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 |
|
A9 F1 I2 R1
|
760 |
52.7 |
2744488 |
90.2% |
2475528 |
105.0 |
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 | 95.2%
| 135.6
/ ‑0.2
| 42 | coding (518/3594 nt) | evgS | hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
| Reads supporting (aligned to +/- strand): ref base . (1/1); new base C (21/19); total (22/20) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.42e-01 |
CTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACATCATTACCAG > NC_000913/2484753‑2485023
|
cTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTa < 2:130073/139‑1 (MQ=255)
gccgccTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑c‑ccc < 1:1127076/139‑1 (MQ=255)
ccgccTCTTAATAATGAGATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑c‑cccc > 1:1050718/1‑139 (MQ=255)
ccgccTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑c‑cccc > 2:999859/1‑139 (MQ=255)
ccgccTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑c‑cccc < 2:1318965/139‑1 (MQ=255)
cgccTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑c‑ccccc > 1:260554/1‑139 (MQ=255)
tctTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑c‑ccccccaga < 1:380787/139‑5 (MQ=255)
ctTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑c‑ccccccagac < 2:1326444/139‑6 (MQ=255)
tataagagacagttGCTGCAACCAAACCATTGATAATTACGTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCATAACCACTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACg < 2:914722/127‑1 (MQ=255)
cATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑c‑ccccccagac > 1:1226200/1‑123 (MQ=255)
cATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑c‑ccccccagac < 2:1226200/128‑6 (MQ=255)
ttGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATtcatc > 2:960346/1‑139 (MQ=255)
ctgcAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCC‑CCCCCAGACGAGGTAATTCatcaa > 1:1175219/1‑139 (MQ=255)
aaaccaTTGATAATTGCCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTACTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATtcatctgtctcttata > 1:914722/1‑128 (MQ=255)
aaaccaTTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCa < 2:1050718/139‑1 (MQ=255)
aTTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCC‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAg < 2:1175219/139‑1 (MQ=255)
ttACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTa > 1:348931/1‑139 (MQ=255)
tACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTAt > 1:1284699/1‑139 (MQ=255)
aCCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTAtc < 2:348931/139‑1 (MQ=255)
tCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAg > 2:690033/1‑123 (MQ=255)
tCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAg < 1:690033/123‑1 (MQ=255)
aaCCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTtata < 2:260554/139‑1 (MQ=255)
ccTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGc > 1:24671/1‑139 (MQ=255)
ttCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCAt > 2:617616/1‑139 (MQ=255)
gACTGAATGCAACCGCTTACCTCACCAAAGCCAGTAAGTAATGCTCAGGTACCAAATTAC‑C‑CCCCCAGTCGAGGTAATTCATCAATCATTTCCAAAAGTATCAAGTATCACTTTTACAAATTTATATCAGGCATTAGCa < 1:362996/139‑1 (MQ=255)
gACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCa > 1:268428/1‑139 (MQ=255)
tCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATcc > 1:1368582/1‑139 (MQ=255)
tGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑c‑ccccccaga > 2:685149/1‑58 (MQ=255)
tGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑c‑ccccccaga < 1:685149/62‑5 (MQ=255)
gACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAACAATTTCCAAAGGCAACAATTACCTCTTTTACAATTTTATATAAGCCATTAGCATCCTTCTCAg > 1:818254/1‑139 (MQ=255)
cGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTAt < 2:10658/95‑1 (MQ=255)
cGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTAt > 1:10658/1‑95 (MQ=255)
cTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTggg > 2:381758/1‑139 (MQ=255)
ttACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAAGTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGc < 1:864438/139‑1 (MQ=255)
cAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGc < 1:475594/74‑1 (MQ=255)
cAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGc > 2:475594/1‑74 (MQ=255)
cAGTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTa < 1:960346/139‑1 (MQ=255)
cAGTAAATATTGCTCGGGTAGCAAATTA‑‑CACCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACTAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTa < 2:923899/139‑1 (MQ=255)
gTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTAtt > 2:1052664/1‑139 (MQ=255)
gTAAATATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTAtt > 2:282652/1‑139 (MQ=255)
aaaTATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGAtt > 1:703169/1‑129 (MQ=255)
aaaTATTGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGAtt < 2:703169/129‑1 (MQ=255)
ttGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGgtagta < 2:1368582/139‑1 (MQ=255)
ttGCTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGgtagta < 2:1284699/139‑1 (MQ=255)
ttGCTCGGGTAGCAAATTA‑‑‑‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAAc > 2:1360735/1‑139 (MQ=255)
cTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCa < 1:871366/96‑1 (MQ=255)
cTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCa > 2:871366/1‑96 (MQ=255)
cTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAAca < 2:24671/139‑1 (MQ=255)
cTCGGGTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAAca > 1:67533/1‑139 (MQ=255)
gTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTAc > 2:282246/1‑69 (MQ=255)
gTAGCAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTAc < 1:282246/69‑1 (MQ=255)
cAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGcaa > 2:1216579/1‑49 (MQ=255)
cAAATTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGcaa < 1:1216579/49‑1 (MQ=255)
aaaTTAC‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACATCATTACcag < 1:1052664/139‑1 (MQ=255)
|
CTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑C‑CCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACATCATTACCAG > NC_000913/2484753‑2485023
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ 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
