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 |
|
A12 F56 I1 R1
|
165 |
53.8 |
2611523 |
96.4% |
2517508 |
99.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,964,868 |
T→C |
K96K (AAA→AAG) |
thyA ← |
thymidylate synthetase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,964,868 | 0 | T | C | 93.9%
| 102.8
/ ‑1.6
| 34 | K96K (AAA→AAG) | thyA | thymidylate synthetase |
| Reads supporting (aligned to +/- strand): ref base T (1/1); new base C (14/17); total (16/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01 |
TAATGCGGCGCGAATCCGGGTCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGTTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAGCAATGTTAG > NC_000913/2964771‑2964956
|
taatGCGGCGCGAATCCGGGTCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGctt < 1:83974/100‑1 (MQ=255)
tGCGGCGCGAATCCGGGTCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTAcc > 2:419759/1‑100 (MQ=255)
tGCGGCGCGAATCCGGGTCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTAcc < 2:1151204/100‑1 (MQ=255)
gcggcgCGAATCCGGGTCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCa < 2:561367/100‑1 (MQ=255)
cgcgAATCCGGGTCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATaca < 2:420666/100‑1 (MQ=255)
gggTCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGa < 1:799113/100‑1 (MQ=255)
gTCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAgg < 1:953577/100‑1 (MQ=255)
tCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGt > 2:8873/1‑100 (MQ=255)
cGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGATGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTc < 1:424240/100‑1 (MQ=255)
cGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGATGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTc < 1:424243/100‑1 (MQ=255)
ggTTCAGTTCCGTAGTGATCTGGTCAATCTGACGACCATCTGGCGTTGGCCAGGCGCGCCACTTCTTACCATACGCTGGCCCGGGGTCGCCGGTTTc < 2:1010103/97‑1 (MQ=255)
ggTTCAGTACCGTAGTGATCTGGTCAATATCCCGACCATCTGGCTTTGGCCAGGCGCGCCACTGGTTACCATACACTGGCCCGAGGTCGcc > 2:1102832/1‑91 (MQ=255)
ttCATTACCGTAGTGAGCTTGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCgg < 1:564585/100‑1 (MQ=255)
tCAGTACCGCAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGc < 1:531810/100‑1 (MQ=255)
gTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGt > 1:211079/1‑100 (MQ=255)
tGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCa > 1:1008793/1‑100 (MQ=255)
tCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGAt > 2:728637/1‑100 (MQ=255)
gTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACGCTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTg > 2:505453/1‑100 (MQ=255)
gTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTg > 1:438951/1‑100 (MQ=255)
tGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTg > 2:829625/1‑99 (MQ=255)
gacgacCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGACCCATTCGTCCCAGATGGTGACATTGtt > 1:564556/1‑100 (MQ=255)
cgacCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGtttt > 1:1164717/1‑100 (MQ=255)
acCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCg < 1:146326/100‑1 (MQ=255)
cATCTGGCGTTGGCTAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCg < 2:362096/98‑1 (MQ=255)
tCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATCCACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTa < 1:419763/100‑1 (MQ=255)
ggCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGAt > 2:898504/1‑100 (MQ=255)
gTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAg > 1:1119919/1‑100 (MQ=255)
ttGGCCGGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAGc < 1:775694/100‑1 (MQ=255)
cgatctggCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAGCa < 1:271704/94‑1 (MQ=255)
ggCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAGCaa > 1:40755/1‑100 (MQ=255)
ccAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAGCAATg < 2:309947/100‑1 (MQ=255)
cAGGCGCGCCACTGTTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAGCAATGt > 1:55303/1‑100 (MQ=255)
ggCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAGCaagatcg > 2:271701/1‑95 (MQ=255)
gcgcgcCTCTGTTTCCCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTGGATAAGCAATGTTAg < 2:600478/100‑1 (MQ=255)
cgcgcCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAGCAATGTTAg < 2:621578/99‑1 (MQ=255)
|
TAATGCGGCGCGAATCCGGGTCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGTTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAGCAATGTTAG > NC_000913/2964771‑2964956
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
