Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F2 I206 R1
|
206 |
23.7 |
1314362 |
96.8% |
1272302 |
86.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
539,975 |
A→G |
D258D (GAT→GAC) |
allC ← |
allantoate deiminase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 539,975 | 0 | A | G | 100.0%
| 89.4
/ NA
| 28 | D258D (GAT→GAC) | allC | allantoate deiminase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (15/13); total (15/13) |
CAATCAATGGTGAACGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCGT > NZ_CP009273/539889‑540061
|
caatcaatGGTGAACGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCg > 2:550874/1‑90 (MQ=255)
aatGGTGAACGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCAt < 2:315723/90‑1 (MQ=255)
atGGTGAACGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATc > 2:152927/1‑90 (MQ=255)
gAACGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCtttt > 2:656521/1‑90 (MQ=255)
tGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCtt > 2:134064/1‑90 (MQ=255)
ggCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTcgaccgac > 1:76971/1‑90 (MQ=255)
gCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACt > 1:217556/1‑90 (MQ=255)
aTTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTcgacc > 2:602990/1‑70 (MQ=255)
aTTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTcgacc < 1:602990/70‑1 (MQ=255)
aTTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACt > 2:35440/1‑90 (MQ=255)
tCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGa < 1:134064/90‑1 (MQ=255)
ggCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTaa < 2:161324/90‑1 (MQ=255)
ctctACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAAc < 2:286978/90‑1 (MQ=255)
aCTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTa < 1:35440/90‑1 (MQ=255)
tGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCac < 2:594576/90‑1 (MQ=255)
gCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCacg > 1:15754/1‑90 (MQ=255)
gCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCac < 1:537413/89‑1 (MQ=255)
gCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCac > 2:537413/1‑89 (MQ=255)
gCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTCTCGACCGACTGATGGCAAATGCGACTGAAAGCg > 1:516561/1‑76 (MQ=255)
gCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTCTCGACCGACTGATGGCAAATGCGACTGAAAGCg < 2:516561/76‑1 (MQ=255)
aaaGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCac < 1:594510/86‑1 (MQ=255)
aaaGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCac > 2:594510/1‑86 (MQ=255)
aGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGaa > 1:650130/1‑62 (MQ=255)
aGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGaa < 2:650130/62‑1 (MQ=255)
aCCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATc < 2:278299/90‑1 (MQ=255)
aGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGc > 2:546814/1‑90 (MQ=255)
aGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGc > 1:505577/1‑90 (MQ=255)
cGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCgt < 1:656521/90‑1 (MQ=255)
|
CAATCAATGGTGAACGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCGT > NZ_CP009273/539889‑540061
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCGTGGTGCCTGCA > NZ_CP009273/539906‑540071
|
GGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGAC > SRR3722088.77752/1‑100 (MQ=60)
GTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACT > SRR3722088.219739/1‑100 (MQ=60)
taagagacagCATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGC < SRR3722088.610414/90‑1 (MQ=60)
CATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACT > SRR3722088.397203/1‑100 (MQ=60)
TCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAAC < SRR3722088.135454/100‑1 (MQ=60)
GCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACG > SRR3722088.15927/1‑100 (MQ=60)
GCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTCTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCtgt > SRR3722088.522792/1‑97 (MQ=60)
ACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGAT < SRR3722088.35812/100‑1 (MQ=60)
TGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACC < SRR3722088.543953/100‑1 (MQ=60)
TGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACC < SRR3722088.601826/100‑1 (MQ=60)
GCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTctgtctcttatacacatc > SRR3722088.658177/1‑82 (MQ=60)
GGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGC > SRR3722088.511657/1‑100 (MQ=60)
CAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGctgtctcttatacacatctccgagcccacgagaccgtac > SRR3722088.581727/1‑61 (MQ=60)
CGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCGTGGTGCCTGCA < SRR3722088.664651/100‑1 (MQ=60)
|
GGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCGTGGTGCCTGCA > NZ_CP009273/539906‑540071
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
