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 |
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%
| 52.4
/ NA
| 18 | I137V (ATC→GTC) | mntH | Nramp family divalent metal transporter |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (10/8); total (10/8) |
CGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCAC > NZ_CP009273/2505690‑2505842
|
cgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCTGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc > 1:277420/1‑90 (MQ=255)
cgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc < 1:338091/90‑1 (MQ=255)
cgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc < 2:55956/90‑1 (MQ=255)
cgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc > 1:523044/1‑90 (MQ=255)
cgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc < 1:537183/90‑1 (MQ=255)
caGTAACCCGCCAATCACTTTCCCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACcgc > 1:448570/1‑90 (MQ=255)
gTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCgcgc > 1:394203/1‑90 (MQ=255)
gTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCgcgc > 1:571244/1‑90 (MQ=255)
ccGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc > 2:577555/1‑70 (MQ=255)
ccGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc < 1:577555/70‑1 (MQ=255)
ccGCCAATCACTTTCTCCAGCGGTTTTTACCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGc > 2:573176/1‑90 (MQ=255)
gCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGcaa > 1:465247/1‑90 (MQ=255)
gCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGcaa > 2:402101/1‑90 (MQ=255)
ttCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAaca > 2:654197/1‑90 (MQ=255)
gCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGaa > 1:578443/1‑90 (MQ=255)
ggTTTTTGCCCGCGACGTTGCCGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATg < 1:624592/90‑1 (MQ=255)
ggTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATg < 2:44924/90‑1 (MQ=255)
ggTTTTTACCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATg < 1:573176/90‑1 (MQ=255)
ttGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGttt < 2:578443/90‑1 (MQ=255)
gcgACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTaa > 2:458950/1‑86 (MQ=255)
gcgACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTaa < 1:458950/86‑1 (MQ=255)
gcgACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAAcc > 1:482738/1‑90 (MQ=255)
cagcaTTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATcgccgc < 2:394203/90‑1 (MQ=255)
cagcaTTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATcgccgc < 1:210486/90‑1 (MQ=255)
gcaTTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCAc < 1:402101/90‑1 (MQ=255)
|
CGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCAC > NZ_CP009273/2505690‑2505842
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 31 ≤ 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
ATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTC > NZ_CP009273/2505680‑2505852
|
ATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCTGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCC > SRR3722088.280097/1‑100 (MQ=60)
ATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCC > SRR3722088.81867/1‑100 (MQ=60)
ATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCC > SRR3722088.529368/1‑100 (MQ=60)
taagagacagCAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCAC < SRR3722088.584637/90‑1 (MQ=60)
CGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCAC < SRR3722088.341629/100‑1 (MQ=60)
CGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCAC < SRR3722088.543720/100‑1 (MQ=60)
CAACAAACAACAGTAACCCGCCAATCACTTTCCCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGC > SRR3722088.453782/1‑100 (MQ=60)
ACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGC > SRR3722088.398441/1‑100 (MQ=60)
ACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGC > SRR3722088.578249/1‑100 (MQ=60)
ACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAA > SRR3722088.470699/1‑100 (MQ=60)
ACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCCACAACGAAACACCAAGAA > SRR3722088.585536/1‑100 (MQ=60)
GGTTTTTGCCCGCGACGTTGCCGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAAC < SRR3722088.632301/100‑1 (MQ=60)
GGTTTTTACCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAAC < SRR3722088.580207/100‑1 (MQ=60)
GTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACC > SRR3722088.488485/1‑100 (MQ=60)
GCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGC < SRR3722088.464318/100‑1 (MQ=60)
CAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAAT < SRR3722088.212596/100‑1 (MQ=60)
GCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTC < SRR3722088.406488/100‑1 (MQ=60)
|
ATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTC > NZ_CP009273/2505680‑2505852
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
