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Arabidopsis thaliana vs Leersia perrieri LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Leersia perrieri (Leersia perrieri, Lperr_V1.4) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. Arabidopsis thaliana 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

ParameterArabidopsis thalianaLeersia perrieri
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 108,346 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 93,480,492 out of 119,667,750
Covered: 26,187,258 out of 119,667,750

Uncovered: 14,451,781 out of 33,775,569
Matches: 12,552,935 out of 33,775,569
Mismatches: 6,369,591 out of 33,775,569
Insertions: 401,262 out of 33,775,569
Identity over aligned base-pairs: 65.0%

Leersia perrieri

Uncovered: 238,908,214 out of 266,687,832
Covered: 27,779,618 out of 266,687,832

Uncovered: 17,640,812 out of 36,898,596
Matches: 12,397,578 out of 36,898,596
Mismatches: 6,381,281 out of 36,898,596
Insertions: 478,925 out of 36,898,596
Identity over aligned base-pairs: 64.4%

Block size distribution

Size range All 108,346 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
892
4.6 kb
10 bp - 100 bp
16,296
1.1 Mb
2,724
191.8 kb
100 bp - 1 kb
84,661
28.5 Mb
19,914
8.5 Mb
1 kb - 10 kb
6,497
9.4 Mb
14,304
29.9 Mb
10 kb - 100 kb
35
426.5 kb