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 |
2,447,222 |
G→A |
54.2% |
pseudogene (834/1647 nt) |
ilvG ← |
Mutation in protein compared to W3110: p.Glu327_Ilefs*223 Restoration of IlvG found in MG1655 (548 amino acids), fusion of N‑ter and C‑ter fragments ECK3760:JW3740+JW3741:b4488; large subunit of acetolactate synthase II |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,447,222 | 0 | G | A | 54.2%
| 3.5
/ 48.5
| 59 | pseudogene (834/1647 nt) | ilvG | Mutation in protein compared to W3110: p.Glu327_Ilefs*223 Restoration of IlvG found in MG1655 (548 amino acids), fusion of N‑ter and C‑ter fragments ECK3760:JW3740+JW3741:b4488; large subunit of acetolactate synthase II |
| Reads supporting (aligned to +/- strand): ref base G (21/6); new base A (19/13); total (40/19) |
| Fisher's exact test for biased strand distribution p-value = 1.68e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ATCCATATGGATAACACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCG > minE/2447174‑2447282
|
atCCATATGGATAACACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGGCGGTCACCCGGTCATCAAAACg < 1:126508/69‑1 (MQ=255)
tatGGATAACACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCa < 1:1097760/68‑1 (MQ=255)
tatGGATAACACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCa < 1:1475799/68‑1 (MQ=255)
tGGATAACACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCCCCCGGTCATCAAAACGTGCAcc > 1:1839755/1‑68 (MQ=255)
tGGATAACACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCAccc > 1:2416502/1‑69 (MQ=255)
tGGATAACACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCAccc > 1:1151336/1‑69 (MQ=255)
tGGATAACACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCAccc > 1:1462919/1‑69 (MQ=255)
gATAACACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCa < 1:2505710/68‑1 (MQ=255)
gATAACACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCa < 1:3307126/68‑1 (MQ=255)
aaCACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCCCCCGGTCATCAAAACGTGCACCCACGGc > 1:2215951/1‑69 (MQ=255)
aaCACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGc > 1:1030015/1‑69 (MQ=255)
aaCACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGc > 1:1632383/1‑69 (MQ=255)
aaCACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGc > 1:2615687/1‑69 (MQ=255)
aaCACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGc > 1:2720970/1‑69 (MQ=255)
aaCACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGc > 1:1475579/1‑69 (MQ=255)
aaCACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGc > 1:3417582/1‑69 (MQ=255)
aaCACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGc > 1:1063832/1‑69 (MQ=255)
aaCACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGc > 1:1048079/1‑69 (MQ=255)
aaCACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGc > 1:511476/1‑69 (MQ=255)
aaCACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCAAGGc > 1:2190983/1‑69 (MQ=255)
aaCACTGGCGTGTGGTGCGAAGGTGTTAAGTTTGACGGTCACCCGGTCATCAAAACGTGCAccc > 1:1903081/1‑64 (MQ=39)
cGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACt > 1:3180236/1‑69 (MQ=255)
cGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACt > 1:1301261/1‑69 (MQ=255)
gtgtTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCa > 1:1468409/1‑43 (MQ=255)
gtgtTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGc > 1:509229/1‑69 (MQ=255)
gtgtTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGc > 1:841321/1‑69 (MQ=255)
gtgtTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGc < 1:1141188/69‑1 (MQ=255)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCGCGGCGATCAGTAGATCGCACTCCTGCActg > 1:3284917/1‑66 (MQ=25)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:2077265/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:759418/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:628462/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:1101481/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:3297696/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:3278031/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:1452978/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:3092447/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:2988825/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:283948/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:1604107/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:2153053/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:1731173/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:1917465/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:2371885/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:2354101/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:2726628/1‑66 (MQ=37)
cAGTTTGCCAGTAACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:3426814/1‑66 (MQ=255)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTTCACtgcg < 1:2315502/65‑1 (MQ=25)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:2331725/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:101782/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:531515/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:520747/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:1047772/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:1051650/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:479703/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:2379793/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:3225984/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:179519/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:3074879/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:1528856/65‑1 (MQ=37)
|
ATCCATATGGATAACACTGGCGTGTGGTGCGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCG > minE/2447174‑2447282
|
| 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
