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 |
|
A12 F28 I1 R1
|
227 |
52.0 |
1764248 |
99.3% |
1751898 |
138.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,304,813 |
(C)7→9 |
coding (1005/1245 nt) |
mtr ← |
tryptophan:H(+) symporter Mtr |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,304,806 | 1 | . | C | 96.0%
| 78.2
/ ‑5.5
| 25 | L338V (CTG→GTG) | mtr | tryptophan:H(+) symporter Mtr |
| Reads supporting (aligned to +/- strand): ref base . (0/0); major base C (14/10); minor base T (0/1); total (14/11) |
| Fisher's exact test for biased strand distribution p-value = 4.40e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | NC_000913 | 3,304,806 | 2 | . | C | 100.0%
| 84.8
/ NA
| 25 | L338V (CTG→GTG) | mtr | tryptophan:H(+) symporter Mtr |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (14/11); total (14/11) |
CCCAGACGCGGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑‑‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAACTCGC > NC_000913/3304671‑3304935
||
cccAGACGCGGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑‑‑cccc > 1:837411/1‑140 (MQ=255)
cAGACGCGGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑‑‑cccccc > 1:273916/1‑140 (MQ=255)
gCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGc < 1:611182/140‑1 (MQ=255)
cTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCa < 2:146462/140‑1 (MQ=255)
tACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATg < 2:837411/140‑1 (MQ=255)
cGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAg < 1:523122/140‑1 (MQ=255)
ccGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAg < 1:656782/127‑1 (MQ=255)
ccGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAg > 2:656782/1‑127 (MQ=255)
ccGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCg > 2:875693/1‑140 (MQ=255)
ccGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCg > 1:228991/1‑140 (MQ=255)
ccGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCg > 2:833415/1‑140 (MQ=255)
ggAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAg < 1:299730/140‑1 (MQ=255)
cAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAAc > 2:632124/1‑140 (MQ=255)
cGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAg < 1:875693/140‑1 (MQ=255)
cTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGAt > 1:440886/1‑131 (MQ=255)
cTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGAt < 2:440886/131‑1 (MQ=255)
cTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGGCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGAt > 2:26126/1‑140 (MQ=255)
aaCCAACATAACCAAAGGCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGt < 2:556227/140‑1 (MQ=255)
cAATGGCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCa > 2:807367/1‑140 (MQ=255)
aaTGGCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAg > 1:8493/1‑140 (MQ=255)
ggCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGt > 2:309869/1‑124 (MQ=255)
ggCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGt < 1:309869/124‑1 (MQ=255)
ggCGTACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGt > 2:738116/1‑140 (MQ=255)
tACAGGAATCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACg > 2:477118/1‑140 (MQ=255)
aGGAATCCGTTCGGGAACAACAGTCCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGcc < 2:875122/140‑1 (MQ=255)
aTCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGga > 2:821140/1‑140 (MQ=255)
aTCCGTTCGGGAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGga > 2:243291/1‑140 (MQ=255)
gAACAACAGCC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCAGAGTGGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAACTCGc > 2:768107/1‑140 (MQ=255)
||
CCCAGACGCGGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑‑‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAACTCGC > NC_000913/3304671‑3304935
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
