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 |
|
A2 F27 I0 R1
|
51 |
79.9 |
2053078 |
82.8% |
1699948 |
215.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
4,378,890 |
C→A |
23.8% |
A19S (GCT→TCT) |
ampC ← |
penicillin‑binding protein; beta‑lactamase, intrinsically weak |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 4,378,890 | 0 | C | A | 23.8%
| 86.5
/ 6.2
| 40 | A19S (GCT→TCT) | ampC | penicillin‑binding protein; beta‑lactamase, intrinsically weak |
| Reads supporting (aligned to +/- strand): ref base C (21/9); new base A (2/8); total (23/17) |
| Fisher's exact test for biased strand distribution p-value = 9.29e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01 |
CCTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGAACATAGGGTCTGGTTTCC‑ATACAAAACGGCCCGCCATAGGCGGGCCGGATTTACATTGGCGATGCGTTAGA‑TTGTAACGACACCAATCAGCGTGACAACTGTCAGGATAGCAGCCAGACCGTAGAAAACCCATTTGCCCGCAGGTACGTGGATTTTCAGATCGTGCATCGCGTGGTGCATA > NC_000913/4378655‑4379121
|
ccTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTACTAAGGTTTACCCTGATAAATTACCGCCACCGCCCTACCCGGGATCTTTTGTTGTCCTATAAGCGGGGTAATTGTGCGATGAACAAAATGTTTTATTTGTTGAGGGGCCGCaaa > 2:486529/1‑239 (MQ=255)
aTAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAATTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTCTAAGCGGGGTAATTGTGCGATGTACATAATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCa > 1:421821/1‑239 (MQ=255)
tCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTTGGCGGTGCACAATATCGTTGTTTTTTTTAGGGGCAGAAAATGTGGGGAAAAAggg > 2:95819/1‑238 (MQ=255)
aGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCGGAAAATGTGGAGAAAGAGGGGGtaa‑ttaa > 1:908188/1‑239 (MQ=255)
gCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAgg > 1:778614/1‑239 (MQ=255)
tttGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGAAAAGTAATAAGGTTTACCCTGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCCCTCTAAACGGGGTAATTGTGCGATCCACAATTTCGTTGATTTGTTGCGGGGCCGCAAATGTGGAGCAAGAGGGGGGAATTTAAAAAGGCG‑AGAGcg > 2:22080/1‑236 (MQ=255)
tGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGtaa‑ttaa > 1:536942/1‑191 (MQ=255)
ggCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGCCGTTTTGAACAAAGGGCCTGGTTTCC‑TTACAAACCGGACCGccta > 1:268970/1‑237 (MQ=255)
tgctTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCGGAGCGTCGTTTTGAACATAGGGACTGGTTTCC‑ATACAAAACGGCCCGCCATAgg > 1:96403/1‑239 (MQ=255)
tgctTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGAACATAGGGTCTGGGTTCC‑ATACAAAACGGCCCGCCATAgg > 1:829904/1‑239 (MQ=255)
ctTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGAACATAGGGTCTGGTTTCC‑ATACAAAACGGCCCGCCCTAGCCg > 1:653885/1‑239 (MQ=255)
cAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCaga > 1:368717/1‑160 (MQ=255)
ggTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGAACATAGGGTCTGGTTTCC‑ATACAAAACGGCCCGCCCTAGGCCGGCCGGATTTTCATTgggggatgggtt > 1:638491/1‑229 (MQ=255)
aGTAATAAGGTTTACCCTGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGAACATAGGGTCTGGTGTCC‑ATACAAAACAGCCCGCCCTAGGCGGGCCGGGTTTCACTTGGCCAGGCGTTAAA‑TTg > 1:928860/1‑239 (MQ=255)
tACCCTGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGAACATAGGGGCTGGTTTCC‑ATACAAAACGGCCCGCCATAGGCGGGGCGGGGTTTCAATGTCGATGTGATAGA‑AGGGAACAAGACCaa > 2:970221/1‑239 (MQ=255)
tACCCTGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGAACAAAGGGGCTGGTTTCC‑ATACAAAACGGCCCGCCATAGGCGGGCCGGGTTTTCATTTGCGGAGCGTTGGA‑TTGTTAAGAccccca > 1:678793/1‑237 (MQ=255)
tAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGAACATAGGGTCTGGTTTCC‑ATACAAAACGGCCCGCCATAGGCGGGCCGGATTTACATTTGCGATGCGGTAGA‑TTGTAAAGAGACCAAACAGCGTg > 1:205425/1‑239 (MQ=255)
ttccccccccccgcctTCCCCGGGTTTTTTTGTTGCTTAATAAGCGGGGTAATTGGGCGAAGCACAATATCGTTGATTTGTTGAGGGGCAGCAAAGGTGGAGCAAGAGGCGTTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGAACATGGGGTCTGGTTTCC‑ATACAAAACGGCCCGCCATAGGCGGGCCGGATTTACATTGGCGATGCGTTAGA‑TTGTAACGACACCAATCAGCGTGACa < 2:205425/229‑1 (MQ=255)
ccaccccgccaTCCCCGGGTTTTTTTTTTGCTTTAAAAGGGGGTTAATTGGGGGATGCAAAATGTTGTTTATTTGTTGGGGGGAAGCAAAGGGGGATCAGGGGGCGGTAA‑TTAAAAAGGCGCAGAGGGTCTTTTTGAACATGGGGTC‑GGTTTCCAATACAAAAGGGCCCGCCATAGGCGGGCCGGATTTACATTGGCGATGCGTTAGA‑TTGTAACGACACCAATCAGCGTGACAACTGt < 2:638491/234‑1 (MQ=255)
cggcaTCCCCGGGATTTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACATTATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGAACATAGGGTCTGGTTTCC‑ATACAAAACGGCCCGCCATAGGCGGGCCGGATTTACATTGGCGATGCGTTAGA‑TTGTAACGACACCAATCAGCGTGACAACTGTCAGGAt < 1:486529/236‑1 (MQ=255)
cgccaTACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGAACAt < 1:430276/135‑1 (MQ=255)
cgccaTACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGAAAAt > 2:430276/1‑135 (MQ=255)
ccctttccccGGGTTTTTTTGTTGCTCTAAAGGGGGGGTAATTGTGGGATGCAAAATATGGTGGATTGGTTGAGGGGGAGAAAATGTGGAGAAAGGGGGGGTAA‑TTAATAAGGCCCAGGGCGTGGTTTTGAACATAGGGTCTGGTTTCC‑ATACAAAACGGCCCGCCATAGGCGGGCCGGATTTACATTGGCGATGCGTTAGA‑TTGTAACGACACCAATCAGCGTGACAACTGTCAGGAt < 2:829904/232‑1 (MQ=255)
gggATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAgg > 1:4935/1‑88 (MQ=255)
gggATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAgg < 2:4935/88‑1 (MQ=255)
gggATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGa > 2:916224/1‑121 (MQ=255)
gggATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGa < 1:916224/121‑1 (MQ=255)
gggATCTTTGGTTGCTCTATAGGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGAAAATGGGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGAACATAGGGTCTGGTTTCC‑ATACAAAACGGCCCGCCATAGGCGGGCCGGATTTACATTGGCGATGCGTTAGA‑TTGTAACGACACCAATCAGCGTGACAACTGTCAGGATAGCAGCCAGa < 1:970221/239‑1 (MQ=255)
ttataAGCGGGGTAATTGTGCGATGCAAAATATCGTTGATTTGTTGGGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGAACATAGGGTCTGGTTTCC‑ATACAAAACGGCCCGCCATAGGCGGGCCGGATTTACATTGGCGATGCGTTAGA‑TTGTAACGACACCAATCAGCGTGACAACTGTCAGGATAGCAGCCAGACCGTAGa < 1:759755/229‑1 (MQ=255)
ggTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGAACATAGGGTCTGGTTTCC‑ATACAAAACGGCCCGCCATAGGCGGGCCGGGTTTACATTTGCGATGCGTTTGATTTGAACCGAC‑CCAATCAACGGGACAACTGTCAGGAAAGAAGCCAAACCCTGAAAAAACCACTTGGCCGCCgg > 1:887233/1‑239 (MQ=255)
gTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGAACATAGGGTCTGGTTTCC‑ATACAAAACGGCCCGCCATAGGCGGGCCGGGTTTACATTTGCGCTGCGTTAGA‑ATTTAAAGACACCAATCAGCGGGACAAACCTCAGGGTAGCAACCAGACCGTTAAAAAACCACTTTCCCCCAggg > 1:979529/1‑238 (MQ=255)
gTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGAACATAGGGTCTGGTTTCC‑ATACAAAACGGCCCGCCATAGGCGGGCCGGATTTACATTGGCGAACGGTTAGA‑TTGTAAAGAAACCAAACAGCGTGGCAAATGGCCGGGTAACAGCCAAACCCTAGAAAACCCATTTGCCCCCAggg > 1:475811/1‑238 (MQ=255)
aTTGTGGGACGCAAAATCTTGTTGATTGTTTGGGGGGAAGAAAATGGGGAGAAAGGGGCGGTAA‑TTAATAAGGCGAAGAGCGTCGTTTTGAACATAGGGTCTGGTTTCC‑ATACAAAACGGCCCGCCATAGGCGGGCCGGATTTACATTGGCGATGCGTTAGA‑TTGTAACGACACCAATCAGCGTGACAACTGTCAGGATAGCAGCCAGACCGTAGAAAACCCATTTGCCCGCAGGTACg < 1:288296/239‑1 (MQ=255)
tttttggagggggCAACAAAGGGGGAGCAAGGGGCGGTAA‑TTAATAAGGCCCAGGGCGTCGTTTTGAACATGGGGTCTGGTTTCC‑ATAAAAAACGGCCCGCCATAGGCGGGCCGGATTTACATTGGCGATGCGTTAGA‑TTGTAACGACACCAATCAGCGTGACAACTGTCAGGATAGCAGCCAGACCGTAGAAAACCCATTTGCCCGCAGGTACGTGGATTTTCAGATCGTGCATcgcg < 1:88309/230‑1 (MQ=255)
tttGTTGAGGGGCAGAAAATGGGGAGCAAGAGGGAGTAA‑TTAATAAGGCGCAGGGCGTCGTTTTGAAAATAGGGTCTGGTTTCC‑ATACAAAACGGCCCGCCATAGGCGGGCCGGATTTACATTGGCGATGCGTTAGA‑TTGTAACGACACCAATCAGCGTGACAACTGTCAGGATAGCAGCCAGACCGTAGAAAACCCATTTGCCCGCAGGTACGTGGATTTTCAGATCGTGCATCGCgt < 1:24730/239‑1 (MQ=255)
tttgGGGGGAAGAAAAGGGGGAGAAAGGGGGGGGAA‑TAAAGAAGGGGCAGAGCGTGGTTTGGAAAATGGGGTTTGGTTTCC‑ATAAAAAACGGGCCGCCATAGGCGGGCCGGATTTACATTGGCGATGCGTTAGA‑TTGTAACGACACCAATCAGCGTGACAACTGTCAGGATAGCAGCCAGACCGTAGAAAACCCATTTGCCCGCAGGTACGTGGATTTTCAGATCGTGCATCGCgtggt < 2:926589/238‑1 (MQ=255)
ggtgAGGGGAAGAAAATGGGGAGCAAGGGGCGGAAA‑TTAAAAAGGCGAAGGGCGTCGTTTTGAACAAAGGGTCTGGTTTCC‑ATACAAAACGGCCCGCCATAGGCGGGCCGGATTTACATTGGCGATGCGTTAGA‑TTGTAACGACACCAATCAGCGTGACAACTGTCAGGATAGCAGCCAGACCGTAGAAAACCCATTTGCCCGCAGGTACGTGGATTTTCAGATCGTGCATCGCgtggt < 1:95819/237‑1 (MQ=255)
ttgAGGGGCAGAAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGAACATAGGGTCTGGTTTCC‑ATACAAAACGGCCCGCCATAGGCGGGCCGGATTTACATTGGCGATGCGTTAGa < 1:138649/133‑1 (MQ=255)
ggggCAAAAAAGGGGGAGAAAGAGGTGGTAA‑TTAATAGGGGCCAGAGCGTCTTTTTGAACAGAGGTTTTGGTTTCC‑ATACAAAACGGCCCGCCATAGGCGGGCCGGATTTACATTGGCGATGCGTTAGA‑TTGTAACGACACCAATCAGCGTGACAACTGTCAGGATAGCAGCCAGACCGTAGAAAACCCATTTGCCCGCAGGTACGTGGATTTTCAGATCGTGCATCGCGTGGTGCAt < 1:598813/238‑1 (MQ=255)
gggCAGCAAATGGGGAGCAAGGGTCGGTAA‑TTAAAAAGGCGCAGAGCGTGGTTTTGAACATAGGTTGTGGTTTCC‑ATACAAAACGGCCCGCCATAGGCGGGCCGGATTTACATTGGCGATGCGTTAGA‑TTGTAACGACACCAATCAGCGTGACAACTGTCAGGATAGCAGCCAGACCGTAGAAAACCCATTTGCCCGCAGGTACGTGGATTTTCAGATCGTGCATCGCGTGGTGCATa < 1:932181/238‑1 (MQ=255)
|
CCTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAA‑TTAATAAGGCGCAGAGCGTCGTTTTGAACATAGGGTCTGGTTTCC‑ATACAAAACGGCCCGCCATAGGCGGGCCGGATTTACATTGGCGATGCGTTAGA‑TTGTAACGACACCAATCAGCGTGACAACTGTCAGGATAGCAGCCAGACCGTAGAAAACCCATTTGCCCGCAGGTACGTGGATTTTCAGATCGTGCATCGCGTGGTGCATA > NC_000913/4378655‑4379121
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
