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 |
1,343,146 |
C→T |
42.5% |
E371E (GAG→GAA) |
wzc ← |
protein‑tyrosine kinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,343,146 | 0 | C | T | 42.5%
| 12.7
/ 32.6
| 47 | E371E (GAG→GAA) | wzc | protein‑tyrosine kinase |
| Reads supporting (aligned to +/- strand): ref base C (16/11); new base T (12/8); total (28/19) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTGCATATAGACCTGCTGACCAGACTCGACATCGCGGGTCAGACGGACAATCTCCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCGTTAAGTTTGGCTTTTTCGTCTTCCAGCGCCTG > minE/1343095‑1343214
|
ttGCATATAGACCTGCTGACCAGACTCGACATCGCGGGTCAGACGGACAATCTCCTGCTGGGTTTTCgg < 1:1994932/69‑1 (MQ=255)
ttGCATATAGACCTGCTGACCAGACTCGACATCGCGGGTCAGACGGACAATCTCCTGCTGGGTTTTCgg < 1:2710014/69‑1 (MQ=255)
ttGCATATAGACCTGCTGACCAGACTCGACATCGCGGGTCAGACGGACAATCTCCTGCTGGGTTTTCgg < 1:2806911/69‑1 (MQ=255)
tGCATATAGACCTGCTGACCAGACTCGACATCGCGGGTCAGACGGACAATCTCCTGCTGGGTTTTCGGc > 1:1723066/1‑69 (MQ=255)
gCATATAGACCTGCTGACCAGACTCGACATCGCGGGTCAGACGGACAATCTCCTGCTGGGTTTTCGGc > 1:1308740/1‑68 (MQ=255)
gCATATAGACCTGCTGACCAGACTCGACATCGCGGGTCAGACGGACAATCTCCTGCTGGGTTTTCGGCa > 1:2446878/1‑69 (MQ=255)
gCATATAGACCTGCTGACCAGACTCGACATCGCGGGTCAGACGGACAATCTCCTGCTGGGTTTTCGGCa > 1:738858/1‑69 (MQ=255)
gCATATAGACCTGCTGACCAGACTCGACATCGCGGGTCAGACGGACAATCTCCTGCTGGGTTTTCGGCa > 1:3099923/1‑69 (MQ=255)
taGACCTGCTGGCCAGACTCGACATCGCGGGTCAGACGGACAATTTCCTGCTGGGTTTTCGGCATCGcc > 1:2084798/1‑69 (MQ=255)
taGACCTGCTGCCCAGACTCGACATCGCGGGTCAGACGGACAATTTCCTGCTGGGTTTTCGGCATCGcc > 1:3134331/1‑69 (MQ=255)
taGACCTGCTGCCCAGACTCGACATCGCGGGTCAGACGGACAATTTCCTGCTGGGTTTTCGGCATCGcc > 1:2584214/1‑69 (MQ=255)
taGACCTGCTGCCCAGACTCGACATCGCGGGTCAGACGGACAATTTCCTGCTGGGTTTTCGGCATCGcc > 1:2590420/1‑69 (MQ=255)
taGACCTGCTGCCCAGACTCGACATCGCGGGTCAGACGGACAATTTCCTGCTGGGTTTTCGGCATCGcc > 1:2657371/1‑69 (MQ=255)
taGACCTGCTGCCCAGACTCGACATCGCGGGTCAGACGGACAATTTCCTGCTGGGTTTTCGGCATCGcc > 1:1848090/1‑69 (MQ=255)
taGACCTGCTGCCCAGACTCGACATCGCGGGTCAGACGGACAATTTCCTGCTGGGTTTTCGGCATCGcc > 1:324501/1‑69 (MQ=255)
taGACCTGCTGCCCAGACTCGACATCGCGGGTCAGACGGACAATTTCCTGCTGGGTTTTCGGCATCGcc > 1:343506/1‑69 (MQ=255)
taGACCTGCTGCCCAGACTCGACATCGCGGGTCAGACGGACAATTTCCTGCTGGGTTTTCGGCATCGcc > 1:364206/1‑69 (MQ=255)
taGACCTGCTGCCCAGACTCGACATCGCGGGTCAGACGGACAATTTCCTGCTGGGTTTTCGGCATCGcc > 1:515056/1‑69 (MQ=255)
taGACCTGCTGCCCAGACTCGACATCGCGGGTCAGACGGACAATTTCCTGCTGGGTTTTCGGCATCGcc > 1:1112010/1‑69 (MQ=255)
taGACCTGCTGCCCAGACTCGACATCGCGGGTCAGACGGACAATTTCCTGCTGGGTTTTCGGCATCGcc > 1:1004572/1‑69 (MQ=255)
ctgACCAGACTCGACATCGCGGGTCAGACGGACAATCTCCTGCTGGGTTTTCGGCATCGCCGTTAcgcg > 1:918581/1‑69 (MQ=255)
ctgACCAGACTCGACATCGCGGGTCAGACGGACAATCTCCTGCTGGGTTTTCGGCATCGCCGTTAcgcg > 1:2954729/1‑69 (MQ=255)
ctgACCAGACTCGACATCGCGGGTCAGACGGACAATCTCCTGCTGGGTTTTCGGCATCGCCGTTAcgcg > 1:3308067/1‑69 (MQ=255)
ctgACCAGACTCGACATCGCGGGTCAGACGGACAATCTCCTGCTGGGTTTTCGGCATCGCCGTTAcgcg > 1:357955/1‑69 (MQ=255)
ctgACCAGACTCGACATCGCGGGTCAGACGGACAATCTCCTGCTGGGTTTTCGGCATCGCCGTTAcgcg > 1:1238687/1‑69 (MQ=255)
ctgACCAGACTCGACATCGCGGGTCAGACGGACAATCTCCTGCTGGGTTTTCGGCATCGCCGTTAcgcg > 1:1804029/1‑69 (MQ=255)
ctgACCAGACTCGACATCGCGGGTCAGACGGACAATCTCCTGCTGGGTTTTCGGCATCGCCGTTAcga > 1:1497420/1‑67 (MQ=255)
gACCAGACTCGACATCGCGGGTCAGACGGACAATCTCCTGCTGGGTTTTCGGCATCGCCGTTAcgcg < 1:1092091/67‑1 (MQ=255)
aCTCGACATCGCGGGTCAGACGGACAATCTCCTGCTGGGTTTTCGGCATCGCCGTTAcgcg < 1:426043/61‑1 (MQ=255)
tctaCATCGCGGGTCAGACGGACAATTTCCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCATTAAGt < 1:1496815/66‑1 (MQ=255)
tCGACATCGCGGGTCAGACGGACAATTTCCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCATTAAGt < 1:2330304/69‑1 (MQ=255)
tCGACATCGCGGGTCAGACGGACAATTTCCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCATTAAGt < 1:1391586/69‑1 (MQ=255)
tCGACATCGCGGGTCAGACGGACAATTTCCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCATTAAGt < 1:3343776/69‑1 (MQ=255)
tCGACATCGCGGGTCAGACGGACAATTTCCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCATTAAGt < 1:3243366/69‑1 (MQ=255)
tCGACATCGCGGGTCAGACGGACAATTTCCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCATTAAGt < 1:318559/69‑1 (MQ=255)
tCGACATCGCGGGTCAGACGGACAATTTCCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCATTAAGt < 1:1946518/69‑1 (MQ=255)
gcgGGTCAGACGGACAATCTCCTGCTTGGTTTTCGGCATCGCCGTTACGCGACCGTTAAGTTTGGCttt > 1:2687661/1‑69 (MQ=255)
gcgGGTCAGACGGACAATCTCCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCGTTAAGTTTGGCttt > 1:1728398/1‑69 (MQ=255)
aGACGGACAATTTCCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCATTAAGt < 1:1861056/54‑1 (MQ=255)
cGGACAATCTCCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCGTTAAGTTTGGCTTTTTCGTCTTcc < 1:1994130/69‑1 (MQ=255)
cGGACAATCTCCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCGTTAAGTTTGGCTTTTTCGTCTTcc < 1:1474175/69‑1 (MQ=255)
cGGACAATCTCCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCGTTAAGTTTGGCTTTTTCGTCTTcc < 1:2026964/69‑1 (MQ=255)
cGGACAATCTCCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCGTTAAGTTTGGCTTTTTCGTCTTcc < 1:2151202/69‑1 (MQ=255)
ggACAATCTCCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCGTTAAGTTTGGCTTTTTCGTCTTcc < 1:2372111/68‑1 (MQ=255)
gACAATCTCCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCGTTAAGTTTGGCTTTTTCGTCTTCCa > 1:2597712/1‑68 (MQ=255)
gACAATCTCCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCGTTAAGTTTGGCTTTTTCGTCTTCCAg > 1:3163152/1‑69 (MQ=255)
aCAATCTCCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCGTTAAGTTTGGCTTTTTCGTCTTCCAgc < 1:2910318/69‑1 (MQ=255)
ctcCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCGTTAAGTTTGGCTTTTTCGTCTTCCAGCGCCTg > 1:317493/1‑69 (MQ=255)
ctcCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCGTTAAGTTTGGCTTTTTCGTCTTCCAGCGCCTg > 1:1705222/1‑69 (MQ=255)
ctcCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCGTTAAGTTTGGCTTTTTCGTCTTCCAGCGCCTg > 1:3307350/1‑69 (MQ=255)
ctcCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCGTTAAGTTTGGCTTTTTCGTCTTCCAGCGCCTg > 1:1338962/1‑69 (MQ=255)
|
TTGCATATAGACCTGCTGACCAGACTCGACATCGCGGGTCAGACGGACAATCTCCTGCTGGGTTTTCGGCATCGCCGTTACGCGACCGTTAAGTTTGGCTTTTTCGTCTTCCAGCGCCTG > minE/1343095‑1343214
|
| 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
