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 |
1,485,543 |
A→C |
44.5% |
A99A (GCT→GCG) |
menF ← |
isochorismate synthase 2 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,485,543 | 0 | A | C | 44.5%
| 4.1
/ 70.3
| 63 | A99A (GCT→GCG) | menF | isochorismate synthase 2 |
| Reads supporting (aligned to +/- strand): ref base A (11/24); new base C (7/21); total (18/45) |
| Fisher's exact test for biased strand distribution p-value = 7.80e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.53e-01 |
GCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTG > minE/1485478‑1485608
|
gCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCa > 1:1668593/1‑69 (MQ=255)
acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa < 1:817730/69‑1 (MQ=255)
acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa < 1:1937171/69‑1 (MQ=255)
acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa < 1:2106015/69‑1 (MQ=255)
acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa < 1:2534474/69‑1 (MQ=255)
acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa < 1:1806531/69‑1 (MQ=255)
acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa < 1:2745576/69‑1 (MQ=255)
acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa < 1:1295613/69‑1 (MQ=255)
ccAGGCGTGGTAAAAGTAAATTGCCCTGCGACGGGTCAAACGc > 1:2464112/1‑43 (MQ=255)
ccAGGCGTGGTAAAAGTAAATTGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCgg > 1:3052186/1‑69 (MQ=255)
ccAGGCGTGGTAAAAGTAAATTGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCgg > 1:3036130/1‑69 (MQ=255)
ccAGGCGTGGTAAAAGTAAATTGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCgg > 1:2909552/1‑69 (MQ=255)
ccAGGCGTGGTAAAAGTAAATTGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCgg > 1:2820126/1‑69 (MQ=255)
ccAGGCGTGGTAAAAGTAAATTGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCgg > 1:343526/1‑69 (MQ=255)
ccAGGCGTGGTAAAAGTAAATTGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCgg > 1:681207/1‑69 (MQ=255)
ccAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCa > 1:2792288/1‑44 (MQ=255)
ccAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCa > 1:3145361/1‑44 (MQ=255)
ccAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCa > 1:3267705/1‑44 (MQ=255)
ccAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCa > 1:243178/1‑44 (MQ=255)
ccAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCa > 1:860818/1‑44 (MQ=255)
ccAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCa > 1:1594694/1‑44 (MQ=255)
ccAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCa > 1:1880900/1‑44 (MQ=255)
ccAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCa > 1:1876927/1‑44 (MQ=255)
tAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCgg > 1:840529/1‑69 (MQ=255)
tAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCgg > 1:2733437/1‑69 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTTGCg < 1:1469996/68‑1 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGct < 1:3303947/68‑2 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg < 1:412988/68‑1 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg < 1:140717/68‑1 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg < 1:19309/68‑1 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg < 1:3206394/68‑1 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg < 1:3337505/68‑1 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg < 1:383293/68‑1 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg < 1:1343013/68‑1 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg < 1:508823/68‑1 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg < 1:583848/68‑1 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg < 1:625286/68‑1 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg < 1:760297/68‑1 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg < 1:1139814/68‑1 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg < 1:1078814/68‑1 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg < 1:1525590/68‑1 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg < 1:2307967/68‑1 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg < 1:1790532/68‑1 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg < 1:2346580/68‑1 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg < 1:262064/68‑1 (MQ=255)
ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTAGGCGTGTTCCGGGTGCTGGCg < 1:3204369/68‑1 (MQ=255)
aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt < 1:2980039/68‑1 (MQ=255)
aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt < 1:1908063/68‑1 (MQ=255)
aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt < 1:2222449/68‑1 (MQ=255)
aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt < 1:833508/68‑1 (MQ=255)
aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt < 1:802064/68‑1 (MQ=255)
aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt < 1:634954/68‑1 (MQ=255)
aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt < 1:2317539/68‑1 (MQ=255)
aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt < 1:1844442/68‑1 (MQ=255)
aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt < 1:289291/68‑1 (MQ=255)
aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt < 1:2926232/68‑1 (MQ=255)
tCAAAAGCATTCAGCGCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGcc < 1:2854663/69‑1 (MQ=255)
tCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGcc < 1:2642397/69‑1 (MQ=255)
tCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGcc < 1:1328937/69‑1 (MQ=255)
tCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGAGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGcc < 1:3435975/69‑1 (MQ=255)
cAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAAc < 1:336524/60‑1 (MQ=255)
cAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAAc < 1:2531223/60‑1 (MQ=255)
cAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAAc < 1:1522691/60‑1 (MQ=255)
aaaaGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAAc < 1:1271180/59‑1 (MQ=255)
aaaaGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAAc < 1:3255755/59‑1 (MQ=255)
aaaaGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTg < 1:1294149/69‑1 (MQ=255)
aaaaGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTg < 1:3262548/69‑1 (MQ=255)
aaaaGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTg < 1:2306614/69‑1 (MQ=255)
aaaaGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTCTGCCTg < 1:5780/69‑1 (MQ=255)
|
GCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTG > minE/1485478‑1485608
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
