kb - 1 Mb
9
903.8 kb
24
5.5 Mb
10 Mb - 100 Mb
12
228.5 Mb