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 |
2,447,261 |
C→T |
50.6% |
pseudogene (795/1647 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 | 2,447,261 | 0 | C | T | 50.6%
| ‑6.2
/ 69.5
| 75 | pseudogene (795/1647 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 C (22/15); new base T (25/13); total (47/28) |
| Fisher's exact test for biased strand distribution p-value = 6.37e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01 |
CGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGCCATGCATTCCCAGCATGCCCAGATAGTA > minE/2447203‑2447329
|
cGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACt > 1:1301261/1‑69 (MQ=255)
cGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACt > 1:3180236/1‑69 (MQ=255)
gtgtTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGc > 1:841321/1‑69 (MQ=255)
gtgtTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGc < 1:1141188/69‑1 (MQ=255)
gtgtTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGc > 1:509229/1‑69 (MQ=255)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCGCGGCGATCAGTAGATCGCACTCCTGCActg > 1:3284917/1‑66 (MQ=25)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:1604107/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:2354101/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:2371885/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:2153053/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:3297696/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:2077265/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:3278031/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:1917465/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:1731173/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:3092447/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:1452978/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:2726628/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:628462/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:759418/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:1101481/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:283948/1‑66 (MQ=37)
cAGTTTGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:2988825/1‑66 (MQ=37)
cAGTTTGCCAGTAACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCActg > 1:3426814/1‑66 (MQ=255)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTTCACtgcg < 1:2315502/65‑1 (MQ=25)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:1047772/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:3225984/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:3074879/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:2379793/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:101782/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:2331725/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:479703/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:179519/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:520747/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:1528856/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:531515/65‑1 (MQ=37)
tGCCAGTCACCCGGTCATCAAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACtgcg < 1:1051650/65‑1 (MQ=37)
cacaCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTcgccgc > 1:764155/1‑69 (MQ=255)
cACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTcgccgc > 1:328175/1‑69 (MQ=255)
cACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTcgccgc > 1:427607/1‑69 (MQ=255)
cACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTcgccgc > 1:539459/1‑69 (MQ=255)
cACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTcgccgc > 1:2785814/1‑69 (MQ=255)
cACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTcgccgc > 1:1983789/1‑69 (MQ=255)
cACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTcgccgc > 1:2886710/1‑69 (MQ=255)
cACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTcgccgc > 1:2707859/1‑69 (MQ=255)
cACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTcgccgc > 1:1059379/1‑69 (MQ=255)
cACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTcgccgc > 1:1363081/1‑69 (MQ=255)
cACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTcgccgc > 1:2342289/1‑69 (MQ=255)
cACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTcgccgc > 1:2381462/1‑69 (MQ=255)
catcaAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGTGAAGTTCGCCGCTTTGGTGc < 1:351597/69‑1 (MQ=255)
catcaAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGc < 1:3254901/69‑1 (MQ=255)
catcaAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGc < 1:1083168/69‑1 (MQ=255)
catcaAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGc < 1:333618/69‑1 (MQ=255)
catcaAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGc < 1:1968187/69‑1 (MQ=255)
catcaAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGc < 1:3174420/69‑1 (MQ=255)
catcaAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGc < 1:3072130/69‑1 (MQ=255)
caAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACTGCGAAGTTCGCCGCTTTGGTGccg > 1:1483585/1‑67 (MQ=255)
caAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACTGCGAAGTTCGCCGCTTTGGTGccg > 1:573745/1‑67 (MQ=255)
caAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACTGCGAAGTTCGCCGCTTTGGTGccg > 1:872374/1‑67 (MQ=255)
caAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACTGCGAAGTTCGCCGCTTTGGTGccg > 1:2693802/1‑67 (MQ=255)
caAAACGTGCGCCCACGGCGATCAGTAGATCGCACTCCTGCACTGCGAAGTTCGCCGCTTTGGTGccg > 1:2844618/1‑67 (MQ=255)
caAAACGTGCGCCCAAGGCGATCAGTAGATCGCACTCCTGCACTGCGAAGTTCGCCGCTTTGGTGccg > 1:887406/1‑67 (MQ=255)
caAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGtt > 1:1360454/1‑52 (MQ=255)
caAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGCCa > 1:478196/1‑68 (MQ=255)
caAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGCCa > 1:2109375/1‑68 (MQ=255)
caAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGCCa > 1:3241463/1‑68 (MQ=255)
caAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGCCa > 1:2553596/1‑68 (MQ=255)
aaaaCGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTcgccgc < 1:695869/57‑1 (MQ=255)
aaaaCGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGCCATg < 1:482346/69‑1 (MQ=255)
gCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGCCATGCATTccc < 1:24943/69‑1 (MQ=255)
cGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGCCATGCATTCCCAGCATGCCCa < 1:889996/69‑1 (MQ=255)
cGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGCCATGCATTCCCAGCATGCCCa < 1:3051945/69‑1 (MQ=255)
cAGCAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGCCATGCATTCCCAGCATGCCCAGAt > 1:1355157/1‑68 (MQ=255)
aGCAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGCCATGCATTCCCAGCATGCCCAGATAg < 1:2155940/69‑1 (MQ=255)
gCAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGCCATGCATTCCCAGCATGCCCAGATAg < 1:49966/68‑1 (MQ=255)
cAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGCCATGCATTCCCAGCATGCCCAGATAGTa < 1:1569663/69‑1 (MQ=255)
cAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGCCATGCATTCCCAGCATGCCCAGATAGTa < 1:792264/69‑1 (MQ=255)
cAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGCCATGCATTCCCAGCATGCCCAGATAGTa < 1:2044694/69‑1 (MQ=255)
cAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGCCATGCATTCCCAGCATGCCCAGATAGTa < 1:2075889/69‑1 (MQ=255)
|
CGAAGGTGTTCAGTTTGCCGGTCACCCGGTCATCAAAACGTGCACCCACGGCGATCAGCAAGTCGCACTCCTGCACCGCGAAGTTCGCCGCTTTGGTGCCATGCATTCCCAGCATGCCCAGATAGTA > minE/2447203‑2447329
|
| 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
