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 |
1,125,241 |
C→T |
42.8% |
S132N (AGC→AAC) |
pheT ← |
phenylalanine tRNA synthetase, beta subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,125,241 | 0 | C | T | 42.8%
| 14.4
/ 33.9
| 49 | S132N (AGC→AAC) | pheT | phenylalanine tRNA synthetase, beta subunit |
| Reads supporting (aligned to +/- strand): ref base C (19/9); new base T (9/12); total (28/21) |
| Fisher's exact test for biased strand distribution p-value = 9.19e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.23e-01 |
AAGTTTCAGGTATTCACGGATATCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAGCACAGCATCCCTTCAGAC > minE/1125177‑1125294
|
aaGTTTCAGGTGTTCACGGATATCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCtgtg > 1:415096/1‑69 (MQ=255)
aaGTTTCAGGTATTCACGGATATCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCtgtg > 1:3278753/1‑69 (MQ=255)
aaGTTTCAGGTATTCACGGATATCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCtgt > 1:116204/1‑68 (MQ=255)
cACGGATATCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATg > 1:564620/1‑68 (MQ=255)
cACGGATATCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATg > 1:1652933/1‑68 (MQ=255)
cGGATATCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCTTCAGAAATGcc < 1:3323942/68‑1 (MQ=255)
cGGATATCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGcc < 1:3414831/68‑1 (MQ=255)
cGGATATCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGcc < 1:3361924/68‑1 (MQ=255)
cGGATATCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGcc < 1:1724095/68‑1 (MQ=255)
cGGATATCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGcc < 1:1725806/68‑1 (MQ=255)
cGGATATCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGcc < 1:3164256/68‑1 (MQ=255)
cGGATATCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGcc < 1:2755185/68‑1 (MQ=255)
cGGATATCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGcc < 1:2530374/68‑1 (MQ=255)
tCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGtt > 1:694876/1‑67 (MQ=255)
tCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGtt > 1:3311181/1‑67 (MQ=255)
tCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGtt > 1:2162765/1‑67 (MQ=255)
cGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAg > 1:1076854/1‑67 (MQ=255)
cGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAg > 1:2094388/1‑67 (MQ=255)
cGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAg > 1:1323974/1‑67 (MQ=255)
cGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAg > 1:30896/1‑67 (MQ=255)
cGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAg > 1:2731303/1‑67 (MQ=255)
cGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAg > 1:2015503/1‑67 (MQ=255)
cGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAg > 1:298326/1‑67 (MQ=255)
ggCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAGcac > 1:428574/1‑69 (MQ=255)
ccGCAGGCAGCTCGATAATGCCGTTATGATCGTCAGa > 1:2432646/1‑37 (MQ=25)
ccGCAGGCAGCTCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCagag > 1:3306439/1‑53 (MQ=25)
ccGCAGGCAGCTCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCagag > 1:3264922/1‑53 (MQ=25)
ccGCAGGCAGCTCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCagag > 1:3341988/1‑53 (MQ=25)
ccGCAGGCAGCTCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCagag > 1:3088946/1‑53 (MQ=25)
ccGCAGGCAGCTCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCagag > 1:1498079/1‑53 (MQ=25)
ccGCAGGCAGCTCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCagag > 1:2916455/1‑53 (MQ=25)
ccGCAGGCAGCTCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCagag > 1:537066/1‑53 (MQ=25)
ccGCAGGCAGCTCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCagag > 1:2477322/1‑53 (MQ=25)
cGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGcc < 1:2600140/42‑1 (MQ=255)
cGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAGCACAGCATccc > 1:1717746/1‑69 (MQ=255)
cGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAGCACAGCATccc > 1:1722096/1‑69 (MQ=255)
cGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAGCACAGCATccc > 1:233506/1‑69 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:173811/66‑1 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:3180252/66‑1 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:1762375/66‑1 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:3073148/66‑1 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:1484348/66‑1 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:2989078/66‑1 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:483426/66‑1 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:2585884/66‑1 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:2567512/66‑1 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:655831/66‑1 (MQ=255)
ctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:1455608/66‑1 (MQ=255)
ctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:2381613/66‑1 (MQ=255)
|
AAGTTTCAGGTATTCACGGATATCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAGCACAGCATCCCTTCAGAC > minE/1125177‑1125294
|
| 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
