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 |
2,856,279 |
G→A |
28.1% |
V184V (GTG→GTA) |
yjeF → |
predicted carbohydrate kinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,856,279 | 0 | G | A | 28.1%
| 38.6
/ 12.9
| 39 | V184V (GTG→GTA) | yjeF | predicted carbohydrate kinase |
| Reads supporting (aligned to +/- strand): ref base G (15/13); new base A (8/3); total (23/16) |
| Fisher's exact test for biased strand distribution p-value = 4.71e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCGCCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCACTTTTATTGCGCTGAAACCAGGCTTGCTCACTGGAAAAGCGCGGGA > minE/2856211‑2856347
|
gcgcCGATTGTGGCGGTTGATATCCCTTCCGGCCTGGTGGCTGAAACTGGCGCTACGCCAGGCGCGGTg < 1:1493169/69‑1 (MQ=255)
gcgcCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTg < 1:2492914/69‑1 (MQ=255)
ccGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATc < 1:249248/69‑1 (MQ=255)
ccGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATc < 1:3075717/69‑1 (MQ=255)
ccGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATc < 1:3132028/69‑1 (MQ=255)
cGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATc < 1:1144937/68‑1 (MQ=255)
ggTTGATATCCCTTCCGGCCTTCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACGCCGATca < 1:1560561/69‑1 (MQ=255)
ggTTGATATCCCTTCCGGCCTTCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACGCCGATca < 1:3174994/69‑1 (MQ=255)
ggTTGATATCCCTTCCGGCCTTCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACGCCGATca < 1:2085929/69‑1 (MQ=255)
ggTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATca < 1:1731322/69‑1 (MQ=255)
ggTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATca < 1:2548041/69‑1 (MQ=255)
ggTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATca < 1:181512/69‑1 (MQ=255)
ggTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATca < 1:2413889/69‑1 (MQ=255)
ggTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATca < 1:210930/69‑1 (MQ=255)
tGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCacac < 1:2564684/69‑1 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATc > 1:2105390/1‑49 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:307571/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:2676173/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:3364749/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:416763/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:862682/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:2637709/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:3108754/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:3258970/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:2516643/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:1283409/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:145180/1‑69 (MQ=255)
cccTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCAc > 1:1520773/1‑69 (MQ=255)
cGGCCTTCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACg > 1:112088/1‑47 (MQ=37)
cGGCCTTCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACGCCGATCACACCATCACTTTTAt > 1:3081678/1‑69 (MQ=255)
cGGCCTTCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACGCCGATCACACCATCACTTTTAt > 1:3270839/1‑69 (MQ=255)
cGGCCTTCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACGCCGATCACACCATCACTTTTAt > 1:2050734/1‑69 (MQ=255)
cGGCCTTCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACGCCGATCACACCATCACTTTTAt > 1:403633/1‑69 (MQ=255)
cGGCCTTCTGGCTGAAACCGGCGCTACGCCAGGCGCGGTAATCAACGCCGATCACACCATCACTTTTAt > 1:855165/1‑69 (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)
ggCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCACTTTTATTGCGCTGAAACCAGGCtt > 1:1479019/1‑68 (MQ=255)
ggCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCACTTTTATTGCGCTGAAACCAGGCTTg > 1:1786658/1‑69 (MQ=255)
gATCAACGCCGATCACACCATCACTTTTATTGCGCTGAAACCAGGCTTGCTCACTGGAAAAGCGCGGGa < 1:1816412/69‑1 (MQ=255)
|
GCGCCGATTGTGGCGGTTGATATCCCTTCCGGCCTGCTGGCTGAAACTGGCGCTACGCCAGGCGCGGTGATCAACGCCGATCACACCATCACTTTTATTGCGCTGAAACCAGGCTTGCTCACTGGAAAAGCGCGGGA > minE/2856211‑2856347
|
| 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
