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 |
2,856,258 |
T→C |
20.2% |
T177T (ACT→ACC) |
yjeF → |
predicted carbohydrate kinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,856,258 | 0 | T | C | 20.2%
| 75.8
/ 11.7
| 54 | T177T (ACT→ACC) | yjeF | predicted carbohydrate kinase |
| Reads supporting (aligned to +/- strand): ref base T (22/21); new base C (8/3); total (30/24) |
| Fisher's exact test for biased strand distribution p-value = 3.10e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AATTCCCATCCTGCGCCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCACTTTTATTGCGCTGAAACCA > minE/2856199‑2856321
|
aaTTCCCATCCTGCGCCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTAc > 1:728795/1‑68 (MQ=255)
aaTTCCCATCCTGCGCCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTAc > 1:2281798/1‑68 (MQ=255)
aaTTCCCATCCTGCGCCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTAc > 1:2148915/1‑68 (MQ=255)
aaTTCCCATCCTGCGCCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTAc > 1:2453345/1‑68 (MQ=255)
aaTTCCCATCCTGCGCCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTAc > 1:665332/1‑68 (MQ=255)
aaTTCCCATCCTGCGCCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTAc > 1:3377064/1‑68 (MQ=255)
aaTTCCCATCCTGCGCCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACg < 1:2283987/69‑1 (MQ=255)
aaTTCCCATCCTGCGCCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACg < 1:1430144/69‑1 (MQ=255)
aaTTCCCATCCTGCGCCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACg < 1:715750/69‑1 (MQ=255)
aaTTCCCATCCTGCGCCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACg < 1:3005301/69‑1 (MQ=255)
aTTCCCATCCTGCGCCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACg < 1:938684/68‑1 (MQ=255)
aTTCCCATCCTGCGCCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACg < 1:1381210/68‑1 (MQ=255)
cccATCCTGCGCCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAg > 1:60958/1‑69 (MQ=255)
cccATCCTGCGCCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAg > 1:1476236/1‑69 (MQ=255)
cccATCCTGCGCCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAg > 1:1369430/1‑69 (MQ=255)
gcgcCGATTGTGGCGGTTGATATCCCTTCCGGCCTGGTGGCTGAAACTGGCGCTACGCCAGGCGCGGTg < 1:1493169/69‑1 (MQ=255)
gcgcCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTg < 1:2492914/69‑1 (MQ=255)
ccGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATc < 1:3132028/69‑1 (MQ=255)
ccGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATc < 1:3075717/69‑1 (MQ=255)
ccGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATc < 1:249248/69‑1 (MQ=255)
cGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATc < 1:1144937/68‑1 (MQ=255)
ggTTGATATCCCTTCCGGCCTTCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACGCCGATca < 1:2085929/69‑1 (MQ=255)
ggTTGATATCCCTTCCGGCCTTCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACGCCGATca < 1:1560561/69‑1 (MQ=255)
ggTTGATATCCCTTCCGGCCTTCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACGCCGATca < 1:3174994/69‑1 (MQ=255)
ggTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATca < 1:2413889/69‑1 (MQ=255)
ggTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATca < 1:210930/69‑1 (MQ=255)
ggTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATca < 1:2548041/69‑1 (MQ=255)
ggTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATca < 1:1731322/69‑1 (MQ=255)
ggTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATca < 1:181512/69‑1 (MQ=255)
tGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCacac < 1:2564684/69‑1 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATc > 1:2105390/1‑49 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:416763/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:3364749/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:3258970/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:1520773/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:3108754/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:145180/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:307571/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:1283409/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:862682/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:2676173/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:2637709/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:2516643/1‑69 (MQ=255)
cGGCCTTCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACg > 1:112088/1‑47 (MQ=37)
cGGCCTTCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACGCCGATCACACCATCACTTTTAt > 1:403633/1‑69 (MQ=255)
cGGCCTTCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACGCCGATCACACCATCACTTTTAt > 1:3270839/1‑69 (MQ=255)
cGGCCTTCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACGCCGATCACACCATCACTTTTAt > 1:3081678/1‑69 (MQ=255)
cGGCCTTCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACGCCGATCACACCATCACTTTTAt > 1:855165/1‑69 (MQ=255)
cGGCCTTCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACGCCGATCACACCATCACTTTTAt > 1:2050734/1‑69 (MQ=255)
cGGCCTTCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACGCCGATCACACCATCACTTTTAt > 1:236725/1‑69 (MQ=255)
cGGCCTGCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACGCCGATCACACCATCACTTTTAt > 1:435836/1‑69 (MQ=255)
tggctgAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCACTTTTAt < 1:3119278/61‑1 (MQ=255)
gAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCACTTTTATTGCGCTGAAACCa < 1:1721865/69‑1 (MQ=255)
gAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCACTTTTATTGCGCTGAAACCa < 1:3025660/69‑1 (MQ=255)
|
AATTCCCATCCTGCGCCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCACTTTTATTGCGCTGAAACCA > minE/2856199‑2856321
|
| 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
