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 |
268,248 |
A→G |
41.6% |
I133I (ATT→ATC) |
dxs ← |
1‑deoxyxylulose‑5‑phosphate synthase, thiamine‑requiring, FAD‑requiring |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 268,248 | 0 | A | G | 41.6%
| 12.5
/ 33.1
| 48 | I133I (ATT→ATC) | dxs | 1‑deoxyxylulose‑5‑phosphate synthase, thiamine‑requiring, FAD‑requiring |
| Reads supporting (aligned to +/- strand): ref base A (12/16); new base G (11/9); total (23/25) |
| Fisher's exact test for biased strand distribution p-value = 5.59e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01 |
TAATCGCGCCATCGCCAATGACACAGACGGTGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCGGCACTGATGGAGGTTGATGAATGCCCGACGCTTAATAC > minE/268181‑268298
|
tAATCGCGCCATCGCCAATGACACAGACGGTGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCa < 1:623854/68‑1 (MQ=255)
aaTCGCGCCATCGCCAATGACACAGACGGTGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAAt > 1:2944143/1‑69 (MQ=255)
cgcgCCATCGCCAATGACACAGACGGTGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATAcc < 1:934551/69‑1 (MQ=255)
gcCATCGCCAATGACACAGACGGTGCGGCGATTTTTGCCTTCTTTCTCGGCAGCAACTGCGATCCCAAt < 1:564752/69‑1 (MQ=255)
gcCATCGCCAATGACACAGACGGTGCGGCGATTTTTGCCTTCTTTCTCGGCAGCAACTGCGATCCCAAt < 1:3163126/69‑1 (MQ=255)
gcCATCGCCAATGACACAGACGGTGCGGCGATTTTTGCCTTCTTTCTCGGCAGCAACTGCGATCCCAAt < 1:2536042/69‑1 (MQ=255)
ccATCGCCAATGACACAGACGGTGCGGCGATTTTTGCCTTCTTTCTCGGCAGCAACTGCGATCCCAAt < 1:2365986/68‑1 (MQ=255)
gCCAATGACACAGACGGTGCGGCTATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCgg > 1:204622/1‑68 (MQ=255)
gCCAATGACACAGACGGTGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCgg > 1:156228/1‑68 (MQ=255)
gCCAATGACACAGACGGTGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCgg < 1:3149840/68‑1 (MQ=255)
gCCAATGACACAGACGGTGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCgg > 1:1747242/1‑68 (MQ=255)
gCCAATGACACAGACGGTGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCgg < 1:1003877/68‑1 (MQ=255)
gCCAATGACACAGACGGTGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCgg < 1:1997009/68‑1 (MQ=255)
gCCAATGACACAGACGGTGCGGCGATTTTTGCCTTATTTTTCGGCAGCAACCGCAATACCAATTCCgg < 1:2153394/68‑1 (MQ=255)
aaTGACACAGACGGTGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCGGCACt < 1:26749/69‑1 (MQ=255)
aaTGACACAGACGGTGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCGGCACt < 1:1350571/69‑1 (MQ=255)
aaTGACACAGACGGTGCGGCGATTTTTGCCTTCTTTCTCGGCAGCAACTGCGATCCCAAt > 1:2067511/1‑60 (MQ=255)
aaTGACACAGACGGTGCGGCGATTTTTGCCTTCTTTCTCGGCAGCAACTGCGATCCCAATTCCGGCACt > 1:813747/1‑69 (MQ=255)
aaTGACACAGACGGTGCGGCGATTTTTGCCTTCTTTCTCGGCAGCAACTGCGATCCCAATTCCGGCACt > 1:2348271/1‑69 (MQ=255)
aaTGACACAGACGGTGCGGCGATTTTTGCCTTCTTTCTCGGCAGCAACTGCGATCCCAATTCCGGCACt > 1:1653720/1‑69 (MQ=255)
aaTGACACAGACGGTGCGGCGATTTTTGCCTTCTTTCTCGGCAGCAACTGCGATCCCAATTCCGGCACt > 1:859591/1‑69 (MQ=255)
aaTGACACAGACGGTGCGGCGATTTTTGCCTTCTTTCTCGGCAGCAACTGCGATCCCAATTCCGGCACt > 1:2913380/1‑69 (MQ=255)
gACACAGACGGTGCGGCGATTTTTGCCTTGTTTTTCGGCAGCAACCGCAATACCAATTCCGGCACTGa > 1:2904175/1‑68 (MQ=255)
gACACAGACGGTGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCGGCACTGa > 1:1901467/1‑68 (MQ=255)
gACACAGACGGTGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCGGCACTGa > 1:484887/1‑68 (MQ=255)
gACACAGACGGTGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCGGCACTGa > 1:3330574/1‑68 (MQ=255)
gACACAGACGGTGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCGGCACTGa > 1:3246796/1‑68 (MQ=255)
gACACAGACGGTGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCGGCACTGa > 1:2172970/1‑68 (MQ=255)
gACACAGACGGTGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCGGCACTGa > 1:2089793/1‑68 (MQ=255)
gACACAGACGGTGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCGGCACTGa > 1:2387713/1‑68 (MQ=255)
tGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCGGCACTGATGGAGGTtgatg < 1:3370984/69‑1 (MQ=255)
tGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCGGCACTGATGGAGGTtgatg < 1:3368578/69‑1 (MQ=255)
tGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCGGCACTGATGGAGGTtgatg < 1:3367076/69‑1 (MQ=255)
gcgATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCgg < 1:2680659/47‑1 (MQ=255)
gcgATTTTTGCCTTCTTTCTCGGCAGCAACTGCGATCCCAATTCCGGCACTGATGGAGGTTGATGAAt < 1:2473658/68‑1 (MQ=255)
gcgATTTTTGCCTTCTTTCTCGGCAGCAACTGCGATCCCAATTCCGGCACTGATGGAGGTTGATGAAt < 1:3085491/68‑1 (MQ=255)
gcgATTTTTGCCTTCTTTCTCGGCAGCAACTGCGATCCCAATTCCGGCACTGATGGAGGTTGATGAAt < 1:2679693/68‑1 (MQ=255)
gcgATTTTTGCCTTCTTTCTCGGCAGCAACTGCGATCCCAATTCCGGCACTGATGGAGGTTGATGAAt < 1:2827641/68‑1 (MQ=255)
gcgATTTTTGCCTTCTTTCTCGGCAGCAACTGCGATCCCAATTCCGGCACTGATGGAGGTTGATGAAt < 1:126922/68‑1 (MQ=255)
ttctttctCGGCAGCAACTGCGATCCCAATTCCGGCACTGATGGAGGTTGATGAATGCCCGACGCTTaa > 1:908564/1‑69 (MQ=255)
ttctttctCGGCAGCAACTGCGATCCCAATTCCGGCACTGATGGAGGTTGATGAATGCCCGACGCTTaa > 1:3156395/1‑69 (MQ=255)
ttctttctCGGCAGCAACTGCGATCCCAATTCCGGCACTGATGGAGGTTGATGAATGCCCGACGCTTaa > 1:1974350/1‑69 (MQ=255)
ttctttctCGGCAGCAACTGCGATCCCAATTCCGGCACTGATGGAGGTTGATGAATGCCCGACGCTTaa > 1:602324/1‑69 (MQ=255)
ttctttctCGGCAGCAACTGCGATCCCAATTCCGGCACTGATGGAGGTTGATGAATGCCCGACGCTTaa > 1:2185265/1‑69 (MQ=255)
ttttCGGCAGCAACCGCAATACCAATTCCGGCACTGATGGAGGTTGATGAATGCCCGACGCTTAATAc < 1:1253161/68‑1 (MQ=255)
ttttCGGCAGCAACCGCAATACCAATTCCGGCACTGATGGAGGTTGATGAATGCCCGACGCTTAATAc < 1:740743/68‑1 (MQ=255)
ttttCGGCAGCAACCGCAATACCAATTCCGGCACTGATGGAGGTTGATGAATGCCCGACGCTTAATAc < 1:1737907/68‑1 (MQ=255)
ttttCGGCAGCAACCGCAATACCAATTCCGGCACTGATGGAGGTTGATGAATGCCCGACGCTTAATAc < 1:2422566/68‑1 (MQ=255)
ttttCGGCAGCAACCGCAATACCAATTCCGGCACTGATGGAGGTTGATGAATGCCCGACGCTTAATAc < 1:2212631/68‑1 (MQ=255)
|
TAATCGCGCCATCGCCAATGACACAGACGGTGCGGCGATTTTTGCCTTCTTTTTCGGCAGCAACCGCAATACCAATTCCGGCACTGATGGAGGTTGATGAATGCCCGACGCTTAATAC > minE/268181‑268298
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
