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 |
1,324,798 |
A→G |
41.3% |
G312G (GGT→GGC) |
wcaL ← |
predicted glycosyl transferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,324,798 | 0 | A | G | 41.3%
| 22.0
/ 48.1
| 69 | G312G (GGT→GGC) | wcaL | predicted glycosyl transferase |
| Reads supporting (aligned to +/- strand): ref base A (22/18); new base G (21/7); total (43/26) |
| Fisher's exact test for biased strand distribution p-value = 1.27e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01 |
AGAAACCACCGGAATACCGACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGCGTCGTCGAGCATCGCTTTCACTT > minE/1324735‑1324862
|
aGAAACAACCGGAATGCCAACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCGCCATc < 1:1122592/69‑1 (MQ=255)
aGAAACAACCGGAATGCCAACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCGCCATc < 1:1055690/69‑1 (MQ=255)
aGAAACAACCGGAATGCCAACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCGCCATc < 1:2687776/69‑1 (MQ=255)
aGAAACAACCGGAATGCCAACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCGCCATc < 1:1337886/69‑1 (MQ=255)
aGAAACAACCGGAATGCCAACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCGCCATc < 1:3129397/69‑1 (MQ=255)
aaCCACCGGAATACCGACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCg < 1:1337752/68‑1 (MQ=255)
aaCCACCGGAATACCGACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCg < 1:311820/68‑1 (MQ=255)
aTACCGACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAAcc > 1:1707095/1‑69 (MQ=255)
aTACCGACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAAcc > 1:2048600/1‑69 (MQ=255)
aTACCGACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAAcc > 1:207221/1‑69 (MQ=255)
aTACCGACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAAcc > 1:2719324/1‑69 (MQ=255)
aTACCGACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAAcc < 1:136674/69‑1 (MQ=255)
aTACCGACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAAcc < 1:3314398/69‑1 (MQ=255)
aTACCGACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAAcc > 1:627193/1‑69 (MQ=255)
aTACCGACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAAcc > 1:736713/1‑69 (MQ=255)
aTACCGACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAAcc < 1:1263523/69‑1 (MQ=255)
aTACCGACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAAcc > 1:791934/1‑69 (MQ=255)
aTACCGACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAAc > 1:63301/1‑68 (MQ=255)
ccgaccgCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCTCCATc < 1:2235744/53‑1 (MQ=255)
ccgaccgCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATc < 1:938498/53‑1 (MQ=255)
ccgaccgCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATc < 1:1684574/53‑1 (MQ=255)
ccgaccgCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATc < 1:514166/53‑1 (MQ=255)
ccgaccgCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATc < 1:56769/53‑1 (MQ=255)
ccgaccgCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATc < 1:201984/53‑1 (MQ=255)
ccgaccgCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATc < 1:1582664/53‑1 (MQ=255)
ccgaccgCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATc < 1:2056913/53‑1 (MQ=255)
ccgaccgCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAACCGAt > 1:3029512/1‑69 (MQ=255)
ccgaccgCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAACCGAt > 1:242742/1‑69 (MQ=255)
ccgaccgCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAACCGAt > 1:2336996/1‑69 (MQ=255)
ccgaccgCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAACCGAt > 1:1271837/1‑69 (MQ=255)
ccgaccgCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAACCGAt > 1:1847/1‑69 (MQ=255)
ccgaccgCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAACAGAt > 1:1775085/1‑69 (MQ=255)
gCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAACCg > 1:2078925/1‑55 (MQ=255)
gCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAACCGATGGCAACAGGaa > 1:1948225/1‑68 (MQ=255)
gCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAACCGATGGCAACAGGaa > 1:1397731/1‑68 (MQ=255)
gCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAACCGATGGCAACAGGaa > 1:1278198/1‑68 (MQ=255)
cTTCCATTAGCGCCACCGGAATACCTTCCATATCGCCATc < 1:2242520/40‑1 (MQ=255)
cTTACATTAGCGCCAACTGAATACCTTCCATATCGCCATc < 1:1200532/40‑1 (MQ=25)
tCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAAcc < 1:225243/51‑1 (MQ=255)
aGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCcgcg > 1:1810243/1‑69 (MQ=255)
aGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCcgcg > 1:2062361/1‑69 (MQ=255)
cACCGGAATACCTTCCATATGGCCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:2270203/1‑66 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCCGCACCTGTAAc > 1:2178633/1‑39 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:936966/1‑66 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:1263927/1‑66 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:484625/1‑66 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:367619/1‑66 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:3307521/1‑66 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:3174123/1‑66 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:3136052/1‑66 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:2675910/1‑66 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:3002986/1‑66 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:2802173/1‑66 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:1511083/1‑66 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:2714298/1‑66 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:2021210/1‑66 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:1677677/1‑66 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:2276022/1‑66 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:2367031/1‑66 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:1408214/1‑66 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:2455702/1‑66 (MQ=255)
cACCGGAATACCTTCCATATCGCCATCAGCACCTGTAACCGATGGCAACAGGAAGACATCCGcgtca > 1:512763/1‑66 (MQ=255)
ccTTCCATATCACCATCCGCACCTGAAACCGATGGCAACAGGAAGACATCcg > 1:1683747/1‑52 (MQ=255)
ttCCATATCACCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGCGTCGTCGAGCATCGCttt < 1:2118346/69‑1 (MQ=255)
ttCCATATCACCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGCGTCGTCGAGCATCGCttt < 1:351068/69‑1 (MQ=255)
ttCCATATCACCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGCGTCGTCGAGCATCGCttt < 1:13381/69‑1 (MQ=255)
ttCCATATCACCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGCGTCGTCGAGCATCGCttt < 1:1721952/69‑1 (MQ=255)
ccATATCACCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGCGTCGTCGAGCATCGCTTTCa > 1:1548079/1‑69 (MQ=255)
tatCACCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGCGTCGTCGAGCATCGCTTTCACtt < 1:2609683/69‑1 (MQ=255)
|
AGAAACCACCGGAATACCGACCGCCATCGCTTCCATTAGCGCCACCGGAATACCTTCCATATCACCATCCGCACCTGTAACCGATGGCAACAGGAAGACATCCGCGTCGTCGAGCATCGCTTTCACTT > minE/1324735‑1324862
|
| 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
