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 |
445,484 |
T→C |
56.1% |
V744V (GTA→GTG) |
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 | 445,484 | 0 | T | C | 56.1%
| 10.9
/ 35.8
| 50 | V744V (GTA→GTG) | kdpD | fused sensory histidine kinase in two‑component regulatory system with KdpE |
| Reads supporting (aligned to +/- strand): ref base T (10/12); new base C (4/24); total (14/36) |
| Fisher's exact test for biased strand distribution p-value = 2.53e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AGAAAGATTGATGGGCGACGATAAACCCGGTTCCAGCATTTGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAACCACTCTTTCTTCAAATTAAAGCCGCCGGACTGAATTCGCGCCATA > minE/445427‑445547
|
agaAAGATTGATGGGCGACGATAAACCCGGTTCCAGCATTTGCAGCGCGCTGCCGACCACTTCTTCCa > 1:2827993/1‑68 (MQ=255)
agaAAGATTGATGGGCGACGATAAACCCGGTTCCAGCATTTGCAGCGCGCTGCCGACCACTTCTTCCAg > 1:940090/1‑69 (MQ=255)
agaAAGATTGATGGGCGACGATAAACCCGGTTCCAGCATTTGCAGCGCGCTGCCGACCACTTCTTCCAg > 1:2454250/1‑69 (MQ=255)
agaAAGATTGATGGGCGACGATAAACCCGGTTCCAGCATTTGCAGCGCGCTGCCGACCACTTCTTCCAg > 1:3415099/1‑69 (MQ=255)
ttGATGGGCGACGATAAACCCGGTTCCAGCATTTGCAGCGCGCTTCCGACTACTTCTTCCAGCGTTAAc < 1:2396229/69‑1 (MQ=255)
ttGATGGGCGACGATAAACCCGGTTCCAGCATTTGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAAc < 1:2328282/69‑1 (MQ=255)
ttGATGGGCGACGATAAACCCGGTTCCAGCATTTGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAAc < 1:1417814/69‑1 (MQ=255)
ttGATGGGCGACGATAAACCCGGTTCCAGCATTTGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAAc < 1:817775/69‑1 (MQ=255)
ttGATGGGCGACGATAAACCCGGTTCCAGCATTTGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAAc < 1:1246334/69‑1 (MQ=255)
ttGATGGGCGACGATAAACCCGGTTCCAGCATTTGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAAc < 1:1640513/69‑1 (MQ=255)
aTGGGCGACGATAAACCCGGTTCCAGCATTTGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAACCAc > 1:1325851/1‑69 (MQ=255)
aTGGGCGACGATAAACCCGGTTCCAGCATTTGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAACCAc > 1:2515655/1‑69 (MQ=255)
aTGGGCGACGATAAACCCGGTTCCAGCATTTGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAACCAc > 1:707689/1‑69 (MQ=255)
cgacgaTAAACCCGGTTCCAGCATTTGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAACCACtcttt < 1:2257118/69‑1 (MQ=255)
aaaCCCGGTTCCAGCATTTGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAACCACTCTTTCTTCaa > 1:2272014/1‑68 (MQ=255)
gTTCCAGCATTTGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAACCACTCTTTCTTCAAATTAAAgc > 1:2960362/1‑69 (MQ=255)
tGCAGCGCGCTGCCGACTACTTCTTCCATCGTTAACCACTCTTTCTTCAAATTAAAGCCGCCGGACTGa > 1:2092128/1‑69 (MQ=255)
tGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAACCACtctttc > 1:2920677/1‑45 (MQ=255)
tGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAACCACTCTTTCTTCAAATTAAAGCCGCCGGACTGa > 1:561032/1‑69 (MQ=255)
tGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAACCACTCTTTCTTCAAATTAAAGCCGCCGGACTGa > 1:1533727/1‑69 (MQ=255)
tGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAACCACTCTTTCTTCAAATTAAAGCCGCCGGACTGa > 1:2435880/1‑69 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:2828260/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:799801/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:1170635/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:3082984/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:3379840/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:3394483/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:580201/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:658497/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:704801/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:741082/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:275532/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:1251760/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:1315787/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:1412013/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:1889575/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:1954883/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:2104334/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:2114041/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:2176962/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:2209128/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:2284351/42‑1 (MQ=255)
tGCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:2576844/42‑1 (MQ=255)
gCAGCGCGCTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:302227/41‑1 (MQ=255)
cgcgcTGCCGACCACTTCTTCCAGCGTTAACCActct < 1:2814172/37‑1 (MQ=255)
gACTACTTCTTCCAGCGTTAACCACTCTTTCTTCAAATTAAAGCCGCCGGACTGAATTCGCGCCata < 1:18318/67‑1 (MQ=255)
gACTACTTCTTCCAGCGTTAACCACTCTTTCTTCAAATTAAAGCCGCCGGACTGAATTCGCGCCata < 1:1759716/67‑1 (MQ=255)
gACTACTTCTTCCAGCGTTAACCACTCTTTCTTCAAATTAAAGCCGCCGGACTGAATTCGCGCCata < 1:1625432/67‑1 (MQ=255)
gACTACTTCTTCCAGCGTTAACCACTCTTTCTTCAAATTAAAGCCGCCGGACTGAATTCGCGCCata < 1:243477/67‑1 (MQ=255)
gACTACTTCTTCCAGCGTTAACCACTCTTTCTTCAAATTAAAGCCGCCGGACTGAATTCGCGCCata < 1:116830/67‑1 (MQ=255)
|
AGAAAGATTGATGGGCGACGATAAACCCGGTTCCAGCATTTGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAACCACTCTTTCTTCAAATTAAAGCCGCCGGACTGAATTCGCGCCATA > minE/445427‑445547
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
