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 |
|
A2 F5 I176 R1
|
180 |
42.9 |
1710034 |
96.5% |
1650182 |
119.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,006,907 |
T→C |
D496D (GAT→GAC) |
uup → |
ABC transporter ATP‑binding protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,006,907 | 0 | T | C | 100.0%
| 70.7
/ NA
| 21 | D496D (GAT→GAC) | uup | ABC transporter ATP‑binding protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (9/12); total (9/12) |
CTCAAACCAAGCAACTTATTGATTCTTGACGAACCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGATCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAATTGGTCGTTATGTCGGCGGTTATCATGATGCCCGTGGTCAGCAAGAGCAGTATGTGGCGCTCAAACAGCCT > NZ_CP009273/1006785‑1007036
|
cTCAAACCAAGCAACTTATTGATTCTTGACGAACCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGAt < 1:477799/138‑1 (MQ=255)
cTCAAACCAAGCAACTTATTGATTCTTGACGAACCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGAt < 2:726361/138‑1 (MQ=255)
aaaCCAAGCAACTTATTGATTCTTGACGAACCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATaa < 2:778390/137‑1 (MQ=255)
aaaCCAAGCAACTTATTGATTCTTGACGAACCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAaca < 2:345771/139‑1 (MQ=255)
gCAACTTATTGATTCTTGACGAACCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGAt > 1:337278/1‑128 (MQ=255)
gCAACTTATTGATTCTTGACGAACCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGAt < 2:337278/128‑1 (MQ=255)
cAACTTATTGATTCTTGACGAACCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTACa < 1:823175/139‑1 (MQ=255)
cTTGACGAACCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCt > 2:502060/1‑139 (MQ=255)
cTTGACGAACCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCt > 1:166673/1‑139 (MQ=255)
aCCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTAc > 1:359911/1‑117 (MQ=255)
aCCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTAc < 2:359911/117‑1 (MQ=255)
cGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAATTGGTCGTTATGTcgg < 2:253376/139‑1 (MQ=255)
ctgGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAATTGGTCGTTATGTCGGCGGTTATCatg > 2:492042/1‑139 (MQ=255)
aagaaCTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAATTGGTCGTTATGTCGGCGGTTATCATGATGc < 2:166673/139‑1 (MQ=255)
cGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAAtt < 1:803207/100‑1 (MQ=255)
cGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAAtt > 2:803207/1‑100 (MQ=255)
ggCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAATTGGTCGTTATGTCGGCGGTTATCATGATGCCCGTGGTCAGCAAGAGCAGTAtg > 1:689643/1‑139 (MQ=255)
ttGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAATTGGTCGTTATGTCGGCGGTTATCATGATGCCCGTGGTCAGCAAGAGCAGTATGTGGCGCTc < 1:345298/138‑1 (MQ=255)
tAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAATTGGTCGTTATGTc < 1:839434/82‑1 (MQ=255)
tAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAATTGGTCGTTATGTc > 2:839434/1‑82 (MQ=255)
tAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAATTGGTCGTTATGTCGGCGGTTATCATGATGCCCGTGGTCACCAAGAGAAGCATGTGGGGCTCAAACAAccc > 1:74063/1‑138 (MQ=255)
|
CTCAAACCAAGCAACTTATTGATTCTTGACGAACCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGATCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAATTGGTCGTTATGTCGGCGGTTATCATGATGCCCGTGGTCAGCAAGAGCAGTATGTGGCGCTCAAACAGCCT > NZ_CP009273/1006785‑1007036
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CCTCAAACCAAGCAACTTATTGATTCTTGACGAACCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGATCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAATTGGTCGTTATGTCGGCGGTTATCATGATGCCCGTGGTCAGCAAGAGCAGTATGTGGCGCTCAAACAGCCTGCGGTGAAAAAA > NZ_CP009273/1006784‑1007048
|
CCTCAAACCAAGCAACTTATTGATTCTTGACGAACCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTACC > SRR3722130.342499/1‑151 (MQ=60)
CCTCAAACCAAGCAACTTATTGATTCTTGACGAACCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTAC < SRR3722130.485214/150‑1 (MQ=60)
GCAACTTATTGATTCTTGACGAACCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGAT < SRR3722130.835135/151‑1 (MQ=60)
ACTTATTGATTCTTGACGAACCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTT > SRR3722130.169177/1‑151 (MQ=60)
ATTCTTGACGAACCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGActgtctcttat > SRR3722130.365530/1‑139 (MQ=60)
gtgggctcggagatgtgtataagagacaGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAATTGGTCGTTATGT < SRR3722130.814938/123‑1 (MQ=60)
gagattcgccttagtctcgtgggctcggagatgtgtataagagacaGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAATTGGTCGTTATGTCGGCGGTTATCA < SRR3722130.851596/105‑1 (MQ=60)
cgtgggctcggagatgtgtataagagacagGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAATTGGTCGTTATGTTGGCGGTTATCATGATGCCCGTGGTCAGCAAGAGCAGTAT < SRR3722130.158015/119‑1 (MQ=60)
ACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAATTGGTCGTTATGTCGGCGGTTATCATGATGCCCGTGGTCAGCAAGAGCAGgatgg > SRR3722130.699860/1‑146 (MQ=60)
GTATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAATTGGTCGTTATGTCGGCGGTTATCATGATGCCCGTGGTCACCAAGAGAAGCATGTGGGGCTCAAACAacccg > SRR3722130.75117/1‑146 (MQ=60)
ATTGCTGGTTAGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAATTGGTCGTTATGTCGGCGGTTATCATGATGCCCGTGGTCAGCAAGAGCAGTATGTGGCGCTCAAACAGCCTGC < SRR3722130.350657/150‑1 (MQ=60)
AGCCACGACCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAATTGGTCGTTATGTCGGCGGTTATCATGATGCCCGTGGTCAGCAAGAGCAGTATGTGGCGCTCAAACAGCCTGCGGGGAAAAAA > SRR3722130.302466/1‑150 (MQ=60)
|
CCTCAAACCAAGCAACTTATTGATTCTTGACGAACCGACCAACGATCTTGATGTCGAAACGCTGGAACTGCTGGAAGAACTGATCGACAGCTATCAGGGCACGGTATTGCTGGTTAGCCACGATCGTCAGTTTGTCGATAACACCGTTACAGAATGTTGGATCTTCGAAGGCGGCGGTAAAATTGGTCGTTATGTCGGCGGTTATCATGATGCCCGTGGTCAGCAAGAGCAGTATGTGGCGCTCAAACAGCCTGCGGTGAAAAAA > NZ_CP009273/1006784‑1007048
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
