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 |
|
A1 F3 I122 R1
|
193 |
20.9 |
1228102 |
94.7% |
1163012 |
84.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,649,476 |
A→G |
intergenic (‑78/+128) |
rspA ← / ← ynfA |
starvation‑sensing protein RspA/YnfA family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,649,476 | 0 | A | G | 100.0%
| 58.7
/ NA
| 17 | intergenic (‑78/+128) | rspA/ynfA | starvation‑sensing protein RspA/YnfA family protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (9/8); total (9/8) |
TTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAG > NZ_CP009273/1649394‑1649560
|
ttCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGc > 1:494346/1‑90 (MQ=255)
cATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACaaaaaa < 1:600898/90‑1 (MQ=255)
aTCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACaaaaaaa < 2:458010/90‑1 (MQ=255)
gCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATca > 1:267946/1‑79 (MQ=255)
gCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATca < 2:267946/79‑1 (MQ=255)
tGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGta > 1:326523/1‑90 (MQ=255)
cGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTatat > 1:399012/1‑90 (MQ=255)
gCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTgcgc < 2:399012/90‑1 (MQ=255)
gCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTgcgc < 2:494346/90‑1 (MQ=255)
tGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACaaaa < 1:572747/90‑1 (MQ=255)
tactacCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGa < 2:568944/90‑1 (MQ=255)
aTACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGaa > 1:411388/1‑90 (MQ=255)
aGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCt > 1:475669/1‑90 (MQ=255)
tataAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCttt > 1:123662/1‑90 (MQ=255)
gATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAg > 1:277182/1‑90 (MQ=255)
tCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACaa > 1:288496/1‑61 (MQ=255)
tCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACaa < 2:288496/61‑1 (MQ=255)
|
TTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAG > NZ_CP009273/1649394‑1649560
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CTTTACGATCTTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTG > NZ_CP009273/1649384‑1649563
|
CTTTACGATCTTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGC > SRR3721989.504821/1‑100 (MQ=60)
TCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGC > SRR3721989.272709/1‑100 (MQ=60)
TTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTA > SRR3721989.332739/1‑100 (MQ=60)
CATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATAT > SRR3721989.407135/1‑100 (MQ=60)
CATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATAT < SRR3721989.613957/100‑1 (MQ=60)
TGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAG < SRR3721989.585158/100‑1 (MQ=60)
AGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAA > SRR3721989.419821/1‑100 (MQ=60)
CTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCT > SRR3721989.485688/1‑100 (MQ=60)
ACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTT > SRR3721989.125929/1‑100 (MQ=60)
CAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAG > SRR3721989.282232/1‑100 (MQ=60)
AGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATctgtctcttatacacatct > SRR3721989.293819/1‑81 (MQ=60)
AGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCT > SRR3721989.18251/1‑100 (MQ=60)
GTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTG > SRR3721989.239314/1‑100 (MQ=60)
|
CTTTACGATCTTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTG > NZ_CP009273/1649384‑1649563
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
