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 |
1,681,250 |
G→A |
30.8% |
L1242L (CTG→TTG) |
yfhM ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,681,250 | 0 | G | A | 30.8%
| 75.3
/ 37.7
| 81 | L1242L (CTG→TTG) | yfhM | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (16/40); new base A (17/8); total (33/48) |
| Fisher's exact test for biased strand distribution p-value = 1.32e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.59e-01 |
AAATCCATCACGTAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGCATTTGCAGCAAACGGGAAATGCCGATATCGACC > minE/1681195‑1681308
|
aaaTCCATCACGTAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCaaa > 1:228487/1‑62 (MQ=255)
aaaTCCATCACGTAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCaaa > 1:1835844/1‑62 (MQ=255)
aaaTCCATCACGTAAGCCGTCAGCCAGTACTCTTCATCACCGTTTTTATCCCACAGCGCaaa > 1:2197829/1‑62 (MQ=255)
ccATCACGTAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGtt < 1:3267667/67‑1 (MQ=255)
ccATCACGTAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGtt < 1:2628813/67‑1 (MQ=255)
ccATCACGTAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGtt < 1:1812676/67‑1 (MQ=255)
ccATCACGTAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGtt < 1:1771506/67‑1 (MQ=255)
aCGTAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGtt < 1:3274709/62‑1 (MQ=255)
gTAAGCAGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCTCCGTTATCACGttc < 1:1755576/69‑2 (MQ=255)
tAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGttac < 1:2371071/69‑3 (MQ=255)
tAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGc < 1:1593091/69‑1 (MQ=255)
tAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGc < 1:2965198/69‑1 (MQ=255)
tAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGc < 1:2101065/69‑1 (MQ=255)
tAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGc < 1:1999537/69‑1 (MQ=255)
tAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGc < 1:1854388/69‑1 (MQ=255)
tAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGc < 1:641786/69‑1 (MQ=255)
tAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGc < 1:3388687/69‑1 (MQ=255)
tAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGc < 1:3065867/69‑1 (MQ=255)
tAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGc < 1:3092849/69‑1 (MQ=255)
tAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGc < 1:3433881/69‑1 (MQ=255)
tAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGc < 1:1186464/69‑1 (MQ=255)
tAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGc < 1:2835133/69‑1 (MQ=255)
aGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCTACAGCGCAAAGCCGCCGt < 1:211064/56‑1 (MQ=255)
aGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGt < 1:189862/56‑1 (MQ=255)
aGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGt < 1:447357/56‑1 (MQ=255)
aGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGt < 1:2924451/56‑1 (MQ=255)
aGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGt < 1:2215934/56‑1 (MQ=255)
aGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGt < 1:2165156/56‑1 (MQ=255)
aGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGt < 1:2971021/56‑1 (MQ=255)
aGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGt < 1:601960/56‑1 (MQ=255)
aGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGt < 1:3286757/56‑1 (MQ=255)
aGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGt < 1:3125531/56‑1 (MQ=255)
aGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGt < 1:877312/56‑1 (MQ=255)
aGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGt < 1:1223382/56‑1 (MQ=255)
aGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGt < 1:1152368/56‑1 (MQ=255)
aGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGt < 1:1025186/56‑1 (MQ=255)
gTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGtt < 1:1589621/53‑1 (MQ=255)
ccAGTACTCTTCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATCACGTTGCATTTgcagca < 1:3237849/68‑1 (MQ=255)
ccAGTACTCTTCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATCACGTTGCATTTgcagca < 1:3267875/68‑1 (MQ=255)
ccAGTACTCTTCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATCACGTTGCATTTgcagca < 1:2842054/68‑1 (MQ=255)
ccAGTACTCTTCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATCACGTTGCATTTgcagca < 1:2693188/68‑1 (MQ=255)
ccAGTACTCTTCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATCACGTTGCATTTgcagca < 1:2541107/68‑1 (MQ=255)
ccAGTACTCTTCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATCACGTTGCATTTgcagca < 1:2320159/68‑1 (MQ=255)
ccAGTACTCTTCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATCACGTTGCATTTgcagca < 1:2194578/68‑1 (MQ=255)
ccAGTACTCTTCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATCACGTTGCATTTgcagca < 1:1460651/68‑1 (MQ=255)
cAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGtt < 1:37992/47‑1 (MQ=255)
aGTACTCTTCGTCACCGTTTTTATCCCACAGCGCATAGCCGCCGtt < 1:1571284/46‑1 (MQ=255)
aCTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGCATTTGCAGCAAACgg > 1:288471/1‑68 (MQ=255)
ctctTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGCATTTg > 1:904508/1‑57 (MQ=255)
ctctTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGCATTTg > 1:3423235/1‑57 (MQ=255)
ctctTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGCATTTg > 1:2028637/1‑57 (MQ=255)
ctctTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGCATTTg > 1:669497/1‑57 (MQ=255)
ctctTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGCATTTGCAGCAAACGGGa < 1:587238/69‑1 (MQ=255)
ctctTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGCATTTGCAGCAAACGGGa > 1:792497/1‑69 (MQ=255)
ctctTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGCATTTGCAGCAAACGGGa < 1:2846224/69‑1 (MQ=255)
ctTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGCATTTGCAGCAAACGGGaaa > 1:949304/1‑69 (MQ=255)
ctTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGCATTTGCAGCAAACGGGaaa > 1:965312/1‑69 (MQ=255)
ctTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGCATTTGCAGCAAACGGGaaa > 1:2230637/1‑69 (MQ=255)
ctTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGCATTTGCAGCAAACGGGaaa > 1:2143055/1‑69 (MQ=255)
ttCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTAt > 1:466578/1‑41 (MQ=255)
ttCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATc > 1:594864/1‑42 (MQ=255)
ttCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATc > 1:1024338/1‑42 (MQ=255)
ttCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATc > 1:1120490/1‑42 (MQ=255)
ttCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATc > 1:1222991/1‑42 (MQ=255)
ttCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATc > 1:895233/1‑42 (MQ=255)
ttCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATc > 1:1345394/1‑42 (MQ=255)
ttCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATc > 1:1505883/1‑42 (MQ=255)
ttCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATc > 1:748499/1‑42 (MQ=255)
ttCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATc > 1:154887/1‑42 (MQ=255)
ttCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATc > 1:1789489/1‑42 (MQ=255)
ttCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATc > 1:2126560/1‑42 (MQ=255)
ttCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATc > 1:3171664/1‑42 (MQ=255)
ttCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATc > 1:581139/1‑42 (MQ=255)
ttCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATc > 1:2476304/1‑42 (MQ=255)
ttCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATc > 1:2964904/1‑42 (MQ=255)
ttCGTCACCGTTTTTATCCCACAACGCAAAGCCGCCGTTATc > 1:30364/1‑42 (MQ=255)
tttATCCCACAGCGCAAAGCCGCCGTTATCACGTTGCATTTGCAGCAAACGGGAAATGCCGATATCGa > 1:2220472/1‑68 (MQ=255)
tttATCCCACAGCGCAAAGCCGCCGTTATCACGTTGCATTTGCAGCAAACGGGAAATGCCGATATCGa > 1:778659/1‑68 (MQ=255)
tttATCCCACAGCGCAAAGCCGCCGTTATCACGTTGCATTTGCAGCAAACGGGAAATGCCGATATCGa > 1:2727899/1‑68 (MQ=255)
tATCCCACAGCGCAAAGCCGCCGTTATCACGTTGCATTTGCAGCAAACGGGAAATGCCGATATCGAcc < 1:3054737/68‑1 (MQ=255)
tATCCCACAGCGCAAAGCCGCCGTTATCACGTTGCATTTGCAGCAAACGGGAAATGCCGATATCGAcc < 1:3156669/68‑1 (MQ=255)
|
AAATCCATCACGTAAGCCGTCAGCCAGTACTCTTCGTCACCGTTTTTATCCCACAGCGCAAAGCCGCCGTTATCACGTTGCATTTGCAGCAAACGGGAAATGCCGATATCGACC > minE/1681195‑1681308
|
| 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
