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 |
|
A2 F8 I0 R2
|
296 |
77.6 |
4260404 |
88.1% |
3753415 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
558,918 |
T→C |
26.4% |
P55P (CCT→CCC) |
cmr → |
multidrug efflux system protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 558,918 | 0 | T | C | 26.4%
| 77.4
/ 31.1
| 48 | P55P (CCT→CCC) | cmr | multidrug efflux system protein |
| Reads supporting (aligned to +/- strand): ref base T (18/17); new base C (6/6); total (24/24) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.92e-01 |
TGATTCAACCCGGTATGTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAATGGCTGCTGGGGCCGCTGTCGGATC > minE/558857‑558985
|
tGATTCAACCCGGTATGTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGAt > 1:2735111/1‑70 (MQ=255)
ttGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTggcggg > 1:2658005/1‑71 (MQ=255)
ttGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcggg > 1:716542/1‑71 (MQ=255)
gCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGgcgggcgg < 1:697798/71‑1 (MQ=255)
ccGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTGCTTCGATGACCGCGTATCTGGcgggcggg < 1:246123/71‑1 (MQ=255)
cGTGGTGGAACAATATCATGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGa < 1:2672004/71‑1 (MQ=255)
cGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACtt < 1:3370760/44‑1 (MQ=255)
cGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGcgggcggg < 1:843533/70‑1 (MQ=255)
cGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGa < 1:1437010/71‑1 (MQ=255)
cGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGa < 1:1089076/71‑1 (MQ=255)
gtggAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGtt > 1:3804030/1‑71 (MQ=255)
gtggAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGtt > 1:426023/1‑71 (MQ=255)
aCAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTa > 1:139644/1‑70 (MQ=255)
aCAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTa > 1:2104629/1‑70 (MQ=255)
aCAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTa > 1:49162/1‑70 (MQ=255)
aCAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATg < 1:248231/40‑1 (MQ=255)
aCAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATg < 1:1084517/40‑1 (MQ=255)
aCAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTAc < 1:1865211/71‑1 (MQ=255)
aCAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTAc < 1:4220574/71‑1 (MQ=255)
aCAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTAc < 1:3035592/71‑1 (MQ=255)
aCAATATCAGGCGGGCATTGATTGGGTTCCAACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTAc < 1:83021/71‑1 (MQ=255)
cAATATCAGGCAGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACa < 1:1525963/71‑1 (MQ=255)
atatCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAAt > 1:3554712/1‑71 (MQ=255)
atatCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAAt > 1:2240151/1‑71 (MQ=255)
tatCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGtt < 1:2205862/62‑1 (MQ=255)
tatCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGtt < 1:635993/62‑1 (MQ=255)
tatCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGtt < 1:363909/62‑1 (MQ=255)
cAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAATGgct > 1:218803/1‑71 (MQ=255)
attgattgGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAATGGCTGCTGGGGcc < 1:1249023/71‑1 (MQ=255)
gattgGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACaa < 1:730192/54‑1 (MQ=255)
gattgGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAAt > 1:2650712/1‑55 (MQ=255)
gattgGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAAt > 1:3327582/1‑55 (MQ=255)
gattgGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAAt > 1:2954085/1‑55 (MQ=255)
gattgGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAAt > 1:1011956/1‑55 (MQ=255)
gattgGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAAt > 1:2212872/1‑55 (MQ=255)
gattgGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAAt > 1:1684201/1‑55 (MQ=255)
gattgGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAATGGCTGCTGGGGCCGCt > 1:2416064/1‑71 (MQ=255)
gattgGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAATGGCTGCTGGGGCCGCt > 1:2355532/1‑71 (MQ=255)
gattgGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAATGGCTGCTGGGGCCGCt > 1:1493225/1‑71 (MQ=255)
gattgGGTTCCCACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAATGGCTGCTGGGGCCGc > 1:1027880/1‑70 (MQ=255)
gggTTCCCACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACaa > 1:3039252/1‑50 (MQ=255)
gggTTCCCACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACaa > 1:3696230/1‑50 (MQ=255)
gggTTCCCACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACaa > 1:1592367/1‑50 (MQ=255)
ttCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACaa < 1:3193188/47‑1 (MQ=255)
ttCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACaa < 1:281982/47‑1 (MQ=255)
ttCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACaa < 1:162515/47‑1 (MQ=255)
ttCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACaa < 1:1346597/47‑1 (MQ=255)
ccTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAATGGCTGCTGGGGCCGCTGTCGGATc < 1:1473518/70‑1 (MQ=255)
|
TGATTCAACCCGGTATGTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAATGGCTGCTGGGGCCGCTGTCGGATC > minE/558857‑558985
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
