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 |
2,505,777 |
T→C |
I137V (ATC→GTC) |
mntH ← |
Nramp family divalent metal transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,505,777 | 0 | T | C | 100.0%
| 24.6
/ NA
| 9 | I137V (ATC→GTC) | mntH | Nramp family divalent metal transporter |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (5/4); total (5/4) |
GCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTCCGCCAGGTCG > NZ_CP009273/2505689‑2505862
|
gcgGCAACAAACAACAGTACCCCGCCAATCACTTTCTCCAGCGG‑TTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc < 1:247110/90‑1 (MQ=255)
cgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc > 1:201988/1‑90 (MQ=255)
cgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc < 1:500200/90‑1 (MQ=255)
cgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc > 2:484727/1‑90 (MQ=255)
cgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc > 2:489969/1‑90 (MQ=255)
cgGAAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc < 1:320084/90‑1 (MQ=255)
gTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCgcgc < 1:328720/90‑1 (MQ=255)
gTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCgcgc < 2:61996/90‑1 (MQ=255)
aaCCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGTGccc > 2:466596/1‑90 (MQ=255)
ccAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGcaac < 2:414572/90‑1 (MQ=255)
cccGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTaaa < 2:359702/90‑1 (MQ=255)
ttGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATcgc > 2:238652/1‑90 (MQ=255)
cAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACCCCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTc > 1:415258/1‑90 (MQ=255)
cAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTc > 1:105572/1‑90 (MQ=255)
gcgACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTCCGCCAGGTCg > 1:26781/1‑90 (MQ=255)
|
GCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTCCGCCAGGTCG > NZ_CP009273/2505689‑2505862
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ 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
ATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTCCGCCAGGTCG > NZ_CP009273/2505680‑2505862
|
ATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCC > SRR3722109.204437/1‑100 (MQ=60)
GCGGCAACAAACAACAGTACCCCGCCAATCACTTTCTCCAGCGG‑TTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCAC < SRR3722109.250010/100‑1 (MQ=60)
CGGCAACAAACAACAGTACCCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCAC < SRR3722109.507753/100‑1 (MQ=60)
CGGAAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCAC < SRR3722109.324316/100‑1 (MQ=60)
GTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAA < SRR3722109.333066/100‑1 (MQ=60)
GCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACCCCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTC > SRR3722109.421335/1‑100 (MQ=60)
GCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTC > SRR3722109.106889/1‑100 (MQ=60)
CAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTCCGCCAGGTCG > SRR3722109.27110/1‑100 (MQ=60)
|
ATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTCCGCCAGGTCG > NZ_CP009273/2505680‑2505862
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
