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 |
|
A11 F1 I2 R1
|
760 |
67.6 |
3323148 |
92.7% |
3080558 |
109.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,484,897 |
(C)6→7 |
coding (524/3594 nt) |
evgS → |
hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,484,891 | 1 | . | C | 93.2%
| 141.8
/ 2.7
| 44 | coding (518/3594 nt) | evgS | hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
| Reads supporting (aligned to +/- strand): ref base . (2/1); new base C (18/23); total (20/24) |
| Fisher's exact test for biased strand distribution p-value = 5.83e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.58e-01 |
CGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑CCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACA > NC_000913/2484756‑2485013
|
cgccgcCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑ccc > 2:155155/1‑139 (MQ=255)
cgccgcCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑ccc > 1:919364/1‑139 (MQ=255)
cgccgcCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑ccc > 1:1528109/1‑139 (MQ=255)
ccgccTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑ccc‑cc > 1:820976/1‑139 (MQ=255)
ccTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑ccc‑cccca < 2:820976/139‑3 (MQ=255)
cATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATtca > 2:1141202/1‑139 (MQ=255)
tgctgcAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACGAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATtaatca > 1:1093647/1‑139 (MQ=255)
ctgcAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCatcaat < 1:89771/139‑1 (MQ=255)
ctgcAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCatcaat < 2:635233/139‑1 (MQ=255)
accaatccaTTGATAAGCAATTTTTGGGCGCTGGTAACCAGCCTTCAGGAGTCGATGCGACTGCTGACCTCACCAAAATCAGTAAATATTGCTCGGGTAGCGAATTA‑CCCTACCATACGAGCTAATTCATCAATCAttt > 2:217401/1‑139 (MQ=255)
accaTTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCaaa > 2:697312/1‑139 (MQ=255)
accaTTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCaaa > 1:930060/1‑139 (MQ=255)
tGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAAGCATTTCCAAAAGcaa > 1:1109513/1‑139 (MQ=255)
gATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑ccc‑cc > 2:1176241/1‑101 (MQ=255)
gATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑ccc‑cc < 1:1176241/101‑1 (MQ=255)
tACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑ccc‑cccca < 2:749334/98‑3 (MQ=255)
tACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑ccc‑cccca > 1:749334/1‑96 (MQ=255)
ttCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCatcaa > 1:1502602/1‑111 (MQ=255)
ttCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCatcaa < 2:1502602/111‑1 (MQ=255)
tCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCttt > 1:502432/1‑139 (MQ=255)
cGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTa < 1:155155/139‑1 (MQ=255)
cGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTa < 2:16361/139‑1 (MQ=255)
ggCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTAc > 2:286347/1‑139 (MQ=255)
gcTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑ccc‑cccca < 2:297101/86‑3 (MQ=255)
gcTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑ccc‑cccca > 1:297101/1‑84 (MQ=255)
gACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCa < 1:1141202/139‑1 (MQ=255)
gACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCa < 1:1236880/139‑1 (MQ=255)
tCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATcc > 2:653286/1‑139 (MQ=255)
tGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAg < 2:1047666/91‑1 (MQ=255)
tGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAg > 1:1047666/1‑91 (MQ=255)
tGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGtct > 1:470226/1‑139 (MQ=255)
ttACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGc < 1:697312/139‑1 (MQ=255)
tACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGca < 2:502432/139‑1 (MQ=255)
aCCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAACTTTATATCAGGCATTAGCATCCGTCTCAGCTGGGcac < 2:1109513/139‑1 (MQ=255)
ccTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGcaca < 2:930060/139‑1 (MQ=255)
aCCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGa < 2:415362/139‑1 (MQ=255)
aCCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAAGCATTAGCATCCGTCTCAGCTGGGCACAATGa < 2:1528109/139‑1 (MQ=255)
gTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCt < 1:374291/118‑1 (MQ=255)
gTAAATATTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCt > 2:374291/1‑118 (MQ=255)
atTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAg < 2:817648/59‑1 (MQ=255)
atTGCTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAg > 1:817648/1‑59 (MQ=255)
tGCTCGGGTAGCAAATTA‑CCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAAt < 2:876219/79‑1 (MQ=255)
tGCTCGGGTAGCAAATTA‑CCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAAt > 1:876219/1‑79 (MQ=255)
cTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGcac > 2:860411/1‑114 (MQ=255)
cTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGcac < 1:860411/114‑1 (MQ=255)
cTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAAca < 2:1636227/139‑1 (MQ=255)
cTCGGGTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAAca < 2:1406575/139‑1 (MQ=255)
gggTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGc < 2:170805/53‑1 (MQ=255)
gggTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGc > 1:170805/1‑53 (MQ=255)
gTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCa > 1:976728/1‑91 (MQ=255)
gTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGc > 1:860253/1‑107 (MQ=255)
gTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGc < 2:860253/107‑1 (MQ=255)
gTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGAtt < 1:118690/116‑1 (MQ=255)
gTAGCAAATTACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGAtt > 2:118690/1‑116 (MQ=255)
gTAGCAAATGACCCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCa < 2:976728/91‑1 (MQ=255)
|
CGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑CCC‑CCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACA > NC_000913/2484756‑2485013
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
