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 |
1,626,692 |
A→G |
40.0% |
P263P (CCA→CCG) |
tktB → |
transketolase 2, thiamin‑binding |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,626,692 | 0 | A | G | 40.0%
| 5.6
/ 13.6
| 25 | P263P (CCA→CCG) | tktB | transketolase 2, thiamin‑binding |
| Reads supporting (aligned to +/- strand): ref base A (7/8); new base G (6/4); total (13/12) |
| Fisher's exact test for biased strand distribution p-value = 6.88e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GATTGGCTTTGGTTCGCCGAATAAAGCAGGTAAGGAAGAGGCGCACGGCGCACCACTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGA > minE/1626638‑1626756
|
gATTGGCTTTGGTTCGCCGAATAAAGCAGGTAAGGAAGAGGCGCACGGCGCACCACTGGGGgaagaaga < 1:2671270/69‑1 (MQ=255)
gATTGGCTTTGGTTCGCCGAATAAAGCAGGTAAGGAAGAGGCGCACGGCGCACCACTGGGGgaagaaga > 1:3124634/1‑69 (MQ=255)
gATTGGCTTTGGTTCGCCGAATAAAGCAGGTAAGGAAGAGGCGCACGGCGCACCACTGGGGgaagaaga > 1:74109/1‑69 (MQ=255)
gATTGGCTTTGGTTCGCCGAATAAAGCAGGTAAGGAAGAGGCGCACGGCGCACCACTGGGGgaagaaga > 1:1804191/1‑69 (MQ=255)
gATTGGCTTTGGTTCGCCGAATAAAGCAGGTAAGGAAGAGGCGCACGGCGCACCACTGGGGgaagaaga > 1:2025398/1‑69 (MQ=255)
ttGGCTTTGGTTCGCCGAATAAAGCAGGTAAGGAAGAGGCGCACGGCGCACCACTGGGGgaagaaga < 1:327795/67‑1 (MQ=255)
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 > 1:610834/1‑69 (MQ=255)
aaGAGGCGCACGGCGCACCACTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCAcc > 1:2743024/1‑69 (MQ=255)
ggcgcacggcgcacCGCTGGGGGAAGAAGAAGTAGCTCTGGCACGGCAAAAACTGGGCTGGCACCATcc < 1:1533961/69‑1 (MQ=255)
ggcgcacggcgcacCGCTGGGGGAAGAAGAAGTAGCTCTGGCACGGCAAAAACTGGGCTGGCACCATcc < 1:2907711/69‑1 (MQ=255)
ggcgcacggcgcacCGCTGGGGGAAGAAGAAGTAGCTCTGGCACGGCAAAAACTGGGCTGGCACCATcc < 1:1017237/69‑1 (MQ=255)
gcgcacggcgcacCGCTGGGGGAAGAAGAAGTAGCTCTGGCACGGCAAAAACTGGGCTGGCACCATcc < 1:490712/68‑1 (MQ=255)
cgcacggcgcacCGCTGGGGGAAGAAGAAGTAGCTCTGGCACGTCAAAAACTGGGCTGGCACCATCCGc > 1:2211721/1‑69 (MQ=255)
cgcacggcgcacCGCTGGGGGAAGAAGAAGTAGCTCTGGCACGGCAAAAACTGGGCTGGCACCATCCGc > 1:128389/1‑69 (MQ=255)
cgcacggcgcacCGCTGGGGGAAGAAGAAGTAGCTCTGGCACGGCAAAAACTGGGCTGGCACCATCCGc > 1:953960/1‑69 (MQ=255)
cgcacggcgcacCGCTGGGGGAAGAAGAAGTAGCTCTGGCACGGCAAAAACTGGGCTGGCACCATCCGc > 1:2763271/1‑69 (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 < 1:2587654/69‑1 (MQ=255)
caccacTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTgaga < 1:2830915/69‑1 (MQ=255)
caccacTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTgaga < 1:22755/69‑1 (MQ=255)
caccacTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTgaga < 1:2073839/69‑1 (MQ=255)
caccacTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTgaga < 1:718391/69‑1 (MQ=255)
caccacTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTgaga < 1:1605968/69‑1 (MQ=255)
caccacTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTgaga < 1:1425354/69‑1 (MQ=255)
accacTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTgaga < 1:2386200/68‑1 (MQ=255)
accacTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTgaga < 1:1716010/68‑1 (MQ=255)
|
GATTGGCTTTGGTTCGCCGAATAAAGCAGGTAAGGAAGAGGCGCACGGCGCACCACTGGGGGAAGAAGAAGTGGCGCTGGCACGGCAAAAACTGGGCTGGCACCATCCGCCATTTGAGA > minE/1626638‑1626756
|
| 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
