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Mouse vs Western wild mouse LastZ results

Mouse (Mus musculus, GRCm39) and Western wild mouse (Mus spretus, SPRET_EiJ_v3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 114. Mouse 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)3000
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

ParameterMouseWestern wild mouse
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 565,833 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Mouse

Uncovered: 295,880,023 out of 2,728,222,451
Covered: 2,432,342,428 out of 2,728,222,451

Uncovered: 30,395 out of 36,936,991
Matches: 36,406,697 out of 36,936,991
Mismatches: 473,061 out of 36,936,991
Insertions: 26,838 out of 36,936,991
Identity over aligned base-pairs: 98.6%

Western wild mouse

Uncovered: 256,616,494 out of 2,546,544,085
Covered: 2,289,927,591 out of 2,546,544,085

Uncovered: 400,199 out of 35,765,005
Matches: 34,937,339 out of 35,765,005
Mismatches: 411,129 out of 35,765,005
Insertions: 16,338 out of 35,765,005
Identity over aligned base-pairs: 98.8%

Block size distribution

Size range All 565,833 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7,154
42.6 kb
10 bp - 100 bp
58,222
3.0 Mb
17,449
1.1 Mb
100 bp - 1 kb
154,480
67.7 Mb
39,768
13.9 Mb
1 kb - 10 kb
271,927
1.1 Gb
14,826
43.2 Mb
10 kb - 100 kb
74,000
1.3 Gb
2,855
77.4 Mb
100 kb - 1 Mb
50
6.6 Mb
190
30.0 Mb
1 Mb - 10 Mb
1
4.9 Mb
10 Mb - 100 Mb
5
391.3 Mb
100 Mb - 1 Gb
15
1.9 Gb