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 |
|
A6 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,327,163 |
T→C |
30.9% |
intergenic (‑153/+123) |
wcaK ← / ← wzxC |
predicted pyruvyl transferase/colanic acid exporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,327,163 | 0 | T | C | 30.9%
| 71.8
/ 28.4
| 42 | intergenic (‑153/+123) | wcaK/wzxC | predicted pyruvyl transferase/colanic acid exporter |
| Reads supporting (aligned to +/- strand): ref base T (11/18); new base C (3/10); total (14/28) |
| Fisher's exact test for biased strand distribution p-value = 4.85e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01 |
TCTTATCAGGCCTACAAGACCCGAGCACAGAACCGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACAGGTCCCGAGCACAGAACCGTAG > minE/1327093‑1327226
|
tCTTATCAGCCCTACAAGACCCGAGCACAGAACCGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAtt < 1:1924439/71‑1 (MQ=255)
ttATCAGGCCTACAAGACCCGAGCACAGAACCGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAtt > 1:2375478/1‑69 (MQ=255)
tCAGGCCTACAAGACCCGAGCACAGAACCGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCATTCAGTg > 1:4129314/1‑71 (MQ=255)
ccTACAAGACCCGAGCACAGAACCGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCATTCAGTGCCTGa < 1:1270555/71‑1 (MQ=255)
cTACAAGACCCGAGCACAGAACCGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCATTCAGTGCCTGAt > 1:2301945/1‑71 (MQ=255)
tACAAGACCCGAGCACAGAACCGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCATTCa > 1:2859225/1‑61 (MQ=255)
aaGACCCGAGCACAGAACCGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCATTCAGTGCCTGATGCGa < 1:23414/71‑1 (MQ=255)
caaaaCCGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCATTCAGTGCCTGATGCGACGCTGACGCGt > 1:1589576/4‑70 (MQ=255)
caGAACCGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAtt < 1:4478341/44‑1 (MQ=255)
aGAACCGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAtt < 1:3749507/43‑1 (MQ=255)
aGAACCGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCATTc < 1:2551577/44‑1 (MQ=255)
gAACCGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCATTc < 1:1346503/43‑1 (MQ=255)
gAACCGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCtt < 1:3948198/71‑1 (MQ=255)
accccGTAGGACGGATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCtt < 1:347533/68‑1 (MQ=11)
accccGTAGGACGGATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCt > 1:895719/4‑70 (MQ=11)
cccGTAGGACGTATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTAt < 1:2099847/70‑1 (MQ=11)
cccGTAGGACGGATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTa < 1:2000872/69‑1 (MQ=11)
cccGTAGGACGGATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTAt < 1:2093025/70‑1 (MQ=11)
aCCGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTAt < 1:4782157/71‑1 (MQ=255)
aCCGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTAt < 1:3576398/71‑1 (MQ=255)
ccGTAGGACGGATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTATc < 1:1226928/71‑1 (MQ=11)
ccGTAGGACGGATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTATc < 1:1220100/71‑1 (MQ=11)
cGTAGTACGGATAAGGCGTTCACGCCGCATCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTATc < 1:1832529/70‑1 (MQ=255)
cGTAGGACGGATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTATCa > 1:3286212/1‑71 (MQ=11)
cGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTATCa < 1:5316478/71‑1 (MQ=255)
cGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTATCa < 1:2638605/71‑1 (MQ=255)
gTAGGACGGATAAGGCGTTCACGCCGCATCCGGCATTCAGTGc > 1:1305785/1‑43 (MQ=38)
ccaGGACGGATAAGGCTTTCACGCCTTATCCGACAACAACTGCCTGATGCGACGCTGACGCGTCTTATCAg > 1:5340866/3‑71 (MQ=9)
tAGGACGGATAAGGCGTTCACGCCGCATCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTATCAgg > 1:4931444/1‑71 (MQ=255)
tAGGACGGATAAGGCGTTCACGCCGCATCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTATCAg < 1:3563313/70‑1 (MQ=255)
caGGACGGATAAGGCTTTCACGCCTTATCCGACAACAACTGCCTGATGCGACGCt < 1:4084969/54‑1 (MQ=2)
caGGACGGATAAGGCTTTCACGCCTTATCCGACAACAACTGCCTGATGCGACGCTGACGCGTCTTATCAg < 1:950276/69‑1 (MQ=14)
caGGACGGATAAGGCTTTCACGCCTTATCCGACAACAACTGCCTGATGCGACGCTGACGCGTCTTATCAg < 1:1941816/69‑1 (MQ=14)
ggACGGATAAGGCGTTCACGCCGCATCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTATCAGGc < 1:3405046/70‑1 (MQ=255)
aCGGATAAGGCTTTCACGCCTTATCCGACAACAACTGCCTGATGCGACGCTGAcgc < 1:5170376/56‑1 (MQ=9)
aaGGCGTTCACGCCGCATCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACAGGTc > 1:3858079/1‑71 (MQ=255)
aaGGCGTTCACGCCGCATCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACAGGTc > 1:3192198/1‑71 (MQ=255)
ttCACGCCGCATCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTATCa < 1:5477899/53‑1 (MQ=255)
cACGCCGCATCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTATCAg > 1:3742831/1‑52 (MQ=255)
cgcATCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACAGGTccc < 1:2828115/60‑1 (MQ=255)
cgcATCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACAGGTCCCGAGCACAGAAc < 1:3956110/71‑1 (MQ=255)
cATCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACAGGTCCCGAGCACAGAACCg < 1:4400215/71‑1 (MQ=255)
tCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTATc < 1:4169605/41‑1 (MQ=255)
tCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTATc < 1:478267/41‑1 (MQ=255)
cGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACAGGTCCCGAGCACAGaa > 1:1200941/1‑64 (MQ=255)
cGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACAGGTCCCGAGCACAGAACCGTAg > 1:2889671/1‑70 (MQ=255)
ttCAGTGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAGGTCCCGAGCACAGAACCGTAg < 1:1815605/65‑1 (MQ=255)
ttCAGTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACAGGTCCCGAGca < 1:1959955/54‑1 (MQ=255)
|
TCTTATCAGGCCTACAAGACCCGAGCACAGAACCGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCATTCAGTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACAGGTCCCGAGCACAGAACCGTAG > minE/1327093‑1327226
|
| 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
