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 F56 I1 R1
|
155 |
65.2 |
3164312 |
95.9% |
3034575 |
99.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
4,098,512 |
C→A |
R259R (CGC→CGA) |
rhaS → |
transcriptional activator of rhaBAD and rhaT |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 4,098,512 | 0 | C | A | 96.2%
| 174.8
/ ‑0.2
| 55 | R259R (CGC→CGA) | rhaS | transcriptional activator of rhaBAD and rhaT |
| Reads supporting (aligned to +/- strand): ref base C (1/1); new base A (28/23); total (30/25) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.17e-01 |
GCCCGACATCTGCTACGCCACAGCGAGGCCAGCGTTACTGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGCCGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGAATCTTCTCAACGTATTTGTACGCCATATTGC > NC_000913/4098417‑4098608
|
gCCCGACATCTGCTACGCCACAGCGAGGCCAGCGTTACTGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACgag > 1:1286173/1‑100 (MQ=255)
ccGACATCTGCTACGCCACAGCGAGGCCAGCGTTACTGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGagag > 1:501814/1‑100 (MQ=255)
ccGACATCTGCTACGCCACAGCGAGGCCAGCGTTACTGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGagag > 1:271260/1‑100 (MQ=255)
cGACATCTGCTACGCCACAGCGAGGCCAGCGTTACTGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGt > 1:1418775/1‑100 (MQ=255)
gCTACGCCACAGCGAGGCCAGCGTTACTGACATCGCCCATCGCTGTGGATTCAGCGATAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTg < 2:864375/99‑1 (MQ=255)
cTACGCCACAGCGAGGCCAGCGTTACTGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTg > 2:881404/1‑98 (MQ=255)
cTACGCCACAGCGAGGCCAGCGTTACTGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGt > 1:455604/1‑100 (MQ=255)
tACGCCACAGCGAGGCCAGCGTTACTGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGCCGAGAGTTTAACTGGTc < 2:1511177/100‑1 (MQ=255)
aCGCCACAGCGAGGCCAGCGTTACTGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTATCGACGCTTTTTCGACGAGAGTTTAACTGGTCa < 2:946191/100‑1 (MQ=255)
gCCACAGCGAGGCCAGCGTTACTGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGCCGAGAGTTTAACTGGTCAcc > 2:601786/1‑100 (MQ=255)
acaGCGAGGCCAGCGTTACTGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACcgcg < 1:778488/100‑1 (MQ=255)
aGCGAGGCCAGCGTTACTGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTg > 2:1402775/1‑100 (MQ=255)
gCGAGGCCAGCGTTACTGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGa < 2:1365065/100‑1 (MQ=255)
gCGAGGCCAGCGTTACTGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGa < 1:865677/100‑1 (MQ=255)
aGGCCAGCGTTACTGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGatat > 2:1453849/1‑100 (MQ=255)
ggCCAGCGTTACTGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATAtt < 1:633353/100‑1 (MQ=255)
tACTGACATCGCCTATCGCTGTGGATTCGGCGCCAGTAACCACGTTTCGACGCTTTTTCGGCGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAg < 2:125660/97‑1 (MQ=255)
aCTGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGAc < 1:591049/100‑1 (MQ=255)
cTGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGGTTAACTGGTCACCGCGTGATATTCGCCAGGGACg > 2:1125814/1‑100 (MQ=255)
tGACATCGCCTATCGCTGTGGATTCAGCGACAGTAATCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACgg < 2:805887/100‑1 (MQ=255)
tGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACgg > 2:584790/1‑100 (MQ=255)
gACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACggg < 2:1445098/100‑1 (MQ=255)
gACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACgg > 2:397617/1‑99 (MQ=255)
tCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATgg > 1:419208/1‑100 (MQ=255)
cGCCTAGCGCTGTGGATTCAGCGACAGTAACCACTTTTCGGCGCTTTTTCGACGAGAGTTTAACTGGCCACCGCGTGATATTCGCCAGGGACGGGATggn < 2:1332442/100‑2 (MQ=255)
gCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCt > 1:444554/1‑100 (MQ=255)
tATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTc > 1:1454856/1‑100 (MQ=255)
aTCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCt < 1:388509/100‑1 (MQ=255)
aTCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCt < 1:337412/100‑1 (MQ=255)
gCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCa > 1:970762/1‑100 (MQ=255)
gCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCa < 2:896079/100‑1 (MQ=255)
tgtgGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAAt < 2:271260/100‑1 (MQ=255)
gATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAAcg < 1:912467/100‑1 (MQ=255)
ttCAGCGACAGTAACCACTTTTCGACGCTTTTTTTTTTTTTTTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAAcgc > 2:397350/1‑99 (MQ=255)
tCAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGa < 2:1454848/100‑1 (MQ=255)
cAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGaa > 1:611584/1‑100 (MQ=255)
cAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGaa > 1:883324/1‑100 (MQ=255)
cAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGaa < 1:485725/100‑1 (MQ=255)
cAGCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGaa > 1:1042699/1‑100 (MQ=255)
gCGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGAAtc > 1:1291176/1‑100 (MQ=255)
cGACAGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGAAtct > 1:600258/1‑100 (MQ=255)
aGTAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGAATCTtctc < 1:1519867/100‑1 (MQ=255)
gTAACCACTTTTCGACGCTTTTTCGACGAGAGGTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGAATCTTCTCa > 2:998068/1‑100 (MQ=255)
tAACCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGAATCTtctcca < 1:1067600/100‑3 (MQ=255)
aCCACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGAATCTTCTCAACg > 1:989313/1‑100 (MQ=255)
ccACTTTTCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGAATCTTCTCAACGt > 1:411174/1‑100 (MQ=255)
tttCGACGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGAATCTTCTCAACGTATTTg > 2:1194417/1‑100 (MQ=255)
cGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGAATCTTCTCAACGTATTTGTACGcc > 2:1024336/1‑100 (MQ=255)
cGCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGAATCTTCTCAACGTATTTGTACGcc > 1:383028/1‑100 (MQ=255)
gCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGAATCTTCTCAACGTATTTGTACGCCa > 2:1461166/1‑100 (MQ=255)
gCTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGAATCTTCTCAACGTATTTGTACGCCa < 2:594852/100‑1 (MQ=255)
cTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGAATCTTCTCAACGTATTTGTACGCCat < 1:757622/100‑1 (MQ=255)
cTTTTTCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGAATCTTCTCAACGTATTTGTACGCCat < 1:629361/100‑1 (MQ=255)
tttttCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGTATCTTCTCAACGTATTTGTACGCCata > 1:254126/1‑100 (MQ=255)
tCGACGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGAATCTTCTCAACGTATTTGTACGCCATATTGc < 1:309011/100‑1 (MQ=255)
|
GCCCGACATCTGCTACGCCACAGCGAGGCCAGCGTTACTGACATCGCCTATCGCTGTGGATTCAGCGACAGTAACCACTTTTCGACGCTTTTTCGCCGAGAGTTTAACTGGTCACCGCGTGATATTCGCCAGGGACGGGATGGCTTTCTGCAATAACGCGAATCTTCTCAACGTATTTGTACGCCATATTGC > NC_000913/4098417‑4098608
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
