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 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,859,998 |
T→C |
I305V (ATT→GTT) |
rpoS ← |
RNA polymerase sigma factor RpoS |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,859,998 | 0 | T | C | 100.0%
| 93.1
/ NA
| 29 | I305V (ATT→GTT) | rpoS | RNA polymerase sigma factor RpoS |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (14/15); total (14/15) |
TACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGAC > NZ_CP009273/2859915‑2860084
|
tacttactCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCg > 1:305841/1‑90 (MQ=255)
tactCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAaca < 2:265779/90‑1 (MQ=255)
tactCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAaca < 1:545367/90‑1 (MQ=255)
tactCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAaca < 1:335288/90‑1 (MQ=255)
actCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAacac > 1:158610/1‑90 (MQ=255)
actCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAacac > 2:514876/1‑90 (MQ=255)
ggAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCAc < 2:457318/90‑1 (MQ=255)
tCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCa > 2:116094/1‑90 (MQ=255)
ttCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCa < 1:167903/90‑1 (MQ=255)
ttCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCa < 2:365149/90‑1 (MQ=255)
cAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACg > 2:8529/1‑90 (MQ=255)
cAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACg < 2:403839/90‑1 (MQ=255)
gCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGa < 1:228707/59‑1 (MQ=255)
gCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGa > 2:228707/1‑59 (MQ=255)
gCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGAc > 1:284327/1‑90 (MQ=255)
gCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGAc > 1:277929/1‑90 (MQ=255)
ccTGCGTTAGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTa > 1:419834/1‑90 (MQ=255)
cTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTAc < 2:284327/90‑1 (MQ=255)
tGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACa > 2:578263/1‑90 (MQ=255)
tGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACa > 2:161879/1‑90 (MQ=255)
tGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACa > 1:203169/1‑90 (MQ=255)
gCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACAt < 2:277929/90‑1 (MQ=255)
ttGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTc > 2:384865/1‑90 (MQ=255)
tGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTcc < 2:98442/90‑1 (MQ=255)
gATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAgtgt > 2:221472/1‑90 (MQ=255)
tCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCAAGTGTTGcc < 1:391045/90‑1 (MQ=255)
cGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTAc < 1:144717/90‑1 (MQ=255)
gAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGAc < 1:374314/90‑1 (MQ=255)
gAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGAc < 2:583667/90‑1 (MQ=255)
|
TACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGAC > NZ_CP009273/2859915‑2860084
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GACAGATGCTTACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGACGTGCCAGCAC > NZ_CP009273/2859905‑2860094
|
GACAGATGCTTACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCG > SRR3722109.309826/1‑100 (MQ=60)
ATGCTTACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACAC > SRR3722109.160568/1‑100 (MQ=60)
tcagatgtgtataagagacagTCGATATTCGGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCAC < SRR3722109.231424/79‑1 (MQ=60)
TACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGG < SRR3722109.339728/100‑1 (MQ=60)
TACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGG < SRR3722109.553637/100‑1 (MQ=60)
TCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGAC > SRR3722109.281432/1‑100 (MQ=60)
TCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGAC > SRR3722109.287941/1‑100 (MQ=60)
ATATTCAGCCCCTGCGTTAGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTA > SRR3722109.425989/1‑100 (MQ=60)
ATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACA > SRR3722109.205637/1‑100 (MQ=60)
TTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACAT < SRR3722109.169976/100‑1 (MQ=60)
TCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCAAGTGTTGCCGCTTCGTACC < SRR3722109.396650/100‑1 (MQ=60)
CGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAAC < SRR3722109.146506/100‑1 (MQ=60)
CCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGAC > SRR3722109.172913/1‑100 (MQ=60)
ACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGACGTGCCA > SRR3722109.578747/1‑100 (MQ=60)
GAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGACGTGCCAGCAC < SRR3722109.379599/100‑1 (MQ=60)
|
GACAGATGCTTACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGACGTGCCAGCAC > NZ_CP009273/2859905‑2860094
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
