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 |
2,790,674 |
G→T |
25.8% |
intergenic (+69/‑706) |
pgi → / → ubiC |
glucosephosphate isomerase/chorismate pyruvate lyase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,790,674 | 0 | G | T | 25.8%
| 151.2
/ 30.9
| 62 | intergenic (+69/‑706) | pgi/ubiC | glucosephosphate isomerase/chorismate pyruvate lyase |
| Reads supporting (aligned to +/- strand): ref base G (16/30); new base T (9/7); total (25/37) |
| Fisher's exact test for biased strand distribution p-value = 1.51e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.17e-01 |
AATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCAATTAATACATAGCACG > minE/2790604‑2790744
|
aaTCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGAcgcg > 1:4125487/1‑71 (MQ=255)
tcatcGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCgg > 1:727137/1‑70 (MQ=255)
tcatcGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGt > 1:2088485/1‑71 (MQ=255)
atcGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTcg > 1:4069955/1‑71 (MQ=255)
atcGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTc > 1:5487258/1‑70 (MQ=255)
gATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCtt < 1:1619543/71‑1 (MQ=255)
cgaatGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCtt < 1:784617/68‑1 (MQ=11)
aatGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTAt < 1:801585/70‑1 (MQ=11)
gTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAg < 1:361995/71‑1 (MQ=11)
gTAGGACGGATAAGGCGTTTACGCCGCATCCGGCAACAGATGCCTGATGCGACGCTACCGCGTCTTATCa < 1:5478651/70‑1 (MQ=11)
tAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAgg > 1:2971764/1‑71 (MQ=255)
tAGGACGGATAAGGCGTTTACGCCGCATCCGGCAACAGATGCCTGATGCGACGCTACCGCGTCTTATCAgg > 1:2454585/1‑71 (MQ=11)
tAGGACGGATAAGGCGTTTACGCCGCATCCGGCAACAGATGCCTGATGCGACGCTACCGCGTCTTATCAgg > 1:1950254/1‑71 (MQ=11)
ggacGGATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTATCATGcc < 1:4841860/68‑1 (MQ=1)
gacGGATAAGGCGTTTACGCCGCATCCGGCAACAGATGCCTGATGCGACGCTACCGCGTCTTATCAGGcc > 1:2180215/3‑70 (MQ=14)
cGGATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTATCATGCCTAc < 1:5246677/71‑1 (MQ=11)
ggATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTATCATGCCTACa > 1:4784248/1‑71 (MQ=11)
tAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTATCATGCCTACatag > 1:2545967/1‑68 (MQ=11)
tAAGGCGTTTACGCCGCATCCGGCAACAGATGCCTGATGCGACGCTACCGCGTCTTATCAGGCCTACaaaa > 1:2750305/1‑68 (MQ=11)
ttCACGCCGCATCCGGCAACCTATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTc < 1:1398961/65‑1 (MQ=255)
ttCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTcgc > 1:4074165/1‑44 (MQ=255)
ttCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGcc < 1:2228975/57‑1 (MQ=255)
cACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGccga > 1:4244148/1‑55 (MQ=255)
cACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGcc < 1:2803497/55‑1 (MQ=255)
cACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGa > 1:5346588/1‑71 (MQ=255)
aCGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCg > 1:3721529/1‑69 (MQ=255)
cgccgcATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGata < 1:874482/71‑1 (MQ=255)
gccgcATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATc > 1:1057757/1‑47 (MQ=255)
ccgcATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATg < 1:5328310/71‑1 (MQ=255)
gcATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCa > 1:4982818/1‑45 (MQ=9)
gcATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCa > 1:5204864/1‑45 (MQ=9)
gcATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCa > 1:3962820/1‑45 (MQ=9)
cATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGGCGATGCCGat < 1:5494557/65‑1 (MQ=255)
aTCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACa < 1:3225822/71‑1 (MQ=255)
tCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACa < 1:1666800/70‑1 (MQ=255)
tCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAgg < 1:2415744/44‑1 (MQ=2)
cGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTa > 1:2906940/1‑46 (MQ=255)
cGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCg < 1:1681247/71‑1 (MQ=255)
cGGCAACCGATGCCTGATGCGACGCGGTCGCGTCGTATCAGGCCt > 1:765295/1‑45 (MQ=255)
gCAACCGATGCCTGATGCGACGCGGTCGCGTCTTa > 1:11565/1‑35 (MQ=255)
aaCCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTAtt < 1:4414672/71‑1 (MQ=255)
aCCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTa < 1:1847385/68‑1 (MQ=255)
aCCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTc > 1:5370321/1‑71 (MQ=255)
cGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCg < 1:4107343/64‑1 (MQ=255)
cGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCgg > 1:1782458/1‑71 (MQ=255)
gATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGa > 1:4779939/1‑52 (MQ=255)
gATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACa < 1:2569914/60‑1 (MQ=255)
gATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGc < 1:4389140/71‑1 (MQ=255)
gATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGc < 1:448219/71‑1 (MQ=255)
gATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGc < 1:2539130/71‑1 (MQ=255)
gATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGc < 1:2651410/71‑1 (MQ=255)
aTGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTa < 1:3173683/64‑1 (MQ=255)
ccTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCAAtt < 1:4894105/71‑1 (MQ=255)
tGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTAc < 1:3036693/53‑1 (MQ=255)
tGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTAc < 1:5147233/53‑1 (MQ=255)
tGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCAAt < 1:617128/68‑1 (MQ=255)
tGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCAAt < 1:469343/68‑1 (MQ=255)
gATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTc < 1:2657539/37‑1 (MQ=255)
gATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTc < 1:687379/37‑1 (MQ=255)
aTGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCAATTa > 1:5690586/1‑68 (MQ=255)
gCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCAATTAATAc < 1:3684779/70‑1 (MQ=255)
cGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATg < 1:780192/45‑1 (MQ=255)
cGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATg < 1:806891/45‑1 (MQ=255)
gACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATg < 1:3753386/44‑1 (MQ=255)
cgcgGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTAc > 1:2305667/1‑45 (MQ=255)
cgGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTAGGCAATTAATACATAGCa > 1:5254149/1‑70 (MQ=255)
ggTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCggg < 1:2633056/54‑2 (MQ=255)
ggTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCAATTAATACATAGCACg < 1:4471367/71‑1 (MQ=255)
|
AATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCAATTAATACATAGCACG > minE/2790604‑2790744
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
