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Triticum aestivum vs Aegilops tauschii LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Aegilops tauschii (Aegilops tauschii subsp. strangulata, Aet_v4.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. Triticum aestivum 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 aestivumAegilops 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 3,367,129 alignment blocks

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

Uncovered: 9,459,434,471 out of 14,547,261,565
Covered: 5,087,827,094 out of 14,547,261,565

Uncovered: 2,219,839 out of 133,674,966
Matches: 125,566,624 out of 133,674,966
Mismatches: 5,336,728 out of 133,674,966
Insertions: 551,775 out of 133,674,966
Identity over aligned base-pairs: 95.5%

Aegilops tauschii

Uncovered: 1,049,682,512 out of 4,224,915,394
Covered: 3,175,232,882 out of 4,224,915,394

Uncovered: 276,949 out of 53,210,770
Matches: 52,165,082 out of 53,210,770
Mismatches: 671,604 out of 53,210,770
Insertions: 97,135 out of 53,210,770
Identity over aligned base-pairs: 98.5%

Block size distribution

Size range All 3,367,129 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
46,564
260.2 kb
10 bp - 100 bp
659,475
37.5 Mb
253,501
15.6 Mb
100 bp - 1 kb
1,821,883
718.8 Mb
714,267
277.9 Mb
1 kb - 10 kb
743,374
1.9 Gb
396,515
1.1 Gb
10 kb - 100 kb
94,971
2.5 Gb
17,412
313.8 Mb
100 kb - 1 Mb
862
105.0 Mb
481
118.8 Mb
1 Mb - 10 Mb
56
174.8 Mb
10 Mb - 100 Mb
25
608.5 Mb
100 Mb - 1 Gb
7
2.6 Gb