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 |
|
A1 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,606,841 |
C→T |
68.5% |
A26V (GCC→GTC) |
lsrB → |
AI2 transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,606,841 | 0 | C | T | 68.5%
| 61.8
/ 47.0
| 54 | A26V (GCC→GTC) | lsrB | AI2 transporter |
| Reads supporting (aligned to +/- strand): ref base C (12/5); new base T (19/18); total (31/23) |
| Fisher's exact test for biased strand distribution p-value = 2.42e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.82e-01 |
TCATCGCTTTAAGAAAATCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGG > W3110S.gb/1606773‑1606901
|
tCATCGCTTTAAGAAAATCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCg > 1:1582794/1‑71 (MQ=255)
tAAGAAAATCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCg < 1:1955268/69‑1 (MQ=255)
tAAGAAAATCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCg < 1:1085115/69‑1 (MQ=255)
tAAGAAAATCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCg < 1:1110312/69‑1 (MQ=255)
tAAGAAAATCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCg < 1:473318/69‑1 (MQ=255)
tAAGAAAATCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCg < 1:2636700/69‑1 (MQ=255)
tAAGAAAATCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCg < 1:123662/69‑1 (MQ=255)
tAAGAAAATCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCg < 1:1391254/69‑1 (MQ=255)
tAAGAAAATCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCg < 1:2120533/69‑1 (MQ=255)
tAAGAAAATCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCg < 1:1734733/69‑1 (MQ=255)
tAAGAAAATCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCg < 1:2173072/69‑1 (MQ=255)
aaGAAAATCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCg < 1:3211729/68‑1 (MQ=255)
aGAAAATCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCg < 1:1638219/67‑1 (MQ=255)
aaaaTCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCGTATTGc < 1:1381691/71‑1 (MQ=255)
aTCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCGTATTGCAtt > 1:3249243/1‑71 (MQ=255)
aTCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCAtt < 1:1945610/71‑1 (MQ=255)
aTCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCAtt < 1:2081527/71‑1 (MQ=255)
aTCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCAtt < 1:774424/71‑1 (MQ=255)
acttaGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCGTATTGCATTTATTccc > 1:955232/1‑70 (MQ=255)
acttaGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCGTATTGCATTTATTccc > 1:1502222/1‑70 (MQ=255)
acttaGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCGTATTGCATTTATTccc > 1:181511/1‑70 (MQ=255)
acttaGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCGTATTGCATTTATTccc > 1:1079147/1‑70 (MQ=255)
ttaGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCGTATTGc < 1:2646736/58‑1 (MQ=255)
ttaGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCGTATTGc < 1:417495/58‑1 (MQ=255)
ttaGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCGTATTGc < 1:2019191/58‑1 (MQ=255)
aGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCGTATTGCAt > 1:1797638/1‑58 (MQ=255)
ggCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGt > 1:1747510/1‑71 (MQ=255)
ggCATTGCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCGTATTGCATTTATTACCAAACTGGTTGGCGt > 1:166350/1‑71 (MQ=255)
ttGCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGt > 1:1973536/1‑61 (MQ=255)
ttGCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGt > 1:3489239/1‑61 (MQ=255)
ttGCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGt > 1:2990857/1‑61 (MQ=255)
ttGCCGAAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGt > 1:2005553/1‑61 (MQ=255)
gCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCg < 1:199782/35‑1 (MQ=255)
gCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGAtt > 1:2387153/1‑71 (MQ=255)
gCCGCAATCTCTATGAATGTGCAGGTCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGAtt > 1:3026904/1‑71 (MQ=255)
gCCGCAATCTCTATGAATGTGCAGGCCGCGGAGCGTATTGCATTTa > 1:815969/1‑46 (MQ=255)
gCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCATTTa > 1:704697/1‑46 (MQ=255)
gCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCATTTa > 1:115011/1‑46 (MQ=255)
gCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCATTTa > 1:1024345/1‑46 (MQ=255)
gCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCATTTa > 1:123175/1‑46 (MQ=255)
gCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCATTTa > 1:1725906/1‑46 (MQ=255)
gCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGAtt > 1:1148029/1‑71 (MQ=255)
gCAATCTCTATGAATGTGCAGGTCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGAttttt > 1:612257/1‑71 (MQ=255)
cAATCTCTATGAATGTGCAGGTCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGAtttttt < 1:41813/71‑1 (MQ=255)
cAATCTCTATGAATGTGCAGGTCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGAtttttt < 1:2134892/71‑1 (MQ=255)
tctATGAATGTGCAGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAg > 1:2580033/1‑71 (MQ=255)
tGAATGTGCAGGTCGCAGAGCGTATTGCATTTATTCCCaaa > 1:635320/1‑41 (MQ=255)
tGAATGTGCAGGTCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTg > 1:2455989/1‑53 (MQ=255)
tGAATGTGCAGGTCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTa > 1:1218730/1‑63 (MQ=255)
tGAATGTGCAGGTCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGc < 1:1984903/68‑1 (MQ=255)
aaTGTGCAGGTCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTgg > 1:2679875/1‑71 (MQ=255)
aaTGTGCAGGTCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTgg > 1:2542710/1‑71 (MQ=255)
aaTGTGCAGGTCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTgg > 1:3501145/1‑71 (MQ=255)
aaTGTGCAGGTCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTgg > 1:2297560/1‑71 (MQ=255)
|
TCATCGCTTTAAGAAAATCGCCTTACTTAGCGCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGG > W3110S.gb/1606773‑1606901
|
| 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
