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 |
1,125,264 |
T→C |
57.8% |
E124E (GAA→GAG) |
pheT ← |
phenylalanine tRNA synthetase, beta subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,125,264 | 0 | T | C | 57.8%
| 15.5
/ 35.6
| 52 | E124E (GAA→GAG) | pheT | phenylalanine tRNA synthetase, beta subunit |
| Reads supporting (aligned to +/- strand): ref base T (11/11); new base C (18/12); total (29/23) |
| Fisher's exact test for biased strand distribution p-value = 5.76e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.22e-01 |
TCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCCGCTTTAATTTTGAA > minE/1125199‑1125329
|
tCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGtt > 1:694876/1‑67 (MQ=255)
tCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGtt > 1:2162765/1‑67 (MQ=255)
tCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGtt > 1:3311181/1‑67 (MQ=255)
cGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAg > 1:298326/1‑67 (MQ=255)
cGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAg > 1:1076854/1‑67 (MQ=255)
cGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAg > 1:2731303/1‑67 (MQ=255)
cGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAg > 1:1323974/1‑67 (MQ=255)
cGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAg > 1:30896/1‑67 (MQ=255)
cGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAg > 1:2094388/1‑67 (MQ=255)
cGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAg > 1:2015503/1‑67 (MQ=255)
ggCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAGcac > 1:428574/1‑69 (MQ=255)
ccGCAGGCAGCTCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCagag > 1:2916455/1‑53 (MQ=25)
ccGCAGGCAGCTCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCagag > 1:3088946/1‑53 (MQ=25)
ccGCAGGCAGCTCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCagag > 1:2477322/1‑53 (MQ=25)
ccGCAGGCAGCTCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCagag > 1:3264922/1‑53 (MQ=25)
ccGCAGGCAGCTCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCagag > 1:3306439/1‑53 (MQ=25)
ccGCAGGCAGCTCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCagag > 1:3341988/1‑53 (MQ=25)
ccGCAGGCAGCTCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCagag > 1:537066/1‑53 (MQ=25)
ccGCAGGCAGCTCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCagag > 1:1498079/1‑53 (MQ=25)
cGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAGCACAGCATccc > 1:1722096/1‑69 (MQ=255)
cGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAGCACAGCATccc > 1:1717746/1‑69 (MQ=255)
cGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAGCACAGCATccc > 1:233506/1‑69 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:2989078/66‑1 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:3073148/66‑1 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:655831/66‑1 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:2585884/66‑1 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:2567512/66‑1 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:1484348/66‑1 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:1762375/66‑1 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:3180252/66‑1 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:483426/66‑1 (MQ=255)
agctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:173811/66‑1 (MQ=255)
ctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:2381613/66‑1 (MQ=255)
ctCGATAATGCCGTTATGATCGTCAGAAATTCCCAGCTCAGAGAAGGAGCACAGCATCCCTTCAGAc < 1:1455608/66‑1 (MQ=255)
cAGTTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCCGCTTTAATTTTGa < 1:714089/68‑1 (MQ=255)
cAGTTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCCGCTTTAATTTTGa < 1:78661/68‑1 (MQ=255)
cAGTTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCCGCTTTAATTTTGa < 1:1052488/68‑1 (MQ=255)
cAGTTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCCGCTTTAATTTTGa < 1:2622766/68‑1 (MQ=255)
cAGTTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCCGCTTTAATTTTGa < 1:105597/68‑1 (MQ=255)
cAGTTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCCGCTTTAATTTTGa < 1:2161327/68‑1 (MQ=255)
cAGTTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCCGCTTTAATTTTGa < 1:2151119/68‑1 (MQ=255)
cAGTTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCCGCTTTAATTTTGa < 1:2903409/68‑1 (MQ=255)
cAGTTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCCGCTTTAATTTTGa < 1:1742501/68‑1 (MQ=255)
cAGTTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCCGCTTTAATTTTGa < 1:1738648/68‑1 (MQ=255)
cAGTTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCCGCTTTAATTTTGa < 1:1592577/68‑1 (MQ=255)
cAGCTCAGAGAAGGAGCACCGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCGGCTTTAATTTTGaa > 1:2642069/1‑69 (MQ=255)
cAGCTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCGGCTTTAATTTTGaa > 1:1768335/1‑69 (MQ=255)
cAGCTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCGGCTTTAATTTTGaa > 1:1009840/1‑69 (MQ=255)
cAGCTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCGGCTTTAATTTTGaa > 1:1236685/1‑69 (MQ=255)
cAGCTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCGGCTTTAATTTTGaa > 1:1622183/1‑69 (MQ=255)
cAGCTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCGGCTTTAATTTTGaa > 1:2358737/1‑69 (MQ=255)
cAGCTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCGGCTTTAATTTTGaa > 1:2373511/1‑69 (MQ=255)
cAGCTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCGGCTTTAATTTTGaa > 1:2695349/1‑69 (MQ=255)
cAGCTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCGGCTTTAATTTTGa > 1:608269/1‑68 (MQ=255)
cAGCTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCGGCTTTAATTTTGa > 1:3000799/1‑68 (MQ=255)
|
TCGGTGCCAATCGGCGCATCCGCAGGCAGTTCGATAATGCCGCTGTGATCGTCAGAAATGCCCAGTTCAGAGAAGGAGCACAGCATCCCTTCAGACGGTTCGCCACGCAGTTTCGCCGCTTTAATTTTGAA > minE/1125199‑1125329
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
