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 |
384,352 |
A→G |
40.4% |
L52L (TTA→TTG) ‡ |
ybdB → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 384,352 | 0 | A | G | 40.4%
| 15.6
/ 30.8
| 47 | L52L (TTA→TTG) ‡ | ybdB | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (16/12); new base G (13/6); total (29/18) |
| Fisher's exact test for biased strand distribution p-value = 5.46e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01 |
TCTGGGCGATGATGTGCTGGAAGCCGAAATGCCGGTTGATACCCGTACTCATCAGCCGTTCGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGATCGATGGCCGGATTTATGAT > minE/384286‑384414
|
tCTGGGCGATGATGTGCTGGAAGCCGAAATGCCGGTTGATACCCGTACTCATCAGCCGTTCGGTTtact < 1:1697030/69‑1 (MQ=255)
cttggCGATGATGTGCTGGAAGCCGAAATGCCGGTTGATACCCGTACTCATCAGCCGTTCGGTTtacta < 1:1060457/66‑1 (MQ=255)
cTGGGCGATGATGTGCTGGAAGCCGAAATGCCGGTTGATACCCGTACTCATCAGCCGTTCGGTTtactg < 1:2664233/69‑2 (MQ=255)
cTGGGCGATGATGTGCTGGAAGCCGAAATGCCGGTTGATACCCGTACTCATCAGCCGTTCGGTTtacta < 1:110161/69‑1 (MQ=255)
cTGGGCGATGATGTGCTGGAAGCCGAAATGCCGGTTGATACCCGTACTCATCAGCCGTTCGGTTtacta < 1:1305483/69‑1 (MQ=255)
cTGGGCGATGATGTGCTGGAAGCCGAAATGCCGGTTGATACCCGTACTCATCAGCCGTTCGGTTtacta < 1:1357877/69‑1 (MQ=255)
cTGGGCGATGATGTGCTGGAAGCCGAAATGCCGGTTGATACCCGTACTCATCAGCCGTTCGGTTtacta < 1:2161729/69‑1 (MQ=255)
cTGGGCGATGATGTGCTGGAAGCCGAAATGCCGGTTGATACCCGTACTCATCAGCCGTTCGGTTtacta < 1:1410400/69‑1 (MQ=255)
atgatgTGCTGGAAGCCGAAATGCCGGTTGATACCCGTACTCATCAGCCGTTCGGTTTACTACATggcg > 1:621782/1‑69 (MQ=255)
atgatgTGCTGGAAGCCGAAATGCCGGTTGATACCCGTACTCATCAGCCGTTCGGTTTACTACATggcg > 1:3185648/1‑69 (MQ=255)
gCCGGTTGATACCCGTACTCATCAGCCGTTTGGCCTGCTGCATGGCGGCGCGTCGGCGGCGCTGGCGGa < 1:25466/69‑1 (MQ=255)
gCCGGTTGATACCCGTACTCATCAGCCGTTTGGCCTGCTGCATGGCGGCGCGTCGGCGGCGCTGGCGGa < 1:2352750/69‑1 (MQ=255)
gCCGGTTGATACCCGTACTCATCAGCCGTTTGGCCTGCTGCATGGCGGCGCGTCGGCGGCGCTGGCGGa < 1:2796177/69‑1 (MQ=255)
gCCGGTTGATACCCGTACTCATCAGCCGTTTGGCCTGCTGCATGGCGGCGCGTCGGCGGCGCTGGCGGa < 1:2895583/69‑1 (MQ=255)
gCCGGTTGATACCCGTACTCATCAGCCGTTTGGCCTGCTGCATGGCGGCGCGTCGGCGGCGCTGGCGGa < 1:1294107/69‑1 (MQ=255)
gCCGGTTGATACCCGTACTCATCAGCCGTTTGGCCTGCTGCATGGCGGCGCGTCGGCGGCGCTGGCGGa < 1:1624058/69‑1 (MQ=255)
aCCCGTACTCATCAGCCGTTTGTCCTGCTGCATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGa > 1:1311923/1‑69 (MQ=255)
aCCCGTACTCATCAGCCGTTTGGCCTGCTGCATGGCGGCGCGTCGGCGGCGCTGGCGGa > 1:2864896/1‑59 (MQ=255)
aCCCGTACTCATCAGCCGTTTGGCCTGCTGCATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGa > 1:1770295/1‑69 (MQ=255)
aCCCGTACTCATCAGCCGTTTGGCCTGCTGCATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGa > 1:2566593/1‑69 (MQ=255)
aCCCGTACTCATCAGCCGTTTGGCCTGCTGCATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGa > 1:820897/1‑69 (MQ=255)
aCCCGTACTCATCAGCCGTTTGGCCTGCTGCATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGa > 1:2179374/1‑69 (MQ=255)
aCCCGTACTCATCAGCCGTTTGGCCTGCTGCATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGa > 1:698418/1‑69 (MQ=255)
aCCCGTACTCATCAGCCGTTTGGCCTGCTGCATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGa > 1:2108540/1‑69 (MQ=255)
aCCCGTACTCATCAGCCGTTTGGCCTGCTGCATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGa > 1:2932245/1‑69 (MQ=255)
aCCCGTACTCATCAGCCGTTTGGCCTGCTGCATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGa > 1:2048183/1‑69 (MQ=255)
aCCCGTACTCATCAGCCGTTTGGCCTGCTGCATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGa > 1:3020643/1‑69 (MQ=255)
aCCCGTACTCATCAGCCGTTTGGCCTGCTGCATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGa > 1:164285/1‑69 (MQ=255)
aCCCGTACTCATCAGCCGTTTGGCCTGCTGCATGGCGGCGCGTAGGCGGCGCTGGCGGAAACGCTGGGa > 1:2052158/1‑69 (MQ=255)
aCCCGTACTCATCAGCCGTTCGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTggg < 1:3398627/68‑1 (MQ=255)
aCCCGTACTCATCAGCCGTTCGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTggg < 1:996928/68‑1 (MQ=255)
aCCCGTACTCATCAGCCGTTCGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTggg < 1:1144426/68‑1 (MQ=255)
aCCCGTACTCATCAGCCGTTCGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTggg < 1:2465067/68‑1 (MQ=255)
aCCCGTACTCATCAGCCGTTCGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTggg < 1:1911974/68‑1 (MQ=255)
cTCATCAGCCGTTCGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGATCGATgg > 1:1710759/1‑69 (MQ=255)
cTCATCAGCCGTTCGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGATCGATgg > 1:57925/1‑69 (MQ=255)
cTCATCAGCCGTTCGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGATCGATgg > 1:2070544/1‑69 (MQ=255)
catcaGCCGTTCGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGATCGATGGc > 1:2233600/1‑68 (MQ=255)
catcaGCCGTTCGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGATCGATGGc > 1:1276006/1‑68 (MQ=255)
catcaGCCGTTCGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGATCGATGGc > 1:902590/1‑68 (MQ=255)
catcaGCCGTTCGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGATCGATGGc > 1:914172/1‑68 (MQ=255)
caGCCGTTCGGTTTACTACATGGCGGCGCGTCggcggc < 1:2125408/38‑1 (MQ=255)
caGCCGTTCGGTTTACTACATGGCGGCGCGTCggcggc < 1:2799516/38‑1 (MQ=255)
caGCCGTTCGGTTTACTACATGGCGGCGCGTCggcggc < 1:1905624/38‑1 (MQ=255)
caGCCGTTCGGTTTACTACATGGCGGCGCGTCggcggc < 1:65806/38‑1 (MQ=255)
caGCCGTTCGGTTTACTACATGGCGGCGCGTCggcggc < 1:1364017/38‑1 (MQ=255)
caGCCGTTCGGTTTACTACATGGCGGCGCGTCggcggc < 1:898145/38‑1 (MQ=255)
aGCCGTTCGGTTTACTACATGGCGGCGCGTCggcggc < 1:2978114/37‑1 (MQ=255)
cGTTCGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGATCGATGGCCGGAttt > 1:3247668/1‑68 (MQ=255)
cGTTCGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGATCGATGGCCGGAttt > 1:918300/1‑68 (MQ=255)
cGTTCGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGATCGATGGCCGGAttt > 1:610729/1‑68 (MQ=255)
cGTTCGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGATCGATGGCCGGAttt > 1:1425223/1‑68 (MQ=255)
cGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGATCGATGGCCGGATTTatgat > 1:2420593/1‑69 (MQ=255)
cGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGATCGATGGCCGGATTTatgat > 1:2284065/1‑69 (MQ=255)
cGGTTTACTACATGGCGGCGCGTAGGCGGCGCTGGCGGAAACGCTGGGATCGATGGCCGGATTTatgat > 1:2196675/1‑69 (MQ=255)
|
TCTGGGCGATGATGTGCTGGAAGCCGAAATGCCGGTTGATACCCGTACTCATCAGCCGTTCGGTTTACTACATGGCGGCGCGTCGGCGGCGCTGGCGGAAACGCTGGGATCGATGGCCGGATTTATGAT > minE/384286‑384414
|
| 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
