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 |
755,221 |
C→T |
29.5% |
S180S (AGC→AGT) |
lolC → |
outer membrane‑specific lipoprotein transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 755,221 | 0 | C | T | 29.5%
| 82.6
/ 34.1
| 81 | S180S (AGC→AGT) | lolC | outer membrane‑specific lipoprotein transporter subunit |
| Reads supporting (aligned to +/- strand): ref base C (40/17); new base T (9/15); total (49/32) |
| Fisher's exact test for biased strand distribution p-value = 1.18e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCGGTGATCAAATCCGCGTGATGGTACCATCTGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATGC > minE/755154‑755285
|
gcgGTGATCAAATCCGCGTGATGGTACCATCTGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGcc > 1:2208615/1‑69 (MQ=255)
cAAATCCGCGTGATGGTACCATCTGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCt > 1:269629/1‑68 (MQ=255)
cAAATCCGCGTGATGGTACCATCTGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTg > 1:751234/1‑69 (MQ=255)
cAAATCCGCGTGATGGTACCATCTGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTg > 1:160750/1‑69 (MQ=255)
gTGATGGTGCCATCTGCTAGCCAGTTCACGCCGATGGGGCGTATTCCAAGTCAGCGCCTGTTCAAtgtg < 1:983044/69‑1 (MQ=255)
gTGATGGTGCCATCTGCTAGCCAGTTCACGCCGATGGGGCGTATTCCAAGTCAGCGCCTGTTCAAtgtg < 1:2601517/69‑1 (MQ=255)
gTGATGGTGCCATCTGCTAGCCAGTTCACGCCGATGGGGCGTATTCCAAGTCAGCGCCTGTTCAAtgtg < 1:2715728/69‑1 (MQ=255)
gTGATGGTGCCATCTGCTAGCCAGTTCACGCCGATGGGGCGTATTCCAAGTCAGCGCCTGTTCAAtgtg < 1:2802589/69‑1 (MQ=255)
gTGATGGTGCCATCTGCTAGCCAGTTCACGCCGATGGGGCGTATTCCAAGTCAGCGCCTGTTCAAtgtg < 1:1804723/69‑1 (MQ=255)
gTGATGGTGCCATCTGCTAGCCAGTTCACGCCGATGGGGCGTATTCCAAGTCAGCGCCTGTTCAAtgtg < 1:3162485/69‑1 (MQ=255)
gTGATGGTGCCATCTGCTAGCCAGTTCACGCCGATGGGGCGTATTCCAAGTCAGCGCCTGTTCAAtgtg < 1:3308957/69‑1 (MQ=255)
gTGATGGTGCCATCTGCTAGCCAGTTCACGCCGATGGGGCGTATTCCAAGTCAGCGCCTGTTCAAtgtg < 1:3369185/69‑1 (MQ=255)
gTGATGGTGCCATCTGCTAGCCAGTTCACGCCGATGGGGCGTATTCCAAGTCAGCGCCTGTTCAAtgtg < 1:908232/69‑1 (MQ=255)
gTGATGGTGCCATCTGCTAGCCAGTTCACGCCGATGGGGCGTATTCCAAGTCAGCGCCTGTTCAAtgtg < 1:735242/69‑1 (MQ=255)
gTGATGGTGCCATCTGCTAGCCAGTTCACGCCGATGGGGCGTATTCCAAGTCAGCGCCTGTTCAAtgtg < 1:1466372/69‑1 (MQ=255)
gTGATGGTGCCATCTGCTAGCCAGTTCACGCCGATGGGGCGTATTCCAAGTCAGCGCCTGTTCAAtgtg < 1:796424/69‑1 (MQ=255)
gTGATGGTGCCATCTGCTAGCCAGTTCACGCCGATGGGGCGTATTCCAAGTCAGCGCCTGTTCAAtgtg < 1:1252385/69‑1 (MQ=255)
gTGATGGTACCATCTGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAAtgtg < 1:1558394/69‑1 (MQ=255)
gTGATGGTACCATCTGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAAtgtg < 1:3262208/69‑1 (MQ=255)
gTGATGGTACCATCTGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAAtgtg < 1:2223686/69‑1 (MQ=255)
gTGATGGTACCATCTGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAAtgtg < 1:2117403/69‑1 (MQ=255)
tGATGGTGCCATCTGCTAGCCAGTTCACGCCGATGGGGCGTATTCCAAGTCAGCGCCTGTTCAAtgtg < 1:1404449/68‑1 (MQ=255)
tGATGGTACCATCTGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAAtgtg < 1:2121663/68‑1 (MQ=255)
aCCATCTGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTc > 1:3356066/1‑55 (MQ=255)
aCCATCTGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTc > 1:2016786/1‑55 (MQ=255)
aCCATCTGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTc > 1:2701036/1‑55 (MQ=255)
aCCATCTGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTc > 1:1941960/1‑55 (MQ=255)
aCCATCTGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTc > 1:1773697/1‑55 (MQ=255)
aCCATCTGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTc > 1:1763690/1‑55 (MQ=255)
ccATCTGCTAGCCAGTTCACGCCGATGGGGCGTATTCCAAGTCAGCGCCTGTTCAAtgtg < 1:2706755/60‑1 (MQ=255)
tgacagccagTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTcgc > 1:3144132/4‑69 (MQ=255)
tGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTcgc > 1:1141159/1‑69 (MQ=255)
tGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTcgc > 1:2523232/1‑69 (MQ=255)
tGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTcgc > 1:1323174/1‑69 (MQ=255)
tGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTcgc > 1:467026/1‑69 (MQ=255)
tGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTcgc > 1:205725/1‑69 (MQ=255)
tGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTcgc > 1:3289394/1‑69 (MQ=255)
cACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGa > 1:882883/1‑69 (MQ=255)
ccGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTc < 1:219171/69‑1 (MQ=255)
ccGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTc < 1:853121/69‑1 (MQ=255)
ccGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTc < 1:620347/69‑1 (MQ=255)
ccGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTc < 1:378406/69‑1 (MQ=255)
ccGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTc < 1:332892/69‑1 (MQ=255)
ccGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTc < 1:1940987/69‑1 (MQ=255)
cGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTc < 1:3432281/68‑1 (MQ=255)
tGGGGCGTATTCCAAGTCAGCGCCTGTTCAATGTGATTGTCACTTTcg > 1:1681791/1‑48 (MQ=39)
tGGGGCGTATTCCAAGTCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGAt > 1:867301/1‑68 (MQ=255)
tGGGGCGTATTCCAAGTCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATg > 1:2150335/1‑69 (MQ=255)
tGGGGCGTATTCCAAGTCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATg > 1:82575/1‑69 (MQ=255)
tGGGGCGTATTCCAAGTCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATg > 1:1999123/1‑69 (MQ=255)
tGGGGCGTATTCCAAGTCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATg > 1:891081/1‑69 (MQ=255)
tGGGGCGTATTCCAAGTCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATg > 1:551830/1‑69 (MQ=255)
tGGGGCGTATTCCAAGTCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATg > 1:2710272/1‑69 (MQ=255)
tGGGGCGTATTCCAAGTCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATg > 1:3062304/1‑69 (MQ=255)
gggCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGc < 1:1736756/69‑1 (MQ=255)
gggCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGc < 1:925900/69‑1 (MQ=255)
gggCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGc < 1:1919688/69‑1 (MQ=255)
gCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTc < 1:2655711/61‑1 (MQ=255)
gCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCt < 1:2563520/68‑1 (MQ=255)
ttCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGaaa > 1:879995/1‑69 (MQ=255)
ttCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGaa > 1:268023/1‑68 (MQ=255)
ccAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGAt > 1:2200865/1‑57 (MQ=255)
ccAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAAt > 1:171061/1‑68 (MQ=255)
ccAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATg > 1:1496152/1‑69 (MQ=255)
ccAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATg > 1:1232284/1‑69 (MQ=255)
ccAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATg > 1:404335/1‑69 (MQ=255)
ccAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATg > 1:400767/1‑69 (MQ=255)
ccAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATg > 1:382361/1‑69 (MQ=255)
ccAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATg > 1:1501233/1‑69 (MQ=255)
ccAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATg > 1:2843186/1‑69 (MQ=255)
cAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGt > 1:2171986/1‑52 (MQ=255)
cAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATg > 1:1087486/1‑68 (MQ=255)
cAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATGc > 1:684472/1‑69 (MQ=255)
cAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATGc > 1:722506/1‑69 (MQ=255)
cAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATGc > 1:1460837/1‑69 (MQ=255)
cAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATGc > 1:2584749/1‑69 (MQ=255)
cAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATGc > 1:3286176/1‑69 (MQ=255)
cAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATGc > 1:3252037/1‑69 (MQ=255)
cAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATGc > 1:1782162/1‑69 (MQ=255)
cAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATGc > 1:950298/1‑69 (MQ=255)
cAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATGc > 1:976064/1‑69 (MQ=255)
cAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATGc > 1:2795294/1‑69 (MQ=255)
|
GCGGTGATCAAATCCGCGTGATGGTACCATCTGCCAGCCAGTTCACGCCGATGGGGCGTATTCCAAGCCAGCGCCTGTTCAATGTGATTGGCACTTTCGCCGCCAACAGTGAAGTCGATGGCTATGAAATGC > minE/755154‑755285
|
| 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
