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 |
|
A8 F1 I2 R1
|
765 |
53.2 |
2691310 |
93.4% |
2513683 |
103.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
723,528 |
(T)8→9 |
coding (887/2685 nt) |
kdpD ← |
fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 723,520 | 1 | . | T | 94.9%
| 116.8
/ ‑0.1
| 39 | coding (895/2685 nt) | kdpD | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| Reads supporting (aligned to +/- strand): ref base . (1/1); new base T (20/17); total (21/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.99e-01 |
AATAATCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGATGCATA > NC_000913/723392‑723651
|
aataatCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑tttttttttc > 2:211079/1‑137 (MQ=255)
atCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGt < 2:823474/139‑1 (MQ=255)
ttGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAg < 1:976574/139‑1 (MQ=255)
aTTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTgcag > 2:174723/1‑139 (MQ=255)
tGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTgcagggca > 1:124788/1‑139 (MQ=255)
cACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTGCAGGGCAgggg < 2:124788/139‑1 (MQ=255)
aCGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGGAAGCGGTGCAGGGCAGGGGt > 2:21958/1‑139 (MQ=255)
cGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGtt < 1:211079/139‑1 (MQ=255)
tAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTgcagggcagg > 2:477314/1‑129 (MQ=255)
tAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTgcagggcagg < 1:477314/129‑1 (MQ=255)
tAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTgcagggcag < 2:739499/128‑1 (MQ=255)
tAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTgcagggcag > 1:739499/1‑128 (MQ=255)
cTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAg > 1:972543/1‑102 (MQ=255)
cTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAg < 2:972543/102‑1 (MQ=255)
tctTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACg > 1:838815/1‑139 (MQ=255)
aaGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGc < 2:838815/139‑1 (MQ=255)
ttGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAg < 2:1214513/75‑1 (MQ=255)
ttGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAg > 1:1214513/1‑75 (MQ=255)
ttGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAgcc > 2:1314586/1‑139 (MQ=255)
ttGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAgcc > 2:287167/1‑139 (MQ=255)
tGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTgcagggcagg > 1:792209/1‑88 (MQ=255)
tGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTgcagggcagg < 2:792209/88‑1 (MQ=255)
cGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAg > 2:43531/1‑71 (MQ=255)
cGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAg < 1:43531/71‑1 (MQ=255)
tcCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTGCAGGGCAgggg > 1:504772/1‑83 (MQ=255)
tcCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTGCAGGGCAgggg < 2:504772/83‑1 (MQ=255)
cgcgCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTgc > 1:336418/1‑139 (MQ=255)
aGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGAcc > 1:562979/1‑139 (MQ=255)
tCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAg > 1:774418/1‑104 (MQ=255)
tCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAg < 2:774418/104‑1 (MQ=255)
gACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGc < 2:562979/139‑1 (MQ=255)
cTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGtt < 2:1001675/52‑1 (MQ=255)
cTGAGAATTGCCCGACGTTTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGtt > 1:1001675/1‑52 (MQ=255)
ttGCCCGACGTTTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGa < 1:707206/136‑1 (MQ=255)
ttGCCCGACGTTTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGa > 2:707206/1‑136 (MQ=255)
ttGCCCGACGTTTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGa < 1:126067/136‑1 (MQ=255)
ttGCCCGACGTTTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCCCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGa > 2:126067/1‑136 (MQ=255)
cccGACGTTTTTTTTTCCGGTAAGCGGTgcagggcagg > 2:1134706/1‑38 (MQ=37)
cccGACGTTTTTTTTTCCGGTAAGCGGTgcagggcagg < 1:1134706/38‑1 (MQ=255)
cccGACGTTTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGATGCATa > 2:1250616/1‑139 (MQ=255)
|
AATAATCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGATGCATA > NC_000913/723392‑723651
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
