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Triticum dicoccoides vs Aegilops tauschii LastZ results

Triticum dicoccoides (Triticum dicoccoides, WEWSeq_v.1.0) and Aegilops tauschii (Aegilops tauschii subsp. strangulata, Aet_v4.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. Triticum dicoccoides 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)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
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

ParameterTriticum dicoccoidesAegilops tauschii
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 3,827,860 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Triticum dicoccoides

Uncovered: 7,988,059,492 out of 10,079,039,394
Covered: 2,090,979,902 out of 10,079,039,394

Uncovered: 1,122,760 out of 81,268,905
Matches: 75,635,463 out of 81,268,905
Mismatches: 3,984,775 out of 81,268,905
Insertions: 525,907 out of 81,268,905
Identity over aligned base-pairs: 94.4%

Aegilops tauschii

Uncovered: 3,163,916,779 out of 4,224,915,394
Covered: 1,060,998,615 out of 4,224,915,394

Uncovered: 864,497 out of 53,210,770
Matches: 49,096,495 out of 53,210,770
Mismatches: 2,815,807 out of 53,210,770
Insertions: 433,971 out of 53,210,770
Identity over aligned base-pairs: 93.8%

Block size distribution

Size range All 3,827,860 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
60,562
328.2 kb
10 bp - 100 bp
868,893
48.8 Mb
301,532
18.6 Mb
100 bp - 1 kb
2,118,737
828.0 Mb
819,986
318.3 Mb
1 kb - 10 kb
776,054
1.7 Gb
486,783
1.4 Gb
10 kb - 100 kb
3,581
75.6 Mb
23,602
380.4 Mb
100 kb - 1 Mb
33
4.1 Mb
253
52.8 Mb
1 Mb - 10 Mb
14
60.4 Mb
10 Mb - 100 Mb
13
389.3 Mb