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 |
447,524 |
C→A |
49.8% |
G64G (GGG→GGT) |
kdpD ← |
fused sensory histidine kinase in two‑component regulatory system with KdpE |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 447,524 | 0 | C | A | 49.8%
| 6.5
/ 45.2
| 46 | G64G (GGG→GGT) | kdpD | fused sensory histidine kinase in two‑component regulatory system with KdpE |
| Reads supporting (aligned to +/- strand): ref base C (10/13); new base A (16/7); total (26/20) |
| Fisher's exact test for biased strand distribution p-value = 1.36e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGCCTGGCGTTTTAACGGCAGAACAGCCAGCCCTTCCAGCATGGCGGCGGTATCTTTTCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCGCTGGGCTTC > minE/447464‑447586
|
cGCCTGGCGTTTTAACGGCAGAACAGCCAGCCCTTCCAGCATGGCGGCGGTATCTTTTCGCCCGTGGGt > 1:1361620/1‑69 (MQ=255)
ttAACGGCAGAACAGCCAGCCCTTCCAGCATGGCGGCGGTATCTTTTCGCCCGTGGGTTTCTACCACg > 1:1474324/1‑68 (MQ=255)
tAACGGCAGAACAGCCAGACCTTTCAGCATGGCGGCGGTATCTTTCCGACCGTGGGt > 1:414163/1‑57 (MQ=255)
tAACGGCAGAACAGCCAGACCTTTCAGCATGGCGGCGGTATCTTTCCGACCGTGGGt > 1:2244194/1‑57 (MQ=255)
tAACGGCAGAACAGCCAGACCTTTCAGCATGGCGGCGGTATCTTTCCGACCGTGGGt > 1:3065060/1‑57 (MQ=255)
tAACGGCAGAACAGCCAGACCTTTCAGCATGGCGGCGGTATCTTTCCGACCGTGGGt > 1:2105531/1‑57 (MQ=255)
tAACGGCAGAACAGCCAGACCTTTCAGCATGGCGGCGGTATCTTTCCGACCGTGGGt > 1:2063331/1‑57 (MQ=255)
tAACGGCAGAACAGCCAGACCTTTCAGCATGGCGGCGGTATCTTTCCGACCGTGGGt > 1:2049308/1‑57 (MQ=255)
tAACGGCAGAACAGCCAGACCTTTCAGCATGGCGGCGGTATCTTTCCGACCGTGGGt > 1:1931892/1‑57 (MQ=255)
tAACGGCAGAACAGCCAGACCTTTCAGCATGGCGGCGGTATCTTTCCGACCGTGGGt > 1:2402362/1‑57 (MQ=255)
tAACGGCAGAACAGCCAGACCTTTCAGCATGGCGGCGGTATCTTTCCGACCGTGGGt > 1:3170829/1‑57 (MQ=255)
tAACGGCAGAACAGCCAGACCTTTCAGCATGGCGGCGGTATCTTTCCGACCGTGGGt > 1:3008477/1‑57 (MQ=255)
tAACGGCAGAACAGCCAGACCTTTCAGCATGGCGGCGGTATCTTTCCGACCGTGGGt > 1:2959331/1‑57 (MQ=255)
tAACGGCAGAACAGCCAGACCTTTCAGCATGGCGGCGGTATCTTTCCGACCGTGGGt > 1:613646/1‑57 (MQ=255)
tAACGGCAGAACAGCCAGACCTTTCAGCATGGCGGCGGTATCTTTCCGACCGTGGGt > 1:1097519/1‑57 (MQ=255)
tAACGGCAGAACAGCCAGACCTTTCAGCATGGCGGCGGTATCTTTCCGACCGTGGGt > 1:1056969/1‑57 (MQ=255)
tAACGGCAGAACAGCCAGACCTTTCAGCATGGCGGCGGTATCTTTCCGACCGTGGGt > 1:2934089/1‑57 (MQ=255)
tAACGGCAGAACAGCCAGACCTTTCAGCATGGCGGCGGTATCTTTCCGACCGTGGGt > 1:2881784/1‑57 (MQ=255)
aCAGCCAGCCCTTCCAGCATGGCGGCGGTATCTTTTCGCCCGTGGGTTTCt > 1:2343130/1‑51 (MQ=255)
aCAGCCAGCCCTTCCAGCATGGCGGCGGTATCTTTTCGCCCGTGGGTTTCTACCACGCCAACCACAata > 1:937411/1‑69 (MQ=255)
aCAGCCAGCCCTTCCAGCATGGCGGCGGTATCTTTTCGCCCGTGGGTTTCTACCACGCCAACCACAata > 1:1926024/1‑69 (MQ=255)
ccAGCATGGCGGCGGTATCTTTTCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTgcg > 1:755811/1‑69 (MQ=255)
ggcggTATCTTTTCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTc < 1:2229375/68‑1 (MQ=255)
ggcggTATCTTTTCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTc < 1:2045275/68‑1 (MQ=255)
ggcggTATCTTTTCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTc < 1:470540/68‑1 (MQ=255)
ggcggTATCTTTTCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTc < 1:593848/68‑1 (MQ=255)
ggcggTATCTTTTCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTc < 1:2599199/68‑1 (MQ=255)
ggcggTATCTTTCCTACCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCg < 1:1011434/69‑1 (MQ=255)
ggcggTATCTTTCCGACCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCg < 1:2683148/69‑1 (MQ=255)
ggcggTATCTTTCCGACCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCg < 1:105167/69‑1 (MQ=255)
ggcggTATCTTTCCGACCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCg < 1:433436/69‑1 (MQ=255)
ggcggTATCTTTCCGACCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCg < 1:2413642/69‑1 (MQ=255)
ggcggTATCTTTCCGACCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCg < 1:3044911/69‑1 (MQ=255)
ggcggTATCTTTCCGACCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCg < 1:2263285/69‑1 (MQ=255)
gcggTATCTTTTCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTc < 1:2707101/67‑1 (MQ=255)
tCTTTTCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCGCTGGGCt < 1:2703020/69‑1 (MQ=255)
tCTTTTCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCGCTGGGCt < 1:1127855/69‑1 (MQ=255)
tCTTTTCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCGCTGGGCt < 1:1667805/69‑1 (MQ=255)
tCTTTTCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCGCTGGGCt < 1:1705432/69‑1 (MQ=255)
tCTTTTCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCGCTGGGCt < 1:2417711/69‑1 (MQ=255)
tCTTTTCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCGCTGGGCt < 1:246374/69‑1 (MQ=255)
tCTTTTCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCGCTGGGCt < 1:2615796/69‑1 (MQ=255)
ttttCTCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCGCTGGGCtt > 1:932343/1‑68 (MQ=255)
ttttCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCGCTGGGCtt > 1:1010416/1‑68 (MQ=255)
ttttCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCGCTGGGCTTc > 1:154776/1‑69 (MQ=255)
ttttCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCGCTGGGCTTc > 1:1333548/1‑69 (MQ=255)
|
CGCCTGGCGTTTTAACGGCAGAACAGCCAGCCCTTCCAGCATGGCGGCGGTATCTTTTCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCGCTGGGCTTC > minE/447464‑447586
|
| 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
