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Oryza sativa Japonica Group vs Panicum hallii HAL2 LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Panicum hallii HAL2 (Panicum hallii var. hallii str. HAL2, PhalliiHAL_v2.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 96. 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 GroupPanicum hallii HAL2
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 138,224 alignment blocks

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

Uncovered: 294,738,822 out of 375,049,285
Covered: 80,310,463 out of 375,049,285

Uncovered: 3,383,748 out of 34,349,962
Matches: 24,341,294 out of 34,349,962
Mismatches: 5,864,068 out of 34,349,962
Insertions: 760,852 out of 34,349,962
Identity over aligned base-pairs: 78.6%

Panicum hallii HAL2

Uncovered: 421,618,277 out of 487,473,734
Covered: 65,855,457 out of 487,473,734

Uncovered: 8,501,547 out of 37,739,336
Matches: 23,411,899 out of 37,739,336
Mismatches: 5,201,568 out of 37,739,336
Insertions: 624,322 out of 37,739,336
Identity over aligned base-pairs: 80.1%

Block size distribution

Size range All 138,224 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,254
7.4 kb
10 bp - 100 bp
18,487
1.1 Mb
5,932
409.5 kb
100 bp - 1 kb
91,854
37.5 Mb
22,186
7.4 Mb
1 kb - 10 kb
26,618
47.4 Mb
7,498
18.8 Mb
10 kb - 100 kb
11
156.4 kb
264
6.0 Mb
100 kb - 1 Mb
16
6.2 Mb
1 Mb - 10 Mb
16
47.3 Mb