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 I1 R1
|
63 |
64.8 |
2934156 |
93.7% |
2749304 |
111.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,994,960 |
C→T |
A134T (GCG→ACG) |
uvrY ← |
response regulator in two‑component regulatory system with BarA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,994,960 | 0 | C | T | 97.9%
| 152.3
/ ‑3.9
| 47 | A134T (GCG→ACG) | uvrY | response regulator in two‑component regulatory system with BarA |
| Reads supporting (aligned to +/- strand): ref base C (1/0); new base T (24/22); total (25/22) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.75e-01 |
AGCTGTTCTGAGATCTCATTGACCTTCTGGCCCTTGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGCCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGAACGAATCGCACTCACGACTTCCTGCGGAGCCGCGCCTTTGCTGAGGTAGCCCGCAGCACCGGCCTGCATGACTTTCG > NC_000913/1994839‑1995088
|
aGCTGTTCTGAGATCTCATTGACCTTCTGGCCCTTGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGt > 2:1435428/1‑139 (MQ=255)
aGCTGTTCTGAGATCTCATTGACCTTCTGGCCCTTGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGt < 1:466584/139‑1 (MQ=255)
gTTCTGAGATCTCATTGACCTTCTGGCCCCTGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTCGAGCGATGTCAGa > 1:1149921/1‑139 (MQ=255)
agaTCTCATTGACCTTCTGGCCCTTGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAAt > 1:1150300/1‑139 (MQ=255)
tcATTGACCTTCTGGCCCTTGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCg > 2:303851/1‑120 (MQ=255)
tcATTGACCTTCTGGCCCTTGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCg < 1:303851/120‑1 (MQ=255)
tcATTGACCTTCTGGCCCTTGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGCCATTTGTTGAGCGATGTCAGAAGCAATGTAAc > 1:80909/1‑139 (MQ=255)
gACCTTCTGGCCCTTGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGc < 2:1150300/139‑1 (MQ=255)
tCTGGCCCTTGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAg < 2:879438/117‑1 (MQ=255)
tCTGGCCCTTGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAg > 1:879438/1‑117 (MQ=255)
tGGCCCTTGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGc < 2:38722/132‑1 (MQ=255)
tGGCCCTTGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGc > 1:38722/1‑132 (MQ=255)
ttGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCAt < 1:18215/92‑1 (MQ=255)
ttGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCAt > 2:18215/1‑92 (MQ=255)
ttGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAg > 2:1387014/1‑100 (MQ=255)
ttGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACGGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAg < 1:1387014/100‑1 (MQ=255)
tGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAg > 2:725917/1‑111 (MQ=255)
tGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAg < 1:725917/111‑1 (MQ=255)
tGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGa > 1:1125841/1‑139 (MQ=255)
tGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGa > 1:455155/1‑139 (MQ=255)
gCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGAACGAATCGCACt > 1:1330986/1‑139 (MQ=255)
aaTCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGAACGAATCGCACTCACg < 2:455155/139‑1 (MQ=255)
tCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACg > 1:278842/1‑103 (MQ=255)
tCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACg < 2:278842/103‑1 (MQ=255)
tCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGc > 2:162648/1‑107 (MQ=255)
tCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGc < 1:162648/107‑1 (MQ=255)
aaTTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGAACGAATCGCACTCACGACTTCCt > 2:433408/1‑139 (MQ=255)
aTTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGAACGAATCGCACTCACGACTTCCTg < 2:827310/139‑1 (MQ=255)
ttCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGAACGAATCGCACTCACGACTTCCTGCGGAGcc < 2:1125841/139‑1 (MQ=255)
tCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACg > 1:647037/1‑89 (MQ=255)
tCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACg < 2:647037/89‑1 (MQ=255)
cAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAg > 1:16778/1‑78 (MQ=255)
cAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAg < 2:16778/78‑1 (MQ=255)
aCAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGAACGAATCGCACTCACGACTTCCTGCGGAGCCGCGcc > 1:1634/1‑139 (MQ=255)
aCTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGc > 1:803934/1‑60 (MQ=255)
aCTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGc < 2:803934/60‑1 (MQ=255)
tGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGAACGAATCGCACTCACGACTTCCTGCGGAGCCGCGCCTTTGCTGAGGTAg > 2:469773/1‑139 (MQ=255)
gggCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGAACGAATCGCACTCACGACt < 2:1422352/108‑1 (MQ=255)
gggCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGAACGAATCGCACTCACGACt > 1:1422352/1‑108 (MQ=255)
cTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGAACGAATCGCACTCACGACTTCCTGCGGAGCCGCGCCTTTGCTGAGGTAGCCCg < 1:1151257/139‑1 (MQ=255)
cTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGAACGAATCGCACTCACGACTTCCTGCGGAGCCGCGCCTTTGCTGAGGTAGCCCg < 2:1330986/139‑1 (MQ=255)
ttCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGAACGAATc > 2:634329/1‑76 (MQ=255)
ttCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGAACGAATc < 1:634329/76‑1 (MQ=255)
ttCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGAACGAATCGCACTCACGACTTCCTGCGGAGCCGCGCCTTTGCTGAGGTAGCCCGCAGCACCGGCCTGCATg > 2:798852/1‑139 (MQ=255)
tCGATCTGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGAACGAATCGCACTCACGACTTCCTGCGGAGCCGCGCCTTTGCTGAGGTAGCCCGCAGCACCGGCCTGCATGa > 2:95387/1‑139 (MQ=255)
tGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGAACGAATCGCACTCACGACTTCCTGCGGAGCCGCGCCTTTGCTGAGGTAGCCCGCAGCACCGGCCTGCATGACTTTCg < 2:483395/139‑1 (MQ=255)
tGGCTTAACGTCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGAACGAATCGCACTCACGACTTCCTGCGGAGCCGCGCCTTTGCTGAGGTAGCCCGCAGCACCGGCCTGCATGACTTTCg < 2:785594/139‑1 (MQ=255)
|
AGCTGTTCTGAGATCTCATTGACCTTCTGGCCCTTGGTGATCATCAGCATAATCTGCAATTCACGTTCAGACAAACTGGCAAATGGGCTTTCTGTTTTTTCTGGTTCGATCTGGCTTAACGCCATTTGTTGAGCGATGTCAGAAGCAATGTAACGCTGCCCTGAATAGACAGAACGAATCGCACTCACGACTTCCTGCGGAGCCGCGCCTTTGCTGAGGTAGCCCGCAGCACCGGCCTGCATGACTTTCG > NC_000913/1994839‑1995088
|
| 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
