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Arabidopsis thaliana vs Phaseolus vulgaris LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Phaseolus vulgaris (Phaseolus vulgaris, PhaVulg1_0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 91. 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 thalianaPhaseolus vulgaris
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 137,058 alignment blocks

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

Uncovered: 84,897,697 out of 119,667,750
Covered: 34,770,053 out of 119,667,750

Uncovered: 9,163,754 out of 33,775,569
Matches: 16,478,477 out of 33,775,569
Mismatches: 7,569,924 out of 33,775,569
Insertions: 563,414 out of 33,775,569
Identity over aligned base-pairs: 67.0%

Phaseolus vulgaris

Uncovered: 481,726,169 out of 521,076,696
Covered: 39,350,527 out of 521,076,696

Uncovered: 9,023,437 out of 34,663,348
Matches: 17,191,069 out of 34,663,348
Mismatches: 7,807,657 out of 34,663,348
Insertions: 641,185 out of 34,663,348
Identity over aligned base-pairs: 67.0%

Block size distribution

Size range All 137,058 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,280
6.9 kb
10 bp - 100 bp
20,287
1.3 Mb
4,347
303.0 kb
100 bp - 1 kb
105,570
36.5 Mb
24,235
9.7 Mb
1 kb - 10 kb
9,908
14.9 Mb
16,716
38.8 Mb
10 kb - 100 kb
13
194.8 kb
278
4.2 Mb