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 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,698,732 |
A→G |
41.7% |
P204P (CCA→CCG) |
csiE → |
stationary phase inducible protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,698,732 | 0 | A | G | 41.7%
| 9.1
/ 37.0
| 54 | P204P (CCA→CCG) | csiE | stationary phase inducible protein |
| Reads supporting (aligned to +/- strand): ref base A (24/7); new base G (12/10); total (36/18) |
| Fisher's exact test for biased strand distribution p-value = 1.34e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.23e-05 |
GTAGCGCAGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGTTCCCGATCCATTGCGGGAT > minE/1698679‑1698798
|
gTAGCGCAGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTg < 1:1049177/69‑1 (MQ=255)
gTAGCGCAGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTg < 1:1051242/69‑1 (MQ=255)
gTAGCGCAGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTg < 1:1368505/69‑1 (MQ=255)
gTAGCGCAGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTg < 1:476708/69‑1 (MQ=255)
gTAGCGCAGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTg < 1:687914/69‑1 (MQ=255)
aGCGCAGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGtt > 1:2749013/1‑69 (MQ=255)
aGCGCAGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGtt > 1:2618730/1‑69 (MQ=255)
aGCGCAGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGtt > 1:3135254/1‑69 (MQ=255)
ggAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTg < 1:2306651/61‑1 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCCGCCTGTACCGCCTGATGAGCCACTGTTTATGGCatt > 1:777388/1‑67 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCatt > 1:3238369/1‑67 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCatt > 1:3267100/1‑67 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCatt > 1:1882834/1‑67 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCatt > 1:42679/1‑67 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCatt > 1:1679503/1‑67 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCatt > 1:1423126/1‑67 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCatt > 1:1388438/1‑67 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCatt > 1:2689003/1‑67 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCatt > 1:1122195/1‑67 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCatt > 1:813483/1‑67 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCat > 1:3145432/1‑67 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCtgatg > 1:1217900/1‑50 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATg > 1:249944/1‑64 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCact > 1:2483451/1‑69 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCact > 1:3011443/1‑69 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCact > 1:2322499/1‑69 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCact > 1:660090/1‑69 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCact > 1:733238/1‑69 (MQ=255)
aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCact > 1:1237520/1‑69 (MQ=255)
ttGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTg < 1:3382914/56‑1 (MQ=255)
cGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCATTACtttt < 1:3289979/68‑1 (MQ=255)
cGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCATTACtttt < 1:3378408/68‑1 (MQ=255)
cGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCATTACtttt < 1:854848/68‑1 (MQ=255)
cGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCATTACtttt < 1:933724/68‑1 (MQ=255)
cGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCATTACtttt < 1:2857065/68‑1 (MQ=255)
cGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCATTACtttt < 1:284687/68‑1 (MQ=255)
cGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCATTACtttt < 1:2432042/68‑1 (MQ=255)
cGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCATTACtttt < 1:2299322/68‑1 (MQ=255)
cGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCATTACtttt < 1:183187/68‑1 (MQ=255)
cGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCGCCTGATGAGCCACTGTTTATGGCATTACtttt < 1:207466/68‑1 (MQ=255)
aCTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCtgat > 1:2917334/1‑38 (MQ=255)
aCTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCa > 1:1005066/1‑69 (MQ=255)
aCTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCa > 1:1651592/1‑69 (MQ=255)
aCTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCa > 1:681409/1‑69 (MQ=255)
aCTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCa > 1:654374/1‑69 (MQ=255)
aCTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCa > 1:521133/1‑69 (MQ=255)
aCTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCa > 1:1747179/1‑69 (MQ=255)
aCTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCa > 1:2183761/1‑69 (MQ=255)
aCTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCa > 1:2317392/1‑69 (MQ=255)
aCTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCa > 1:2499701/1‑69 (MQ=255)
aCTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCa > 1:3124902/1‑69 (MQ=255)
aCTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCa > 1:2904236/1‑69 (MQ=255)
atGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCAt > 1:3331989/2‑69 (MQ=255)
ccTGTACCTCCTGATGAGCCACTGTTTATGGCATTACtttt < 1:1704320/41‑1 (MQ=38)
ccaccTGATGAGCCACTGTTTATGGGACTACTTTTTTCCATGTTGCGGGTTCCCGATCCATTGCGGGAt > 1:508826/1‑69 (MQ=255)
ccaccTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGTTCCCGATCCATTGCg > 1:1087641/1‑65 (MQ=255)
ccaccTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGTTCCCGATCCATTGCGGGa > 1:103936/1‑68 (MQ=255)
ccaccTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGTTCCCGATCCATTGCGGGAt > 1:2120799/1‑69 (MQ=255)
ccaccTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGTTCCCGATCCATTGCGGGAt > 1:3054973/1‑69 (MQ=255)
ccaccTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGTTCCCGATCCATTGCGGGAt > 1:1338768/1‑69 (MQ=255)
ccaccTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGTTCCCGATCCATTGCGGGAt > 1:1047604/1‑69 (MQ=255)
|
GTAGCGCAGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGTTCCCGATCCATTGCGGGAT > minE/1698679‑1698798
|
| 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
