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 |
1,004,373 |
G→A |
100% |
L408L (CTG→TTG) |
pntA ← |
pyridine nucleotide transhydrogenase, alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,004,373 | 0 | G | A | 75.1%
| 28.5
/ 6.1
| 28 | L408L (CTG→TTG) | pntA | pyridine nucleotide transhydrogenase, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base G (7/0); new base A (15/6); total (22/6) |
| Fisher's exact test for biased strand distribution p-value = 2.88e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.83e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GGTGAAGTGCCCAAGGAATTCTTTCGGCGCAACGCTTGCCATCCAGCCAAAAAGAATGATTGCCAGCGCCATCAACGCGTATTTACGCCACGGTGAGCAGGTACATTTTTCCTCAGTTTTCACTT > minE/1004308‑1004432
|
ggTGAAGTGCCCAAGGAATTCTTTCGGCGCAACGCTTGCCATCCAGCCAAAAAGAATGATTGCCAgcgc < 1:1868426/69‑1 (MQ=255)
ggTGAAGTGCCCAAGGAATTCTTTCGGCGCAACGCTTGCCATCCAGCCAAAAAGAATGATTGCCAgcgc < 1:699488/69‑1 (MQ=255)
ggTGAAGTGCCCAAGGAATTCTTTCGGCGCAACGCTTGCCATCCAGCCAAAAAGAATGATTGCCAgcgc < 1:1377580/69‑1 (MQ=255)
ggTGAAGTGCCCAAGGAATTCTTTCGGCGCAACGCTTGCCATCCAGCCAAAAAGAATGATTGCCAgcgc < 1:1553768/69‑1 (MQ=255)
cccAAGGAATTCTTTCGGCGCAACGCTTGCCATCCAGCCAAAAAGAATGATTGCCAGCGCCATCAAcg > 1:3124494/1‑68 (MQ=255)
cccAAGGAATTCTTTCGGCGCAACGCTTGCCATCCAGCCAAAAAGAATGATTGCCAGCGCCATCAAcg > 1:1552533/1‑68 (MQ=255)
gAATTCTTTCGGCGCAACGCTTGCCATCCAGCCAAAAAGAATGATTGCCAGCGCCATCAACGCGTAttt > 1:1179917/1‑69 (MQ=255)
gAATTCTTTCGGCGCAACGCTTGCCATCCAGCCAAAAAGAATGATTGCCAGCGCCATCAACGCGTAttt > 1:1168565/1‑69 (MQ=255)
gAATTCTTTCGGCGCAACGCTTGCCATCCAGCCAAAAAGAATGATTGCCAGCGCCATCAACGCGTAttt > 1:565883/1‑69 (MQ=255)
gAATTCTTTCGGCGCAACGCTTGCCATCCAGCCAAAAAGAATGATTGCCAGCGCCATCAACGCGTAttt > 1:498865/1‑69 (MQ=255)
aCGCTTGCCATCCAGCCGAAAAGGATGATTGCCAACTCCATCAACGCGTATTTACGCCACgg > 1:1488776/1‑62 (MQ=255)
aCGCTTGCCATCCAGCCGAAAAGGATGATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCa > 1:3236531/1‑68 (MQ=255)
aCGCTTGCCATCCAGCCGAAAAGGATGATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCa > 1:3150360/1‑68 (MQ=255)
aCGCTTGCCATCCAGCCGAAAAGGATGATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCa > 1:994119/1‑68 (MQ=255)
aCGCTTGCCATCCAGCCGAAAAGGATGATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCa > 1:726296/1‑68 (MQ=255)
aCGCTTGCCATCCAGCCGAAAAGGATGATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCa > 1:2974757/1‑68 (MQ=255)
aCGCTTGCCATCCAGCCGAAAAGGATGATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCa > 1:2729091/1‑68 (MQ=255)
aCGCTTGCCATCCAGCCGAAAAGGATGATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCa > 1:2678233/1‑68 (MQ=255)
aCGCTTGCCATCCAGCCGAAAAGGATGATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCa > 1:2195250/1‑68 (MQ=255)
aCGCTTGCCATCCAGCCGAAAAGGATGATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCa > 1:2126069/1‑68 (MQ=255)
aCGCTTGCCATCCAGCCGAAAAGGATGATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCa > 1:1805832/1‑68 (MQ=255)
aCGCTTGCCATCCAGCCGAAAAGGATGATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCa > 1:1507680/1‑68 (MQ=255)
aCGCTTGCCATCCAGCCGAAAAGGATGATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCa > 1:1352294/1‑68 (MQ=255)
aCGCTTGCCATCCAGCCGAAAAGGATGATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCa > 1:1344651/1‑68 (MQ=255)
aCGCTTGCCATCCAGCCGAAAAGGATGATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCa > 1:1242023/1‑68 (MQ=255)
cAGCCAAAAAGAATGATTGCCAGCGCCATCAACGCGTATTTACGCCACGGTGAGCAGGTACATTTTTc > 1:2856016/1‑68 (MQ=255)
tGATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCAGGCACATTTTTCCTCAGTTTTCACtt < 1:2966570/69‑1 (MQ=255)
tGATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCAGGCACATTTTTCCTCAGTTTTCACtt < 1:3136136/69‑1 (MQ=255)
tGATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCAGGCACATTTTTCCTCAGTTTTCACtt < 1:1656535/69‑1 (MQ=255)
tGATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCAGGCACATTTTTCCTCAGTTTTCACtt < 1:1289870/69‑1 (MQ=255)
tGATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCAGGCACATTTTTCCTCAGTTTTCACtt < 1:1184351/69‑1 (MQ=255)
gATTGCCAACGCCATCAACGCGTATTTACGCCACGGTGAGCAGGCACATTTTTCCTCAGTTTTCACtt < 1:2786118/68‑1 (MQ=255)
|
GGTGAAGTGCCCAAGGAATTCTTTCGGCGCAACGCTTGCCATCCAGCCAAAAAGAATGATTGCCAGCGCCATCAACGCGTATTTACGCCACGGTGAGCAGGTACATTTTTCCTCAGTTTTCACTT > minE/1004308‑1004432
|
| 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
