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Arabidopsis thaliana vs Triticum aestivum LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Triticum aestivum (Triticum aestivum, IWGSC) 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 thalianaTriticum aestivum
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 404,317 alignment blocks

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

Uncovered: 91,022,432 out of 119,667,750
Covered: 28,645,318 out of 119,667,750

Uncovered: 13,464,923 out of 33,775,569
Matches: 12,954,935 out of 33,775,569
Mismatches: 6,888,587 out of 33,775,569
Insertions: 467,124 out of 33,775,569
Identity over aligned base-pairs: 63.8%

Triticum aestivum

Uncovered: 14,422,084,033 out of 14,547,261,565
Covered: 125,177,532 out of 14,547,261,565

Uncovered: 64,557,595 out of 133,674,966
Matches: 44,114,019 out of 133,674,966
Mismatches: 23,397,500 out of 133,674,966
Insertions: 1,605,852 out of 133,674,966
Identity over aligned base-pairs: 63.8%

Block size distribution

Size range All 404,317 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,506
12.8 kb
10 bp - 100 bp
65,897
4.6 Mb
19,522
1.4 Mb
100 bp - 1 kb
313,065
102.4 Mb
116,275
44.5 Mb
1 kb - 10 kb
22,849
33.7 Mb
47,982
93.7 Mb
10 kb - 100 kb
84
1.0 Mb