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 |
|
A5 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,018,964 |
G→A |
58.5% |
A92T (GCG→ACG) |
fliI → |
flagellum‑specific ATP synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,018,964 | 0 | G | A | 58.5%
| 16.9
/ 49.5
| 41 | A92T (GCG→ACG) | fliI | flagellum‑specific ATP synthase |
| Reads supporting (aligned to +/- strand): ref base G (11/6); new base A (11/13); total (22/19) |
| Fisher's exact test for biased strand distribution p-value = 3.42e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01 |
GTTGGCTTTAACGGTCAACGGCTGTTTTTAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCGCGCGTGTTTATGCCAAAAACATTTCGGCAGAAGGGCTGCAAAGCGGCAAGCAGTTGCCGCTCG > W3110S.gb/2018898‑2019027
|
gTTGGCTTTAACGGTCAACGGCTGTTTTTAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGcgcgcg > 1:1328968/1‑71 (MQ=255)
gCTTTAACGGTCAACGGCTGTTTTTAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCGCGCGTGtt < 1:4764689/71‑1 (MQ=255)
ttAACGGTCAACGGCTGTTTTTAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCGCGGCGCGCGTGTTTAt > 1:4614691/1‑71 (MQ=255)
tAACGGTCAACGGCTGTTTTTAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGAGCGCGTGTTTa > 1:4326103/1‑69 (MQ=255)
ggTCAACGGCTGTTTTTAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCACGCgtgt > 1:3689941/1‑62 (MQ=255)
ggTCAACGGCTGTTTTTAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCACGCGTGtt > 1:4570966/1‑63 (MQ=255)
ggTCAACGGCTGTTTTTAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCACGCGTGtt > 1:2315053/1‑63 (MQ=255)
gTCAACGGCTGTTTTTAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCACGCGTGTTTATGCCaaa < 1:3460278/71‑1 (MQ=255)
gTCAACGGCTGTTTTTAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCACGCGTGTTTATGCCaaa < 1:3267434/71‑1 (MQ=255)
aaCGGCTGTTTTTAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCGCGCGTGTTTATGCCAAAAAc < 1:309118/71‑1 (MQ=255)
aaCGGCTGTTTTTAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCACGCGTGTTTATGCCaaaaa < 1:1871949/70‑1 (MQ=255)
cGGCTGTTTTTAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCACGCGTGTTTATGCCAAAAACAt < 1:3481305/71‑1 (MQ=255)
cGGCTGTTTTTAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCACGCGTGTTTATGCCAAAAACAt < 1:2216446/71‑1 (MQ=255)
tttttAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGgcacgc < 1:1279793/46‑1 (MQ=255)
tttAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCGCGCGTGTTTATGCCAAAAACATTTCgg > 1:4718433/1‑68 (MQ=255)
tttAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCGCGCGTGTTTATGCCAAAAACATTTCgg > 1:4658708/1‑68 (MQ=255)
tttAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCGCGCGTGTTTATGCCAAAAACATTTCgg > 1:1311980/1‑68 (MQ=255)
tttAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCGCGCGTGTTTATGCCAAAAACATTTCgg > 1:3255338/1‑68 (MQ=255)
tttAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCGCGCGTGTTTATGCCAAAAACATTTCgg > 1:3615569/1‑68 (MQ=255)
tttAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCACGCgt > 1:4431467/1‑46 (MQ=255)
aTGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCACGCGTGTTTATGCCAAAAACATTTCGGCAGaa > 1:2838721/1‑69 (MQ=255)
ccGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCACGCGTGTTTATGCCAAAAACATTTCGGCAGAAGGGc < 1:1893183/70‑1 (MQ=255)
ccGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCACGCGTGTTTATGCCAAAAACATTTCGGCAGAAGGGCt > 1:1529033/1‑71 (MQ=255)
ggaAGTCGAAGGTGTCCTGCCCGGCACGCGTGTTTATGCCAAAAACATTTCGGCAGAAGGGCTGCAAAGCg > 1:4256109/1‑71 (MQ=255)
aaGTCGAAGGTGTCCTGCCCGGCGCGCGTGTTTATGCCAAAAACATTTCGGCAGaa > 1:252084/1‑56 (MQ=255)
aGTCGAAGGTGTCCTGCCCGGCACGCGTGTTTATGCCAAAAACATTTc > 1:1981955/1‑48 (MQ=255)
gAAGGTGTCCTGCCCGGCGCGCGTGTTTATGCCAAAAACAttt > 1:2175006/1‑43 (MQ=255)
aaGGTGTCCTGCCCGGCACGCGTGTTTATGCCAAAAACATTTCGGCAg < 1:3493957/48‑1 (MQ=255)
aaGGTGTCCTGCCCGGCACGCGTGTTTATGCCAAAAACATTTCGGCAg < 1:232238/48‑1 (MQ=255)
aaGGTGTCCTGCCCGGCACGCGTGTTTATGCCAAAAACATTTCGGCAg < 1:4667183/48‑1 (MQ=255)
aaGGTGTCCTGCCCGGCACGCGTGTTTATGCCAAAAACATTTCGGCAg < 1:4319929/48‑1 (MQ=255)
ggTGTCCTGCCCGGCGCGCGTGTTTATGCCAAAAACATTTCGGCAg < 1:1998895/46‑1 (MQ=255)
gtgtCCTGCCCGGCGCGCGTGTTTATGCCAAAAACATTTCGGCAGAAGGGCTGCAAAGCGGCAAGCa < 1:3946430/67‑1 (MQ=255)
gtgtCCTGCCCGGCGCGCGTGTTTATGCCAAAAACATTTCGGCAGAAGGGCTGCAAAGCGGCAAGCa < 1:222071/67‑1 (MQ=255)
gtgtCCTGCCCGGCACGCGTGTTTATGCCAAAAACAtt < 1:948169/38‑1 (MQ=255)
tCCTGCCCGGCGCGCGTGTTTATGCCAAAAACATTTCGGCAGAAGGGCTGCAAAGCGGCAAGCa < 1:3427556/64‑1 (MQ=255)
cTGCCCGGCGCGCGTGTTTATGCCAAAAACATTTCGGCAGAAGGGCTGCaa > 1:3886959/1‑51 (MQ=255)
cTGCCCGGCGCGCGTGTTTATGCCAAAAACATTTCGGCAGAAGGGCTGCaa > 1:2584697/1‑51 (MQ=255)
cTGCCCGGCACGCGTGTTTATGCCAAAAACATTTCGGc > 1:3470733/1‑38 (MQ=255)
cTGCCCGGCACGCGTGTTTATGCCAAAAACATTTCGGCa > 1:3248494/1‑39 (MQ=255)
cccGGCACGCGTGTTTATGCCAAAAACATTTCGGCAGAAGGGCTGCAAAGCGGCAAGCa < 1:13695/59‑1 (MQ=255)
cccGGCACGCGTGTTTATGCCAAAAACATTTCGGCAGAAGGGCTGCAAAGCGGCAAGCAg > 1:1111877/1‑60 (MQ=255)
cccGGCACGCGTGTTTATGCCAAAAACATTTCGGCAGAAGGGCTGCAAAGCGGCAAGCAGTTGCCGCTCg < 1:3874194/70‑1 (MQ=255)
|
GTTGGCTTTAACGGTCAACGGCTGTTTTTAATGCCGCTGGAGGAAGTCGAAGGTGTCCTGCCCGGCGCGCGTGTTTATGCCAAAAACATTTCGGCAGAAGGGCTGCAAAGCGGCAAGCAGTTGCCGCTCG > W3110S.gb/2018898‑2019027
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
