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 |
|
A12 F1 I1 R1
|
760 |
58.2 |
3022526 |
90.8% |
2744453 |
102.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
4,540,984 |
(A)7→6 |
coding (28/603 nt) |
fimB → |
tyrosine recombinase/inversion of on/off regulator of fimA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 4,540,978 | 0 | A | . | 98.0%
| 194.8
/ ‑2.3
| 50 | coding (22/603 nt) | fimB | tyrosine recombinase/inversion of on/off regulator of fimA |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base . (24/25); total (24/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
TAGTTATTAAGCAAACGTTCGCTTTTATAAACATAATCAGGATAAAAATGTTGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAACAAAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGCCTCATGCAGCACGTAATTATTGTCTGACTTTGCTTTGTTTTATTCATGGTTTCCGGGCGAGTGAAA > NC_000913/4540849‑4541107
|
tagttaTTAAGCAAACGTTCGCTTTTATAAACATAATCAGGATAAAAATGTTGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAACaaaaaaggaa < 2:338371/139‑5 (MQ=255)
tattaAGCAAACGTTCGCTTTTATAAACATAATCAGGATAAAAATGTTGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTc < 1:876014/139‑1 (MQ=255)
aaaCGTTCGCTTTTATAAACATAATCAGGATAAAAATGTTGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGAcc < 2:770629/137‑1 (MQ=255)
aaaCGTTCGCTTTTATAAACATAATCAGGATAAAAATGTTGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGAcc > 1:770629/1‑137 (MQ=255)
aaaCATAATCAGGATAAAAATGTTGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCa < 1:1208156/139‑1 (MQ=255)
tAATCAGGATAAAAATGTTGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCt < 2:944536/139‑1 (MQ=255)
aaTCAGGATAAAAATGTTGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAAt > 2:302508/1‑131 (MQ=255)
aaTCAGGATAAAAATGTTGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAAt < 1:302508/131‑1 (MQ=255)
tCAGGATAAAAATGTTGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCt > 2:544858/1‑136 (MQ=255)
tCAGGATAAAAATGTTGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCt < 1:544858/136‑1 (MQ=255)
cAGGATAAAAATGTTGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTaaa < 1:506603/139‑1 (MQ=255)
gATAAAAATGTTGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAACaaaaaaggaa < 2:1475536/99‑5 (MQ=255)
gATAAAAATGTTGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAACaaaaaaggaa > 1:1475536/1‑95 (MQ=255)
aTAAAAATGTTGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATG‑AGAATAAGGCTGATAACaaaaaagg < 1:245646/95‑3 (MQ=255)
aTAAAAATGTTGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATG‑AGAATAAGGCTGATAACaaaaaagg > 2:245646/1‑93 (MQ=255)
tGTTGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAACaaaaaaggaa < 2:1329883/91‑5 (MQ=255)
tGTTGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAACaaaaaaggaa > 1:1329883/1‑87 (MQ=255)
ttGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATa < 2:924372/103‑1 (MQ=255)
ttGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATa > 1:924372/1‑103 (MQ=255)
ttGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCg > 1:243837/1‑139 (MQ=255)
ttGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCg > 1:232862/1‑139 (MQ=255)
tGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCgg < 2:130019/139‑1 (MQ=255)
tGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCgg < 1:743521/139‑1 (MQ=255)
gCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGCCTCATgc < 2:243837/139‑1 (MQ=255)
tAACCCAGCACAGCTAGTGCGCGTCTGTAGTTATAAGGGAAAAAAGATGAAGAATAAGGCTGGTAACAAAAAAAGGAACTTCCTTACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGCCTCATgca < 2:1286729/139‑1 (MQ=255)
tAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGCCTCATgcag < 2:258810/139‑1 (MQ=255)
aGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAg < 2:487392/86‑1 (MQ=255)
aGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAg > 1:487392/1‑86 (MQ=255)
tcacaGCTAGTGCGCGTCTGTAATTGTAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTg < 1:922677/76‑1 (MQ=255)
gCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTg > 2:922677/1‑77 (MQ=255)
gCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCa < 1:1150433/82‑1 (MQ=255)
gCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCa > 2:1150433/1‑82 (MQ=255)
gCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGCCTCATgcagca > 1:785227/1‑134 (MQ=255)
gCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGCCTCATgcagca < 2:785227/134‑1 (MQ=255)
cTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGt > 2:579010/1‑80 (MQ=255)
cTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGt < 1:579010/80‑1 (MQ=255)
tAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGCCTCATGCAGCACGTAATTATTGt > 1:1032647/1‑139 (MQ=255)
cgTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGGATCACTCCTTAAAGCAGCAAATACCGGGCCTCATGCAGCACGTAATTATTGTCTGActt > 2:914579/1‑139 (MQ=255)
cgTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGCCTCATGCAGCACGTAATTATTGTCTGActt > 1:1315849/1‑139 (MQ=255)
tCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGCCTCATGCAGCACGTAATTATTGTCTGActttg > 1:643358/1‑139 (MQ=255)
tAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGCCTCATGCAGCACg < 1:380084/116‑1 (MQ=255)
tAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGCCTCATGCAGCACg > 2:380084/1‑116 (MQ=255)
aaGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGCCTCATgcagca > 1:948990/1‑107 (MQ=255)
aaGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGCCTCATgcagca < 2:948990/107‑1 (MQ=255)
aGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGc > 1:95141/1‑95 (MQ=255)
aGGGAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGc < 2:95141/95‑1 (MQ=255)
ggAAAAACGTTGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAgcagca < 2:13704/83‑1 (MQ=255)
ggAAAAACGTTGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAgcagca > 1:13704/1‑83 (MQ=255)
ggAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGCCTCATGCAGCACGTAATTATTGTCTGACTTTGCTTTGTTTTATTCa < 2:232862/139‑1 (MQ=255)
ggAAAAACGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGCCTCATGCAGCACGTAATTATTGTCTGACTTTGCTTTGTTTTATTCa > 1:407048/1‑139 (MQ=255)
aaCGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGaaa > 2:1401540/1‑55 (MQ=255)
aaCGATGAAGAATAAGGCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGaaa < 1:1401540/55‑1 (MQ=255)
ggCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCa < 2:1077871/48‑1 (MQ=39)
ggCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCa > 1:1077871/1‑48 (MQ=255)
ggCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGCCTCATGCAGCACGTAat > 2:635198/1‑90 (MQ=255)
ggCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGCCTCATGCAGCACGTAat < 1:635198/90‑1 (MQ=255)
ggCTGATAAC‑AAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGCCTCATGCAGCACGTAATTATTGTCTGACTTTGCTTTGTTTTATTCATGGTTTCCGGGCGAGTGaaa > 2:518024/1‑139 (MQ=255)
|
TAGTTATTAAGCAAACGTTCGCTTTTATAAACATAATCAGGATAAAAATGTTGGATTATTGCTAACCCAGCACAGCTAGTGCGCGTCTGTAATTATAAGGGAAAAACGATGAAGAATAAGGCTGATAACAAAAAAAGGAACTTCCTGACCCATAGTGAAATCGAATCACTCCTTAAAGCAGCAAATACCGGGCCTCATGCAGCACGTAATTATTGTCTGACTTTGCTTTGTTTTATTCATGGTTTCCGGGCGAGTGAAA > NC_000913/4540849‑4541107
|
| 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
