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 |
826,674 |
C→T |
53.7% |
S357S (AGC→AGT) |
ychP → |
predicted invasin |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 826,674 | 0 | C | T | 53.7%
| ‑0.4
/ 32.4
| 41 | S357S (AGC→AGT) | ychP | predicted invasin |
| Reads supporting (aligned to +/- strand): ref base C (9/10); new base T (2/20); total (11/30) |
| Fisher's exact test for biased strand distribution p-value = 1.15e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.45e-01 |
GATTTGGCAGGGCGATACGCAGATATTAAGTTTGACGCCGGGCGCACAAGCCAACAGCGCGGAGGGCTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCG > minE/826617‑826739
|
gATTTGGCAGGGCGATACGCAGATATTAAGTTTGACGCCGGGCGCACAAGCCAACAGCGCGGAGGGCTg > 1:3427943/1‑69 (MQ=255)
tGGCAGGGCGATACGCAGATATTAAGTTTGACGCCGGGCGCACAAGCCAACAGCGCGGAGGGCTGGACg > 1:2888866/1‑69 (MQ=255)
tGGCAGGGCGATACGCAGATATTAAGTTTGACGCCGGGCGCACAAGCCAACAGCGCGGAGGGCTGGACg > 1:2723362/1‑69 (MQ=255)
tGGCAGGGCGATACGCAGATATTAAGTTTGACGCCGGGCGCACAAGCCAACAGCGCGGAGGGCTGGACg > 1:2632073/1‑69 (MQ=255)
tGGCAGGGCGATACGCAGATATTAAGTTTGACGCCGGGCGCACAAGCCAACAGCGCGGAGGGCTGGACg > 1:2529747/1‑69 (MQ=255)
tGGCAGGGCGATACGCAGATATTAAGTTTGACGCCGGGCGCACAAGCCAACAGCGCGGAGGGCTGGACg > 1:498993/1‑69 (MQ=255)
tGGCAGGGCGATACGCAGATATTAAGTTTGACGCCGGGCGCACAAGCCAACAGCGCGGAGGGCTGGACg > 1:3295120/1‑69 (MQ=255)
tGGCAGGGCGATACGCAGATATTAAGTTTGACGCCGGGCGCACAAGCCAACAGCGCGGAGGGCTGGACg > 1:2179344/1‑69 (MQ=255)
aTACGCAGATATTAAGTTTGACGCCGGGCGCACAAGCCAACAGCGCGGAGGGCTGGACGCTGATCATGc < 1:2908444/69‑1 (MQ=255)
aTACGCAGATATTAAGTTTGACGCCGGGCGCACAAGCCAACAGCGCGGAGGGCTGGACGCTGATCATGc < 1:1599626/69‑1 (MQ=255)
tACGCAGATATTAAGTTTGACGCCGGGCGCACAAGCCAACAGCGCGGAGGGCTGGACGCTGATCATGc < 1:2516029/68‑1 (MQ=255)
aCGCAGATATTAAGTTTGACGCCGGGCGCACAAGCCAACAGCGCGGAGGGCTGGACGCTGATCATGCCt < 1:2421512/69‑1 (MQ=255)
atTAAGTTTGACGCCGGGCGCACAAGCCAACAGCGCGGAGGGCTGGACGCTGATCATGCCTGACTgg > 1:1511433/1‑67 (MQ=255)
tGACGCCGGGCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACgg > 1:382767/1‑67 (MQ=255)
tGACGCCGGGCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACgg > 1:505581/1‑67 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:99022/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:2976427/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:481414/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:689717/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:736510/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:739380/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:805196/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:888520/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:1173152/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:1187586/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:1337415/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:2080192/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:193133/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:181466/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:2491143/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:15820/69‑1 (MQ=255)
gggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:1462277/69‑1 (MQ=255)
ggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:501578/68‑1 (MQ=255)
ggCGCACAAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:1443295/68‑1 (MQ=255)
caAGCCAACAGTGAGGAGGGCTGGACGCTGATCATGCCTGACTGGCAAAACGGGGAAGgcgc < 1:400362/62‑1 (MQ=255)
cAGCGCGGAGGGCTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCg < 1:168860/69‑1 (MQ=255)
cAGCGCGGAGGGCTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCg < 1:1022221/69‑1 (MQ=255)
cAGCGCGGAGGGCTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCg < 1:3368590/69‑1 (MQ=255)
cAGCGCGGAGGGCTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCg < 1:2245266/69‑1 (MQ=255)
cAGCGCGGAGGGCTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCg < 1:3091494/69‑1 (MQ=255)
cAGCGCGGAGGGCTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCg < 1:2396266/69‑1 (MQ=255)
|
GATTTGGCAGGGCGATACGCAGATATTAAGTTTGACGCCGGGCGCACAAGCCAACAGCGCGGAGGGCTGGACGCTGATCATGCCTGACTGGCAGAACGGGGAAGGGGCAAGCAATCACTGGCG > minE/826617‑826739
|
| 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
