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 |
|
A35 F1 I1 R1
|
21 |
46.3 |
3071142 |
93.0% |
2856162 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
3,145,849 |
T→C |
intergenic (+180/‑15) |
dnaG → / → rpoD |
DNA primase/RNA polymerase sigma factor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 3,145,849 | 0 | T | C | 98.0%
| 204.9
/ ‑4.3
| 50 | intergenic (+180/‑15) | dnaG/rpoD | DNA primase/RNA polymerase sigma factor |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (24/25); total (24/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01 |
CAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAG > REL606/3145776‑3145921
|
caacCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAgcgt < 2:687395/76‑1 (MQ=255)
acCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTgg > 2:908332/1‑76 (MQ=255)
ccGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGa < 2:1139401/76‑1 (MQ=255)
cGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGAt < 1:1078220/76‑1 (MQ=255)
gTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATa > 1:984699/1‑76 (MQ=255)
ttGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATAc < 1:147050/76‑1 (MQ=255)
gATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGt < 1:1121058/76‑1 (MQ=255)
tCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCACCACCAACCTCATGAAATAAGTGTGGATACCGTCTTa < 2:64017/76‑1 (MQ=255)
tCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTa < 1:630615/76‑1 (MQ=255)
cAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTAt < 2:963232/76‑1 (MQ=255)
cAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTAt < 2:229904/76‑1 (MQ=255)
gCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATgg < 1:1057753/76‑1 (MQ=255)
ttAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGc > 2:613680/1‑76 (MQ=255)
cTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAAccc < 1:1291342/76‑1 (MQ=255)
cTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAAccc < 1:337321/76‑1 (MQ=255)
gAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGc > 2:1480939/1‑76 (MQ=255)
gAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGc > 2:127036/1‑76 (MQ=255)
gAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGc > 1:657992/1‑76 (MQ=255)
aaGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCa < 1:303245/76‑1 (MQ=255)
aaGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCa < 1:342016/76‑1 (MQ=255)
gACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTc < 1:1489148/76‑1 (MQ=255)
gACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTc < 1:422705/76‑1 (MQ=255)
aTCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTcaca > 1:149235/1‑76 (MQ=255)
tCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAg < 1:801431/76‑1 (MQ=255)
tCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAg < 1:1112254/76‑1 (MQ=255)
cGGGTCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGc > 1:3261/1‑76 (MQ=255)
tCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGaa < 1:1464350/76‑1 (MQ=255)
tCAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGaa > 2:870804/1‑76 (MQ=255)
cAATCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGaaa > 2:517354/1‑76 (MQ=255)
aaTCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAAc > 1:1463078/1‑76 (MQ=255)
aaTCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAAc > 2:10306/1‑76 (MQ=255)
aaTCGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAAc > 2:10311/1‑76 (MQ=255)
cGCCCAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAActtc > 1:248697/1‑76 (MQ=255)
cccAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAActtctt > 1:622520/1‑76 (MQ=255)
cAACACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGt > 2:823306/1‑76 (MQ=255)
aaCACCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTc < 1:518134/76‑1 (MQ=255)
acCAACCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCAcc > 1:613376/1‑76 (MQ=255)
aCCTCATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTg < 2:961413/76‑1 (MQ=255)
cATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTaa > 2:167896/1‑76 (MQ=255)
cATGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTaa > 1:1107051/1‑76 (MQ=255)
aTGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAg > 1:1254041/1‑76 (MQ=255)
tGAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAgg < 2:438127/76‑1 (MQ=255)
gAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGa < 1:1526925/76‑1 (MQ=255)
gAAATAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGa > 2:737418/1‑76 (MQ=255)
aaaTAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAg < 2:1353979/76‑1 (MQ=255)
aaTAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGc < 2:1114/76‑1 (MQ=255)
aaTAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGc > 1:923841/1‑76 (MQ=255)
aTAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCa < 1:401000/76‑1 (MQ=255)
tAAGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCaa < 1:218527/76‑1 (MQ=255)
aaGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAg > 1:1226710/1‑76 (MQ=255)
aaGCGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAg > 1:1133236/1‑76 (MQ=255)
|
CAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAG > REL606/3145776‑3145921
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
