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 |
2,418,583 |
G→A |
65.7% |
H25H (CAC→CAT) |
rffM ← |
UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,418,583 | 0 | G | A | 65.7%
| 45.0
/ 36.9
| 67 | H25H (CAC→CAT) | rffM | UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase |
| Reads supporting (aligned to +/- strand): ref base G (16/7); new base A (20/24); total (36/31) |
| Fisher's exact test for biased strand distribution p-value = 7.46e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01 |
TTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTTGGTGCCGTGGTGTTGT > minE/2418524‑2418650
|
ttAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCat < 1:605338/68‑1 (MQ=255)
aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAATCAGATAATCGAGGGCGTGCTGCATATc > 1:1139179/1‑69 (MQ=255)
aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGt > 1:928711/1‑59 (MQ=255)
aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGt > 1:894390/1‑59 (MQ=255)
aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGt > 1:7176/1‑59 (MQ=255)
aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGt > 1:1407153/1‑59 (MQ=255)
aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGt > 1:1866076/1‑59 (MQ=255)
aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCatat > 1:659420/1‑68 (MQ=255)
aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATc > 1:3320247/1‑69 (MQ=255)
aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATc > 1:266261/1‑69 (MQ=255)
aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATc > 1:2349674/1‑69 (MQ=255)
aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATc > 1:2236567/1‑69 (MQ=255)
aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATc > 1:2998012/1‑69 (MQ=255)
aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATc > 1:1777372/1‑69 (MQ=255)
aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATc > 1:3360875/1‑69 (MQ=255)
aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATc > 1:403860/1‑69 (MQ=255)
aaTGGCAACCAGCGTTCCCTGCTTAAGCAGCCCGTCAGCAAACAGATAATCGAGGGCGt > 1:1201702/1‑59 (MQ=255)
aaCCAGCGTTCACTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATCACGcca < 1:3004889/69‑1 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:3353058/1‑68 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:2693614/1‑68 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:3315657/1‑68 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:3365236/1‑68 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:3203072/1‑68 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:3068562/1‑68 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:2873701/1‑68 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:2861585/1‑68 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:547206/1‑68 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:549724/1‑68 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:871707/1‑68 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:2656064/1‑68 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:1408595/1‑68 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:2514188/1‑68 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:1233909/1‑68 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:1643450/1‑68 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:2233342/1‑68 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:1344216/1‑68 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:2028770/1‑68 (MQ=255)
gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa > 1:2116992/1‑68 (MQ=255)
tCAGCAAACAGATAATCGAGGGCGTGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGta < 1:7555/69‑1 (MQ=255)
tCAGCAAACAGATAATCGAGGGCGTGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGta < 1:654126/69‑1 (MQ=255)
tCAGCAAACAGATAATCGAGGGCGTGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGta < 1:2477772/69‑1 (MQ=255)
aaTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:3323747/69‑1 (MQ=255)
aaTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:616884/69‑1 (MQ=255)
aaTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:64912/69‑1 (MQ=255)
aaTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:1355216/69‑1 (MQ=255)
aaTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:1287745/69‑1 (MQ=255)
aaTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:1385529/69‑1 (MQ=255)
aaTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:381683/69‑1 (MQ=255)
aaTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:1245570/69‑1 (MQ=255)
aaTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:16391/69‑1 (MQ=255)
aaTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:168438/69‑1 (MQ=255)
aaTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:2025291/69‑1 (MQ=255)
aaTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:2942758/69‑1 (MQ=255)
aaTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:2907448/69‑1 (MQ=255)
aaTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:2827136/69‑1 (MQ=255)
aaTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCCGTGCCg < 1:438289/69‑1 (MQ=255)
aaTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGGCGGTGCCg < 1:2148347/69‑1 (MQ=255)
aTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:1194798/68‑1 (MQ=255)
aTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:763890/68‑1 (MQ=255)
aTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:1204275/68‑1 (MQ=255)
aTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:2645374/68‑1 (MQ=255)
aTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:1308076/68‑1 (MQ=255)
aTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:521422/68‑1 (MQ=255)
aTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:1569036/68‑1 (MQ=255)
aTCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTCGGTGCCg < 1:2213289/68‑1 (MQ=255)
cGTGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTTGGTGCCGTGGtgttgt < 1:822533/69‑1 (MQ=255)
cGTGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTTGGTGCCGTGGtgttgt < 1:2617605/69‑1 (MQ=255)
|
TTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTATAGGTTGGTGCCGTGGTGTTGT > minE/2418524‑2418650
|
| 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
