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 |
627,664 |
T→C |
26.8% |
R38R (CGT→CGC) |
kdsB → |
3‑deoxy‑manno‑octulosonate cytidylyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 627,664 | 0 | T | C | 26.8%
| 55.0
/ 18.2
| 52 | R38R (CGT→CGC) | kdsB | 3‑deoxy‑manno‑octulosonate cytidylyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (9/29); new base C (5/9); total (14/38) |
| Fisher's exact test for biased strand distribution p-value = 4.85e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.44e-01 |
TGCCCGGTAAACCATTGGTTGATATTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATCATGAGGATGTTGCCCGCGCCGTTG > minE/627597‑627725
|
tGCCCGGTAAACCATTGGTTGATATTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTg < 1:747818/69‑1 (MQ=255)
tGCCCGGTAAACCATTGGTTGATATTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTg < 1:356347/69‑1 (MQ=255)
tGCCCGGTAAACCATTGGTTGATATTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTg < 1:3210488/69‑1 (MQ=255)
tGCCCGGTAAACCATTGGTTGATATTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTg < 1:2982991/69‑1 (MQ=255)
tGCCCGGTAAACCATTGGTTGATATTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTg < 1:3106776/69‑1 (MQ=255)
tGCCCGGTAAACCATTGGTTGATATTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTg < 1:2035811/69‑1 (MQ=255)
gTAAACCATTGGTTGATATTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAg > 1:456905/1‑69 (MQ=255)
ttGGTTGATATTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAg > 1:2818026/1‑69 (MQ=255)
ttGGTTGATATTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAg > 1:3171877/1‑69 (MQ=255)
ttGGTTGATATTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAg > 1:1461174/1‑69 (MQ=255)
ttGGTTGATATTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAg > 1:3046530/1‑69 (MQ=255)
atTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGcatcat < 1:997457/68‑1 (MQ=255)
atTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGcatcat < 1:2533928/68‑1 (MQ=255)
atTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGcatcat < 1:2339208/68‑1 (MQ=255)
atTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGcatcat < 1:2269023/68‑1 (MQ=255)
atTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGcatcat < 1:1401908/68‑1 (MQ=255)
atTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGcatcat < 1:1330004/68‑1 (MQ=255)
atTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGcatcat < 1:594028/68‑1 (MQ=255)
atTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGcatcat < 1:920462/68‑1 (MQ=255)
aaCGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGCATCATCGt > 1:2357370/1‑68 (MQ=255)
aaCGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGCATCATCGt > 1:2357502/1‑68 (MQ=255)
aaCGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGCATCATCGt > 1:2515227/1‑68 (MQ=255)
aaCGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGAGTGAATCAGGTGCCGAGCGCATCATCGt > 1:2696114/1‑68 (MQ=255)
ccATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATc < 1:2687320/69‑1 (MQ=255)
ccATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATc < 1:2804295/69‑1 (MQ=255)
ccATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATc < 1:2972690/69‑1 (MQ=255)
ccATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATc < 1:372989/69‑1 (MQ=255)
ccATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGGGCCGAGCGCATCATCGTGGCAACCGATc < 1:3376166/69‑1 (MQ=255)
aTTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATCATGAg < 1:2506321/69‑1 (MQ=255)
aTTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATCATGAg < 1:1059540/69‑1 (MQ=255)
aTTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATCATGAg < 1:695428/69‑1 (MQ=255)
aTTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATCATGAg < 1:603983/69‑1 (MQ=255)
aTTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATCATGAg < 1:1126311/69‑1 (MQ=255)
aTTGTTCATGTTCTTGAACGCGCGCGCGAATCAGGTGCCGAGCGCATCATCGTGGc < 1:10660/56‑1 (MQ=255)
aTTGTTCATGTTCTTGAACGCGCGCGCGAATCAGGTGCCGAGCGCATCATCGTGGc < 1:1070361/56‑1 (MQ=255)
aTTGTTCATGTTCTTGAACGCGCGCGCGAATCAGGTGCCGAGCGCATCATCGTGGc < 1:681084/56‑1 (MQ=255)
aTTGTTCATGTTCTTGAACGCGCGCGCGAATCAGGTGCCGAGCGCATCATCGTGGc < 1:665520/56‑1 (MQ=255)
aTTGTTCATGTTCTTGAACGCGCGCGCGAATCAGGTGCCGAGCGCATCATCGTGGc < 1:1427589/56‑1 (MQ=255)
aTTGTTCATGTTCTTGAACGCGCGCGCGAATCAGGTGCCGAGCGCATCATCGTGGc < 1:1766570/56‑1 (MQ=255)
aTTGTTCATGTTCTTGAACGCGCGCGCGAATCAGGTGCCGAGCGCATCATCGTGGc < 1:2202435/56‑1 (MQ=255)
aTTGTTCATGTTCTCGAACGCGCGCGCGAATCAGGTGCCGAGCGCATCATCGTGGc < 1:2849809/56‑1 (MQ=255)
ttGTTCATGTTCTTGAACGCGCGCGCGAATCAGGTGCCGAGCGCATCATCGTTGc < 1:3226214/55‑1 (MQ=255)
cTTGAACGCGCGCGCGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATCATGAGGATGTTGCCcgc > 1:1329512/1‑69 (MQ=255)
cTTGAACGCGCGCGCGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATCATGAGGATGTTGCCcgc > 1:1176591/1‑69 (MQ=255)
cTTGAACGCGCGCGCGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATCATGAGGATGTTGCCcgc > 1:2933023/1‑69 (MQ=255)
cTTGAACGCGCGCGCGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATCATGAGGATGTTGCCcgc > 1:729013/1‑69 (MQ=255)
cTTGAACGCGCGCGCGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATCATGAGGATGTTGCCcg > 1:1758334/1‑68 (MQ=255)
cgcgcgcgTGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATCATGAGGATGTTGCCCGCGCCGtt < 1:3396382/69‑1 (MQ=255)
gcgcgcgcGAATCAGGTGCCGAGCGCATCATCGTGGc < 1:112343/37‑1 (MQ=255)
gcgcgcgTGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATCATGAGGATGTTGCCCGCGCCGTTg < 1:1366150/69‑1 (MQ=255)
gcgcgcgTGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATCATGAGGATGTTGCCCGCGCCGTTg < 1:374865/69‑1 (MQ=255)
gcgcgcgTGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATCATGAGGATGTTGCCCGCGCCGTTg < 1:2088929/69‑1 (MQ=255)
gcgcgcgTGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATCATGAGGATGTTGCCCGCGCCGTTg < 1:248013/69‑1 (MQ=255)
|
TGCCCGGTAAACCATTGGTTGATATTAACGGCAAACCCATGATTGTTCATGTTCTTGAACGCGCGCGTGAATCAGGTGCCGAGCGCATCATCGTGGCAACCGATCATGAGGATGTTGCCCGCGCCGTTG > minE/627597‑627725
|
| 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
