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 F3 I95 R1
|
196 |
14.2 |
808436 |
96.0% |
776098 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,922,863 |
A→G |
V34A (GTC→GCC) |
viaA ← |
ATPase RavA stimulator ViaA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,922,863 | 0 | A | G | 90.0%
| 51.6
/ ‑2.6
| 20 | V34A (GTC→GCC) | viaA | ATPase RavA stimulator ViaA |
| Reads supporting (aligned to +/- strand): ref base A (0/2); new base G (5/13); total (5/15) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTCAGCCGACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGACCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAGC > NZ_CP009273/3922779‑3922946
|
ttCAGCCGACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGgccgcc < 2:118649/90‑1 (MQ=255)
aGCCGACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGc < 1:238835/90‑1 (MQ=255)
aGCCGACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGc < 1:240598/90‑1 (MQ=255)
tGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTg < 2:128879/90‑1 (MQ=255)
gCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCcagc < 2:83639/79‑1 (MQ=255)
gCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCcagc > 1:83639/1‑79 (MQ=255)
ggggAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGatca < 2:132236/90‑1 (MQ=255)
gAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCAtct > 1:9114/1‑90 (MQ=255)
atcatcAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTc < 1:51673/90‑1 (MQ=255)
atcaGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGAt < 1:362193/90‑1 (MQ=255)
atcaGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGAt > 2:278143/1‑90 (MQ=255)
caGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCgatga > 1:119666/1‑75 (MQ=255)
caGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCgatga < 2:119666/75‑1 (MQ=255)
gATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATcc > 1:201397/1‑90 (MQ=255)
cGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGcc < 2:331631/90‑1 (MQ=255)
gTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCa < 2:146368/90‑1 (MQ=255)
aaTTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATc < 1:148360/90‑1 (MQ=255)
aaTTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATc < 2:201397/90‑1 (MQ=255)
aaTTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATc < 2:327102/90‑1 (MQ=255)
aaTTTTTCAAAGAAGACCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATc < 1:125295/90‑1 (MQ=255)
aagaagACCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAGc < 1:330057/90‑1 (MQ=255)
|
TTCAGCCGACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGACCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAGC > NZ_CP009273/3922779‑3922946
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ 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
GGACTCGGGCATCTTTCAGCCGACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGACCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAGCGTATCCAGCG > NZ_CP009273/3922765‑3922956
|
GGACTCGGGCATCTTTCAGCCGACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGC > SRR3722235.325063/1‑100 (MQ=60)
AGCCGACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGG < SRR3722235.241857/100‑1 (MQ=60)
AGCCGACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGG < SRR3722235.243656/100‑1 (MQ=60)
CTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGAC > SRR3722235.84610/1‑100 (MQ=60)
CGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCT > SRR3722235.9212/1‑100 (MQ=60)
GGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCctgtc > SRR3722235.121043/1‑95 (MQ=60)
CATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCC > SRR3722235.203861/1‑100 (MQ=60)
ATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCC < SRR3722235.52239/100‑1 (MQ=60)
ATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCT < SRR3722235.367410/100‑1 (MQ=60)
AATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAGCG < SRR3722235.150059/100‑1 (MQ=60)
AATTTTTCAAAGAAGACCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAGCG < SRR3722235.126745/100‑1 (MQ=60)
AAGAAGACCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAGCGTATCCAGCG < SRR3722235.334774/100‑1 (MQ=60)
|
GGACTCGGGCATCTTTCAGCCGACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGACCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAGCGTATCCAGCG > NZ_CP009273/3922765‑3922956
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
