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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
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 | 97.1%
| 101.4
/ ‑3.5
| 35 | I137V (ATC→GTC) | mntH | Nramp family divalent metal transporter |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (12/21); total (14/21) |
| Fisher's exact test for biased strand distribution p-value = 3.82e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.38e-01 |
CGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTC > NZ_CP009273/2505690‑2505852
|
gggCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGCAAAGGCGCGAccc > 1:1042884/2‑90 (MQ=255)
cgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc > 2:890042/1‑90 (MQ=255)
cgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc > 2:1080316/1‑90 (MQ=255)
cgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc > 1:783319/1‑90 (MQ=255)
cgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc < 1:1302854/90‑1 (MQ=255)
cgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc > 2:388185/1‑90 (MQ=255)
cgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc > 1:1455039/1‑90 (MQ=255)
cgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc < 2:651819/90‑1 (MQ=255)
cgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc < 1:320134/90‑1 (MQ=255)
acaaacaaCAGTACCCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTc < 1:425386/90‑1 (MQ=255)
caacaGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCAc < 2:1303288/90‑1 (MQ=255)
caGTACCCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACcgc < 2:1185016/90‑1 (MQ=255)
caGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACcgc < 2:727658/90‑1 (MQ=255)
gTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCgcgc > 2:630309/1‑90 (MQ=255)
gTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCgcgc < 2:284637/90‑1 (MQ=255)
gTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCgcgc > 2:1185692/1‑90 (MQ=255)
cGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGca < 1:388185/90‑1 (MQ=255)
cGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGca < 1:113920/90‑1 (MQ=255)
gCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGcaa > 1:1577760/1‑90 (MQ=255)
gCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGcaa > 1:1342953/1‑90 (MQ=255)
ccAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGcaac < 2:250491/90‑1 (MQ=255)
aCTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGaa < 1:1080316/90‑1 (MQ=255)
aCTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGaa < 2:471225/90‑1 (MQ=255)
aCTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGaa < 2:1455039/90‑1 (MQ=255)
aCTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGaa < 1:766790/90‑1 (MQ=255)
tttCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAac < 2:977216/90‑1 (MQ=255)
tttCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAac < 2:1247635/90‑1 (MQ=255)
tctcCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAacac > 2:1009685/1‑90 (MQ=255)
aGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGa > 2:107572/1‑90 (MQ=255)
ggTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATg < 2:1577760/90‑1 (MQ=255)
ggTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATg < 1:984564/90‑1 (MQ=255)
ggTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATg < 1:1185692/90‑1 (MQ=255)
gTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGa > 2:364560/1‑90 (MQ=255)
ttttGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGt > 2:949880/1‑90 (MQ=255)
gCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTaa < 2:1042224/90‑1 (MQ=255)
ttGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATcgc > 1:1098279/1‑90 (MQ=255)
cagcaTTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATcgccgc < 2:1067927/90‑1 (MQ=255)
cagcaTTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATcgccgc < 2:506831/90‑1 (MQ=255)
cagcaTTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATcgccgc < 2:1105562/90‑1 (MQ=255)
gcaTTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCAc > 1:490237/1‑90 (MQ=255)
aTTAAAATCAGGAAAGTCGCGA‑CCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCaa > 1:1497271/1‑90 (MQ=255)
cAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTc > 2:1480582/1‑90 (MQ=255)
cAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTc > 2:311690/1‑90 (MQ=255)
cAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTc > 1:668778/1‑90 (MQ=255)
|
CGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTC > NZ_CP009273/2505690‑2505852
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ 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
AATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTCCGCCAGGTCGGTTGCCATCGCAA > NZ_CP009273/2505679‑2505875
|
AATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACC < SRR3722078.510577/100‑1 (MQ=60)
ATGTAATCCGGGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGCAAAGGCGCGACCC > SRR3722078.1058455/1‑100 (MQ=60)
ATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCC > SRR3722078.793521/1‑100 (MQ=60)
ATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCC > SRR3722078.1478767/1‑100 (MQ=60)
CGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCAC < SRR3722078.324053/100‑1 (MQ=60)
CGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCAC < SRR3722078.1323626/100‑1 (MQ=60)
ACAAACAACAGTACCCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGC < SRR3722078.430513/100‑1 (MQ=60)
ACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAA > SRR3722078.1364506/1‑100 (MQ=60)
ACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAA > SRR3722078.1603442/1‑100 (MQ=60)
CGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAAC < SRR3722078.115260/100‑1 (MQ=60)
CGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAAC < SRR3722078.392912/100‑1 (MQ=60)
ACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAA < SRR3722078.776677/100‑1 (MQ=60)
ACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAA < SRR3722078.1096663/100‑1 (MQ=60)
GGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAAC < SRR3722078.1204230/100‑1 (MQ=60)
GGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAAC < SRR3722078.998803/100‑1 (MQ=60)
GCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGC > SRR3722078.1114989/1‑100 (MQ=60)
CGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCAC > SRR3722078.496056/1‑100 (MQ=60)
ACGTTGCAGCATTAAAATCAGGAAAGTCGCGA‑CCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAA > SRR3722078.1521674/1‑100 (MQ=60)
GCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTC > SRR3722078.676423/1‑100 (MQ=60)
GGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATctgtctcttataca > SRR3722078.884095/1‑86 (MQ=60)
GTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTCCGCCAGGTCGGTTGCCA > SRR3722078.355883/1‑100 (MQ=60)
ACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTCCGCCAGGTCGGTTGCCATCGCAA > SRR3722078.1027972/1‑100 (MQ=60)
|
AATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTCCGCCAGGTCGGTTGCCATCGCAA > NZ_CP009273/2505679‑2505875
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
