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 |
1,534,037 |
T→C |
62.2% |
D60D (GAT→GAC) |
yfcN → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,534,037 | 0 | T | C | 62.2%
| 31.2
/ 34.3
| 58 | D60D (GAT→GAC) | yfcN | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (9/13); new base C (21/15); total (30/28) |
| Fisher's exact test for biased strand distribution p-value = 2.80e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.27e-01 |
TCAGCGAAGTGCCGGTGAAACGCTTGATCCAGGAGCAGGCTGATGCCAGCCATTATTTCTCCGATGAGTTTCAGCCGTTATTAAATACCGAAGGTCCGGTGAAATATGTTCGCCCGGATGTCAGCCA > minE/1533973‑1534099
|
tCAGCGAAGTGCCGGTGAAACGCTTGATCCAGGAGCAGGCTGATGCCAGCCATTATTTCTCCGATGAGt < 1:1987545/69‑1 (MQ=255)
gTGAAACGCTTGATCCAGGAGCAGGCTGATGCCAGCCATTATTTCTCCGATGAGTTTCAGCCGttatta < 1:2261356/69‑1 (MQ=255)
tGAAACGCTTGATCCAGGAGCAGGCTGATGCCAGCCATTATTTCTCCGATGAGTTTCAGCCGttatta < 1:1273006/68‑1 (MQ=255)
gAAACGCTTGATCCAGGAGCAGGCTGATGCCAGCCATTATTTCTCCGATGAGTTTCAGCCGTTATTaaa > 1:2666129/1‑69 (MQ=255)
gAAACGCTTGATCCAGGAGCAGGCTGATGCCAGCCATTATTTCTCCGATGAGTTTCAGCCGTTATTaaa < 1:1283595/69‑1 (MQ=255)
gAAACGCTTGATCCAGGAGCAGGCTGATGCCAGCCATTATTTCTCCGATGAGTTTCAGCCGTTATTaaa > 1:2022318/1‑69 (MQ=255)
gAAACGCTTGATCCAGGAGCAGGCTGATGCCAGCCATTATTTCTCCGATGAGTTTCAGCCGTTATTaaa > 1:3252062/1‑69 (MQ=255)
ccAGGAGCAGGCTGATGCCAGCCATTATTTCTCCGATGAGTTTCAGCCGTTATTAAATACCGAAGGTcc < 1:3146584/69‑1 (MQ=255)
cAGGAACAGGCCGATGCCAGCCACTATTTTTCGGACGAATTTCAGccat < 1:1684830/49‑3 (MQ=16)
cAGGAACAGGCCGATGCCAGCCACTATTTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCg < 1:1771809/69‑1 (MQ=255)
cAGGAACAGGCCGATGCCAGCCACTATTTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCg < 1:1791028/69‑1 (MQ=255)
cAGGAACAGGCCGATGCCAGCCACTATTTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCg < 1:1856532/69‑1 (MQ=255)
cAGGAACAGGCCGATGCCAGCCACTATTTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCg < 1:1069770/69‑1 (MQ=255)
cAGGAACAGGCCGATGCCAGCCACTATTTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCg < 1:2957544/69‑1 (MQ=255)
cAGGAACAGGCCGATGCCAGCCACTATTTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCg < 1:908151/69‑1 (MQ=255)
cAGGAACAGGCCGATGCCAGCCACTATTTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCg < 1:970670/69‑1 (MQ=255)
aGGAACAGGCCGATGCCAGCCACTATTTTTCGGACTAATTTCAGccat < 1:2855560/48‑3 (MQ=255)
aGGAACAGGCCGATGCCAGCCACTATTTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCg < 1:2234424/68‑1 (MQ=255)
acAGGCCGATGCCAGCCACTATTTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa < 1:2584306/68‑1 (MQ=255)
acAGGCCGATGCCAGCCACTATTTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa < 1:3106075/68‑1 (MQ=255)
acAGGCCGATGCCAGCCACTATTTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa < 1:1514270/68‑1 (MQ=255)
cAGGCTGATGCCAGCCATTATTTCTCCGATGAGTTTCAGCCGTTATTAAATACCGAAGGTCCGGTGaaa < 1:2199187/69‑1 (MQ=255)
cAGGCTGATGCCAGCCATTATTTCTCCGATGAGTTTCAGCCGTTATTAAATACCGAAGGTCCGGTGaaa < 1:1333011/69‑1 (MQ=255)
aGGCCGATGCCAGCCACTATTTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa < 1:337820/67‑1 (MQ=255)
gCTGATGCCAGCCATTATTTCTCCGATGAGTTTCAGCCGTTATTAAATACCGAAGGTCCGGTGAAatat < 1:1593718/69‑1 (MQ=255)
gCTGATGCCAGCCATTATTTCTCCGATGAGTTTCAGCCGTTATTAAATACCGAAGGTCCGGTGAAatat < 1:1551542/69‑1 (MQ=255)
gCTGATGCCAGCCATTATTTCTCCGATGAGTTTCAGCCGTTATTAAATACCGAAGGTCCGGTGAAatat < 1:2186767/69‑1 (MQ=255)
gCTGATGCCAGCCATTATTTCTCCGATGAGTTTCAGCCGTTATTAAATACCGAAGGTCCGGTGAAatat < 1:2190577/69‑1 (MQ=255)
cTGATGCCAGCCATTATTTCTCCGATGAGTTTCAGCCGTTATTAAATACCGAAGGTCCGGTGAAatat < 1:1869473/68‑1 (MQ=255)
aatattTTTCGGACGAATTTCTGCCATTATTGAATACCGAAGGTCCg < 1:242573/45‑1 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:2218377/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:3095200/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:973003/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:86578/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:583138/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:383993/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:2965009/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:3034801/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:1072854/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:1149314/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:2484031/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:2438598/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:2224488/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:2199969/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:1729705/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:1485954/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:2661651/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:128879/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:1348984/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:1412495/1‑49 (MQ=255)
attTTTCGGACGAATTTCAGCCATTATTGAATACCGAAGGTCCGGTCaa > 1:1365489/1‑49 (MQ=255)
attTCTCCGATGAGTTTCAGCCGTTATTAAATACCGAAGGTCCGGTGAAATATGTTCGCCCGGATGTCa > 1:3201637/1‑69 (MQ=255)
attTCTCCGATGAGTTTCAGCCGTTATTAAATACCGAAGGTCCGGTGAAATATGTTCGCCCGGATGTCa > 1:1188298/1‑69 (MQ=255)
attTCTCCGATGAGTTTCAGCCGTTATTAAATACCGAAGGTCCGGTGAAATATGTTCGCCCGGATGTCa > 1:1433596/1‑69 (MQ=255)
attTCTCCGATGAGTTTCAGCCGTTATTAAATACCGAAGGTCCGGTGAAATATGTTCGCCCGGATGTCa > 1:162614/1‑69 (MQ=255)
attTCTCCGATGAGTTTCAGCCGTTATTAAATACCGAAGGTCCGGTGAAATATGTTCGCCCGGATGTCa > 1:2737347/1‑69 (MQ=255)
attTCTCCGATGAGTTTCAGCCGGTATTAAATACCGAAGGTCCGGTg > 1:2533740/1‑47 (MQ=255)
tcCGATGAGTTTCAGCCGTTATTAAATACCGAAGGTCCGGTGAAATATGTTCGCCCGGATGTCAGCCa < 1:3212765/68‑1 (MQ=255)
|
TCAGCGAAGTGCCGGTGAAACGCTTGATCCAGGAGCAGGCTGATGCCAGCCATTATTTCTCCGATGAGTTTCAGCCGTTATTAAATACCGAAGGTCCGGTGAAATATGTTCGCCCGGATGTCAGCCA > minE/1533973‑1534099
|
| 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
