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 |
|
A6 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,716,860 |
A→C |
18.4% |
intergenic (+118/+80) |
yphH → / ← glyA |
predicted DNA‑binding transcriptional regulator/serine hydroxymethyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,716,860 | 0 | A | C | 18.4%
| 122.0
/ 45.9
| 98 | intergenic (+118/+80) | yphH/glyA | predicted DNA‑binding transcriptional regulator/serine hydroxymethyltransferase |
| Reads supporting (aligned to +/- strand): ref base A (46/34); new base C (4/14); total (50/48) |
| Fisher's exact test for biased strand distribution p-value = 8.77e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01 |
AACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACATTGACAGCA > minE/1716792‑1716925
|
aaCGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAg > 1:5357842/1‑71 (MQ=255)
aaCGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAg > 1:621064/1‑71 (MQ=255)
caaaTTGCCTGATGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTg < 1:1070969/70‑1 (MQ=11)
caaaTTGCCTGATGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTg < 1:1355129/70‑1 (MQ=11)
caaaTTGCCTCATGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTg < 1:4129553/70‑1 (MQ=11)
agcttgcctgatgcgcgatGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTg < 1:345139‑M2/51‑1 (MQ=255)
agcttgcctgatgcgcgatGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTg < 1:334856‑M2/51‑1 (MQ=255)
aaaTTGCCTGATGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTg > 1:1029988/1‑70 (MQ=11)
aaaTTGCCTGATGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGt < 1:1405716/71‑1 (MQ=11)
gcttgcctgatgcgcgatGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTg > 1:100149‑M2/19‑69 (MQ=255)
aaTTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGt < 1:1965428/70‑1 (MQ=255)
aaTTGCCTGATGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGt < 1:1123517/70‑1 (MQ=11)
aTTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAg < 1:280107/71‑1 (MQ=255)
ttGCCTGATGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAg > 1:4964856/1‑70 (MQ=11)
ccTGATGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAggac < 1:3626879/70‑3 (MQ=11)
ccTGATGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAgga < 1:5333843/69‑2 (MQ=11)
tGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGa > 1:87508/1‑71 (MQ=255)
atgcgcgatGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATa < 1:276209‑M2/62‑1 (MQ=255)
atgcgcgatGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATa < 1:5482606‑M2/62‑1 (MQ=255)
aTGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGt > 1:3472443/1‑61 (MQ=255)
aTGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGt > 1:3465622/1‑61 (MQ=255)
aTGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGt > 1:5241154/1‑61 (MQ=255)
aTGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGa < 1:64705/69‑1 (MQ=255)
aTGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGAt < 1:5506823/70‑1 (MQ=255)
aTGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGAt < 1:1271959/70‑1 (MQ=255)
aTGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGAt < 1:1233144/70‑1 (MQ=11)
aTGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGAt < 1:4987178/70‑1 (MQ=11)
aTGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATa < 1:2054670/71‑1 (MQ=11)
tgcgcgatGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTg < 1:5484282‑M2/51‑1 (MQ=255)
tgcgcgatGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTg < 1:303370‑M2/51‑1 (MQ=255)
cgcTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAgg > 1:1208984/1‑71 (MQ=255)
cgcTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAg < 1:4010410/70‑1 (MQ=11)
cgcTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAg < 1:3703517/70‑1 (MQ=11)
cgatGCTTATCAGGCCTACA‑GAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGt < 1:2714889‑M2/67‑1 (MQ=255)
atGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGtttt < 1:5031911‑M2/50‑1 (MQ=255)
atGCTTATCAGGCCTACCAGAAGATAGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGtt < 1:4203362‑M2/69‑1 (MQ=255)
aCGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGa > 1:4984271/1‑62 (MQ=255)
aCGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGa > 1:1349458/1‑62 (MQ=255)
aCGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAgga > 1:293058/1‑57 (MQ=2)
aCGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAgga > 1:5119812/1‑57 (MQ=2)
aCGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAgga > 1:5616760/1‑57 (MQ=2)
aCGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAgga > 1:4816340/1‑57 (MQ=2)
aCGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAGGCgct > 1:4413369/1‑69 (MQ=2)
aCGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAGGCgct > 1:1436366/1‑69 (MQ=2)
cGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCaaa > 1:1220582/1‑46 (MQ=255)
cGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCaaa > 1:2113532/1‑46 (MQ=255)
cGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGtt < 1:5436240/70‑1 (MQ=255)
cTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCa > 1:2513460/1‑70 (MQ=255)
cTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCa > 1:4071410/1‑70 (MQ=255)
cTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCAc > 1:3248722/1‑71 (MQ=255)
cTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATATGCGATGTTTTGTAGGACTGATAAGGCGCTcg > 1:5395870/1‑69 (MQ=2)
tATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAgga > 1:109984/1‑52 (MQ=2)
aTCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAGGCGCTcgcg < 1:3798215/69‑1 (MQ=2)
tCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTa < 1:4110570/48‑1 (MQ=11)
cAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAGGCGCTCGcgccg > 1:934475/1‑70 (MQ=2)
aGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAgg > 1:3956611/1‑48 (MQ=11)
aGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAgg > 1:3164094/1‑48 (MQ=11)
ccTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGAt < 1:5218794/51‑1 (MQ=255)
tACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATa < 1:1792834/50‑1 (MQ=255)
tACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATa < 1:529082/50‑1 (MQ=255)
cacGGAGATTGCAATATATTGAATTTGCAAAGTTTTGt > 1:5162570/1‑38 (MQ=255)
cacGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATaa > 1:1550923/1‑49 (MQ=255)
cacGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAg > 1:4125468/1‑50 (MQ=255)
cacGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAg > 1:1556834/1‑50 (MQ=255)
cacGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCgg < 1:5050166/69‑1 (MQ=255)
acGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATaa > 1:5061555/1‑48 (MQ=255)
acGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAt > 1:5566762/1‑71 (MQ=255)
agaagaTTGCAATATATTGAATTTGCACTGTTTT‑TAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATg > 1:1023432/4‑70 (MQ=11)
ggAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGc > 1:3973499/1‑49 (MQ=255)
agaTTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGaac < 1:4980081/71‑1 (MQ=11)
agaTTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGaac < 1:1028001/71‑1 (MQ=11)
agaTTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGaac < 1:1869594/71‑1 (MQ=11)
agaTTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGaac < 1:5502856/71‑1 (MQ=11)
caTTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAGGCGCTCGCGCCGCATCCGGCATCaact < 1:5329792/70‑2 (MQ=11)
caTTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAGGCGCTCGCGCCGCATCCGGCATCaac > 1:3731757/2‑70 (MQ=11)
aTTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAGGCGCTCGCGCCGCATCCGGCATcaacaa < 1:3874039/71‑1 (MQ=11)
aTTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATa < 1:3329907/41‑1 (MQ=255)
tGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGaacaac > 1:1650007/1‑70 (MQ=255)
tGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGaacaac > 1:5574960/1‑70 (MQ=255)
cAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAg > 1:3828834/1‑71 (MQ=255)
aaTATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGc < 1:3284311/71‑1 (MQ=255)
atatatTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGca < 1:3494598/71‑1 (MQ=255)
atatatTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGca < 1:4537113/71‑1 (MQ=255)
atatatTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGca < 1:5076453/71‑1 (MQ=255)
tctatTGAATTTGCGATGTTTTGTAGGACGGATAAGGCGCTCGCGCCGCATCCGGCATcaacaa > 1:2837279/3‑64 (MQ=11)
tctatTGAATTTGCGATGTTTTGTAGGACGGATAAGGCGCTCGCGCCGCATCCGGCATcaacaa > 1:882821/3‑64 (MQ=11)
tatTGAATTTGCGATGTTTTGTAGGACGGATAAGGCGCTCGCGCCGCATCCGGCATCaac > 1:1107182/1‑60 (MQ=11)
tatTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGc > 1:2146612/1‑36 (MQ=40)
tatTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGcaca < 1:4737930/70‑1 (MQ=255)
tatTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACAt < 1:575186/71‑1 (MQ=255)
ctttGGATTTGCAAA‑TTTTGTAGACCGGATAAGGAATTCACGCCGCATCCgg > 1:2539797/3‑52 (MQ=0)
ctttGGATTTGCAAA‑TTTTGTAGACCGGATAAGGAATTCACGCCGCATCCgg > 1:1595834/3‑52 (MQ=0)
ctttGGATTTGCAAA‑TTTTGTAGACCGGATAAGGAATTCACGCCGCATCCgg > 1:1909925/3‑52 (MQ=0)
ctttGGATTTGCAAA‑TTTTGTAGACCGGATAAGGAATTCACGCCGCATCCGGc < 1:2514547/51‑1 (MQ=0)
ttGAATTTGCGATGTTTTGTAGGACGGATAAGGCg < 1:4648181/35‑1 (MQ=14)
ttGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCg > 1:2302650/1‑35 (MQ=40)
ttGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCg > 1:1378075/1‑35 (MQ=40)
gAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACATTGa > 1:3443282/1‑70 (MQ=255)
gaTTTGCAAA‑TTTTGTAGACCGGATAAGGAATTCACGCCGCATCCGGCATCaa > 1:3873219/2‑53 (MQ=11)
tGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACATTGACAGCa > 1:5128176/1‑70 (MQ=255)
|
AACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACATTGACAGCA > minE/1716792‑1716925
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
