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 |
|
A3 F1 I2 R1
|
777 |
59.2 |
2955938 |
92.5% |
2734242 |
106.9 |
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 | 96.4%
| 169.4
/ ‑0.6
| 55 | 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 . (0/2); new base T (24/29); total (24/31) |
| Fisher's exact test for biased strand distribution p-value = 4.99e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01 |
GCGACCGAGAATAATCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑G‑‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGATGCATAA > NC_000913/723383‑723652
|
gCGACCGAGAATAATCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑G‑‑t > 2:73225/1‑139 (MQ=255)
aataatCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑G‑‑ttttttttt < 2:347351/138‑2 (MQ=255)
aataatCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑G‑‑ttttttttt > 1:347351/1‑137 (MQ=255)
ttGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAg < 2:114658/139‑1 (MQ=255)
ttGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAg < 1:24011/139‑1 (MQ=255)
ccGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCgg > 2:557580/1‑139 (MQ=255)
gggaTTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATAAAAAAGTGTTGCCGTCCCCGCCCCCATTTCCTGCGCCAGACGTAAGGCGTTGAGAATTGCCCGACTT‑‑TTTTTTTTCCGGTAAGCGGTg < 2:1450829/137‑1 (MQ=255)
gagaTTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTg < 1:733512/139‑1 (MQ=255)
gagaTTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTg < 1:1367918/139‑1 (MQ=255)
aTGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTgcagggc < 1:474936/139‑1 (MQ=255)
gTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTgcagggcag < 1:557580/139‑1 (MQ=255)
aCGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTg > 2:305713/1‑127 (MQ=255)
aCGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTg < 1:305713/127‑1 (MQ=255)
cGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGtt > 2:1321092/1‑139 (MQ=255)
cGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGtt < 2:369122/139‑1 (MQ=255)
cGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGtt < 1:73225/139‑1 (MQ=255)
cTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGcc < 1:1321092/139‑1 (MQ=255)
tctcTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGa < 2:637440/139‑1 (MQ=255)
tctTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACg > 1:608495/1‑139 (MQ=255)
gCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTAccc > 2:1092557/1‑139 (MQ=255)
cTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAg < 2:485557/90‑1 (MQ=255)
cTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAg > 1:485557/1‑90 (MQ=255)
tgtTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAg > 1:1334565/1‑139 (MQ=255)
tgtTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAg > 1:763837/1‑139 (MQ=255)
tgtTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAg > 2:447214/1‑139 (MQ=255)
tgtTGCCGTCTCCGCGCCCAGTTCATGCGCCAGACGTAAGGCGCTGAGAATGGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCTAGCCGTGACGCCAg > 2:899189/1‑139 (MQ=255)
cGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAgccgcgc > 2:62839/1‑139 (MQ=255)
tctcCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGCC‑GT‑TTTTTTTTTCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAgccgcgccg < 2:763837/139‑1 (MQ=255)
tcCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAg < 1:303903/67‑1 (MQ=255)
tcCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAg > 2:303903/1‑67 (MQ=255)
tcCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAgggg > 1:761843/1‑83 (MQ=255)
tcCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAgggg < 2:761843/83‑1 (MQ=255)
tcCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGttt < 1:1090298/86‑1 (MQ=255)
tcCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGttt > 2:1090298/1‑86 (MQ=255)
gcgcCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTgcg < 1:1092557/139‑1 (MQ=255)
gcgcCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTgcg < 2:487296/139‑1 (MQ=255)
ttCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTgcagggca > 2:1386758/1‑68 (MQ=255)
ttCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTgcagggca < 1:1386758/68‑1 (MQ=255)
ccAGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGCTTTTCGc < 2:608495/139‑1 (MQ=255)
aGACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTg > 1:171791/1‑139 (MQ=255)
gACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTgcagggcagg < 2:199173/59‑1 (MQ=255)
gACGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTgcagggcagg > 1:199173/1‑59 (MQ=255)
cGTAAGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCg < 1:62839/139‑1 (MQ=255)
aaGGCGCTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGgtg > 2:1074521/1‑139 (MQ=255)
cTGAGAATTGCCCGAC‑GTTTTTTTTTTCCAGTAAGCGGTgcagggcag < 2:943466/48‑1 (MQ=25)
cTGAGAATTGCCCGAC‑GTTTTTTTTTTCCAGTAAGCGGTgcagggcag > 1:943466/1‑48 (MQ=37)
cTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTg < 2:1457877/39‑1 (MQ=37)
cTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTg > 1:1457877/1‑39 (MQ=37)
cTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATgg > 2:975075/1‑139 (MQ=255)
cTGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATgg > 2:551658/1‑139 (MQ=255)
tGAGAATTGCCCGACAT‑‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGc < 1:143871/139‑1 (MQ=255)
tGAGAATTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGc < 2:1193593/139‑1 (MQ=255)
aTTGCCCGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGATg < 1:1074521/139‑1 (MQ=255)
cccGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGtt < 1:1095578/42‑1 (MQ=255)
cccGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGtt > 2:1095578/1‑42 (MQ=38)
cccGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGa > 1:1105426/1‑133 (MQ=255)
cccGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGa < 2:1105426/133‑1 (MQ=255)
ccGAC‑GT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCCGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGATGCATaa < 1:899189/139‑1 (MQ=255)
|
GCGACCGAGAATAATCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGAC‑G‑‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGATGCATAA > NC_000913/723383‑723652
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
