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 |
|
A4 F21 I0 R1
|
1009 |
73.8 |
4146436 |
87.4% |
3623985 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,502,353 |
G→A |
22.2% |
S92L (TCA→TTA) |
lrhA ← |
DNA‑binding transcriptional repressor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,502,353 | 0 | G | A | 22.2%
| 151.8
/ 34.6
| 72 | S92L (TCA→TTA) | lrhA | DNA‑binding transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base G (25/31); new base A (9/7); total (34/38) |
| Fisher's exact test for biased strand distribution p-value = 5.71e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GATCGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGAATGC > minE/1502289‑1502416
|
gATCGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtgatgat > 1:127507/1‑70 (MQ=255)
aTCGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtgatgat > 1:3043817/1‑69 (MQ=255)
cGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtgatgatga > 1:2906618/1‑69 (MQ=255)
gTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGc < 1:1164198/70‑1 (MQ=255)
tATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtg < 1:1045374/60‑1 (MQ=255)
tATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtg < 1:1270136/60‑1 (MQ=255)
tATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAg < 1:552872/71‑1 (MQ=255)
aTCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtgatga > 1:3577016/1‑63 (MQ=255)
aTCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGc > 1:1272990/1‑68 (MQ=255)
aTCGACAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGc > 1:1431438/1‑68 (MQ=255)
ggCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCt < 1:421699/71‑1 (MQ=255)
ggCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCt < 1:3479808/71‑1 (MQ=255)
ggCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCt > 1:1097187/1‑71 (MQ=255)
cAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCtca < 1:406869/71‑1 (MQ=255)
aGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCtcat > 1:3764850/1‑71 (MQ=255)
aTTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCtcatca < 1:2460711/71‑1 (MQ=255)
ttCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTcatcat > 1:3509374/1‑71 (MQ=255)
tCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTcatcat > 1:3095715/1‑70 (MQ=255)
tCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTcatcat > 1:763834/1‑70 (MQ=255)
cATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtgat > 1:517099/1‑50 (MQ=255)
tCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAg < 1:3261982/57‑1 (MQ=255)
tCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAg < 1:3946356/57‑1 (MQ=255)
tCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAg < 1:2900952/57‑1 (MQ=255)
tCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCtc < 1:345679/62‑1 (MQ=255)
tGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCtcat > 1:1325794/1‑62 (MQ=255)
gAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACg > 1:297161/1‑71 (MQ=255)
aaGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtgatgatga > 1:496317/1‑49 (MQ=255)
aaGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAg > 1:3962628/1‑50 (MQ=255)
aGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCa < 1:3951875/71‑1 (MQ=255)
gCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAg < 1:943763/48‑1 (MQ=255)
gCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAg < 1:3261038/71‑1 (MQ=255)
ccGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGAt < 1:2112051/71‑1 (MQ=255)
cGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGAtt > 1:2472678/1‑71 (MQ=255)
cGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGAtt < 1:3403401/71‑1 (MQ=255)
gATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGAttt > 1:271082/1‑71 (MQ=255)
gATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGAttt > 1:2270744/1‑71 (MQ=255)
gATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGAttt > 1:39363/1‑71 (MQ=255)
gATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGAttt < 1:3007759/71‑1 (MQ=255)
ttAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAg < 1:1574411/41‑1 (MQ=255)
ttAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTcc < 1:3737669/69‑1 (MQ=255)
ttAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTg < 1:3982525/71‑1 (MQ=255)
aaTACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCtca > 1:4081124/1‑45 (MQ=255)
aaTACGCCCTGAAGATTACTGAACATTAATGATGAGCa > 1:248567/1‑38 (MQ=255)
aaTACGCCCTGAAGATTACTGAACATTAATGATGAGCa > 1:3379453/1‑38 (MQ=255)
aaTACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGc > 1:357095/1‑71 (MQ=255)
tACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCtc < 1:1151736/42‑1 (MQ=255)
tACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCg > 1:3276689/1‑70 (MQ=255)
tACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGt < 1:2977052/71‑1 (MQ=255)
tACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGt < 1:683575/71‑1 (MQ=255)
cGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCt > 1:3943345/1‑64 (MQ=255)
cGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTa < 1:369927/70‑1 (MQ=255)
cccTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAAcc < 1:3672009/71‑1 (MQ=255)
cTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGAtttt > 1:1255800/1‑57 (MQ=255)
tgtaGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTgg < 1:3435233/58‑1 (MQ=255)
gAAGATTACTGAACATTGATGATGAGCAGGCCtcatca < 1:803551/38‑1 (MQ=255)
gAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTaa > 1:3194660/1‑42 (MQ=255)
gAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag > 1:4085703/1‑70 (MQ=255)
gAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag > 1:3872486/1‑70 (MQ=255)
aaGATTACTGAACATTGATGATGAGCAGGCCTCATCATTa > 1:3130497/1‑40 (MQ=255)
aaGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAATCaaga < 1:4127637/70‑1 (MQ=255)
aaGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaaga < 1:1228704/70‑1 (MQ=255)
aaGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag > 1:2103039/1‑69 (MQ=255)
aaGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag > 1:30728/1‑69 (MQ=255)
aaGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag > 1:2132254/1‑69 (MQ=255)
aaGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaa > 1:1571348/1‑68 (MQ=255)
aGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaagaa < 1:2518928/70‑1 (MQ=255)
aGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaa > 1:3263770/1‑67 (MQ=255)
ttACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaa < 1:673678/64‑1 (MQ=255)
ttACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTg < 1:3356336/71‑1 (MQ=255)
ttACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTg < 1:1036205/71‑1 (MQ=255)
ttACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTg < 1:710324/71‑1 (MQ=255)
ttACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTg < 1:3554839/71‑1 (MQ=255)
ttACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTg < 1:739912/71‑1 (MQ=255)
tACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTg > 1:3783988/1‑70 (MQ=255)
aaCATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGt > 1:2640888/1‑63 (MQ=255)
aaCATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTg < 1:1623234/65‑1 (MQ=255)
aaCATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGAATGc > 1:1628875/1‑70 (MQ=255)
aaCATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGAATGc > 1:1576122/1‑70 (MQ=255)
aaaTTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaa < 1:1899810/55‑1 (MQ=255)
ttGATGATGAGCAGGCCTCATCATTAAAACGCAGGAttt < 1:2629314/39‑1 (MQ=255)
|
GATCGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGAATGC > minE/1502289‑1502416
|
| 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
