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 |
1,626,710 |
G→A |
21.4% |
V269V (GTG→GTA) |
tktB → |
transketolase 2, thiamin‑binding |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,626,710 | 0 | G | A | 21.4%
| 70.6
/ 11.3
| 51 | V269V (GTG→GTA) | tktB | transketolase 2, thiamin‑binding |
| Reads supporting (aligned to +/- strand): ref base G (15/25); new base A (6/5); total (21/30) |
| Fisher's exact test for biased strand distribution p-value = 3.27e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.85e-01 |
TTTGGTTCGCCGAATAAAGCAGGTAAGGAAGAGGCGCACGGCGCACCACTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATCCCTAAAGAGATTTAT > minE/1626645‑1626773
|
tttGGTTCGCCGAATAAAGCAGGTAAGGAAGAGGCGCACGGCGCACCACTGGGGGAAGAAGAAGTGgc < 1:1956909/68‑1 (MQ=255)
tAAAGCAGGTAAGGAAGAGGCGCACGGCGCACCACTGGGGGAAGAAGAAGTGGCGCTGGCACGGCaaaa < 1:2169427/69‑1 (MQ=255)
aaaGCAGGTAAGGAAGAGGCGCACGGCGCACCACTGGGGGAAGAAGAAGTGGCGCTGGCACGGCaaaa < 1:3283845/68‑1 (MQ=255)
gTAAGGAAGAGGCGCACGGCGCACCACTGGGGGAAGAAGAAGTGGCGCTGGCACGGCaaaa < 1:1587236/61‑1 (MQ=255)
aaGGAAGAGGCGCACGGCGCACCACTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTgg > 1:1971983/1‑69 (MQ=255)
aaGAGGCGCACGGCGCACCACTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCAcc > 1:2743024/1‑69 (MQ=255)
aaGAGGCGCACGGCGCACCACTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCAcc > 1:610834/1‑69 (MQ=255)
ggcgcacggcgcacCGCTGGGGGAAGAAGAAGTAGCTCTGGCACGGCAAAAACTGGGCTGGCACCATcc < 1:1533961/69‑1 (MQ=255)
ggcgcacggcgcacCGCTGGGGGAAGAAGAAGTAGCTCTGGCACGGCAAAAACTGGGCTGGCACCATcc < 1:1017237/69‑1 (MQ=255)
ggcgcacggcgcacCGCTGGGGGAAGAAGAAGTAGCTCTGGCACGGCAAAAACTGGGCTGGCACCATcc < 1:2907711/69‑1 (MQ=255)
gcgcacggcgcacCGCTGGGGGAAGAAGAAGTAGCTCTGGCACGGCAAAAACTGGGCTGGCACCATcc < 1:490712/68‑1 (MQ=255)
cgcacggcgcacCGCTGGGGGAAGAAGAAGTAGCTCTGGCACGTCAAAAACTGGGCTGGCACCATCCGc > 1:2211721/1‑69 (MQ=255)
cgcacggcgcacCGCTGGGGGAAGAAGAAGTAGCTCTGGCACGGCAAAAACTGGGCTGGCACCATCCGc > 1:2763271/1‑69 (MQ=255)
cgcacggcgcacCGCTGGGGGAAGAAGAAGTAGCTCTGGCACGGCAAAAACTGGGCTGGCACCATCCGc > 1:128389/1‑69 (MQ=255)
cgcacggcgcacCGCTGGGGGAAGAAGAAGTAGCTCTGGCACGGCAAAAACTGGGCTGGCACCATCCGc > 1:953960/1‑69 (MQ=255)
cgcacggcgcacCGCTGGGGGAAGAAGAAGTAGCTCTGGCACGGCAAAAACTGGGCTGGCACCATCCGc > 1:2071657/1‑69 (MQ=255)
cgcacggcgcacCGCTGGGGGAAGAAGAAGTAGCTCTGGCACGGCAAAAACTGGGCTGGCA‑CATCCGcc > 1:2244168/1‑69 (MQ=255)
ggcgcacGACTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGAACCATCCGCCAttt < 1:1644021/69‑1 (MQ=255)
ggcgcacCACTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCAttt < 1:277024/69‑1 (MQ=255)
caccacTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTgaga < 1:718391/69‑1 (MQ=255)
caccacTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTgaga < 1:2587654/69‑1 (MQ=255)
caccacTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTgaga < 1:2830915/69‑1 (MQ=255)
caccacTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTgaga < 1:22755/69‑1 (MQ=255)
caccacTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTgaga < 1:2073839/69‑1 (MQ=255)
caccacTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTgaga < 1:1425354/69‑1 (MQ=255)
caccacTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTgaga < 1:1605968/69‑1 (MQ=255)
accacTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTgaga < 1:2386200/68‑1 (MQ=255)
accacTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTgaga < 1:1716010/68‑1 (MQ=255)
gggggAAGAAGAAGTGGCGCTGGCACGTCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATccc > 1:1675869/1‑66 (MQ=255)
gggggAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTgg > 1:1238034/1‑43 (MQ=255)
gggggAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTgaga > 1:2577763/1‑62 (MQ=255)
gggggAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATccc > 1:369657/1‑66 (MQ=255)
gggggAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATccc > 1:631521/1‑66 (MQ=255)
gggggAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATccc > 1:2681240/1‑66 (MQ=255)
gggggAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATccc > 1:3140632/1‑66 (MQ=255)
gggggAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATccc > 1:2455465/1‑66 (MQ=255)
gggggAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATccc > 1:2540871/1‑66 (MQ=255)
gggggAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATcc > 1:3044081/1‑65 (MQ=255)
aagaagaagTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATCCCTAAAgaga < 1:2204240/69‑1 (MQ=255)
aagaagaagTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATCCCTAAAgaga < 1:2805580/69‑1 (MQ=255)
aagaagaagTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATCCCTAAAgaga < 1:1754023/69‑1 (MQ=255)
gaagaagTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATCCCTAAAGAGAtt > 1:1628338/1‑69 (MQ=255)
gaagaagTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATCCCTAAAGAGAtt > 1:93807/1‑69 (MQ=255)
gaagaagTAGCTCTGGCACGGCAAAAACTGGGCTGGCACCATcc < 1:166314/44‑1 (MQ=38)
agaagTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATCCCTAAAGAGATTTa < 1:368652/69‑1 (MQ=255)
agaagTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATCCCTAAAGAGATTTa < 1:911332/69‑1 (MQ=255)
agaagTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATCCCTAAAGAGATTTa < 1:1268466/69‑1 (MQ=255)
agaagTGGCGCTGGCACGGCAAAAACTGGGCTAGCACCATCCGCCATTTGAGATCCCTAAAGAGATTTa < 1:201284/69‑1 (MQ=255)
gaagTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATCCCTAAAGAGATTTAt < 1:645566/69‑1 (MQ=255)
gaagTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATCCCTAAAGAGATTTAt < 1:682666/69‑1 (MQ=255)
gaagTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATCCCTAAAGAGATTTAt < 1:941856/69‑1 (MQ=255)
|
TTTGGTTCGCCGAATAAAGCAGGTAAGGAAGAGGCGCACGGCGCACCACTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGATCCCTAAAGAGATTTAT > minE/1626645‑1626773
|
| 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
