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 I96 R1
|
172 |
34.7 |
2005794 |
96.2% |
1929573 |
85.4 |
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 | 95.8%
| 72.4
/ ‑3.4
| 24 | intergenic (‑78/+128) | rspA/ynfA | starvation‑sensing protein RspA/YnfA family protein |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base G (10/13); total (11/13) |
| Fisher's exact test for biased strand distribution p-value = 4.58e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.92e-01 |
CGATCTTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTT > NZ_CP009273/1649389‑1649554
|
cGATCTTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGgaa < 2:973358/90‑1 (MQ=255)
tCTTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGgaaaaa > 2:145016/1‑90 (MQ=255)
tCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTg > 2:90973/1‑90 (MQ=255)
cATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACaaaaaa < 2:721444/90‑1 (MQ=255)
cGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAgg < 2:555851/90‑1 (MQ=255)
ttGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGt < 2:317402/90‑1 (MQ=255)
ttGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGt > 1:60480/1‑90 (MQ=255)
cATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCt > 2:392458/1‑90 (MQ=255)
aTGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCtg > 1:968697/1‑90 (MQ=255)
aCGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGtt < 1:639689/90‑1 (MQ=255)
aCTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACaa < 1:90973/90‑1 (MQ=255)
aCTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACaa < 2:317923/90‑1 (MQ=255)
tGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACaaaa < 1:277473/90‑1 (MQ=255)
gAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAg > 1:642803/1‑90 (MQ=255)
gCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGAt < 2:325517/90‑1 (MQ=255)
gCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGAt < 2:742457/90‑1 (MQ=255)
tactacCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGa < 1:426022/90‑1 (MQ=255)
actacCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGaa > 1:580612/1‑90 (MQ=255)
ctacCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGaaa < 1:369967/90‑1 (MQ=255)
tacCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACaa < 1:852512/80‑1 (MQ=255)
tacCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACaa > 2:852512/1‑80 (MQ=255)
cATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACaaaaaaa < 1:918296/46‑1 (MQ=255)
cATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACaaaaaaa > 2:918296/1‑46 (MQ=255)
cATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGa > 1:261478/1‑90 (MQ=255)
aGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCt > 2:452688/1‑90 (MQ=255)
tataAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCttt > 2:408116/1‑90 (MQ=255)
|
CGATCTTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTT > NZ_CP009273/1649389‑1649554
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTT > NZ_CP009273/1649408‑1649575
|
CTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGT > SRR3722236.61330/1‑100 (MQ=60)
ttcgtcggcagcgtcagatgtgtataagagacagGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATT < SRR3722236.934517/66‑1 (MQ=60)
GTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTG > SRR3722236.985781/1‑100 (MQ=60)
CTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAG > SRR3722236.653375/1‑100 (MQ=60)
ACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGAT < SRR3722236.650176/100‑1 (MQ=60)
CAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAA > SRR3722236.589615/1‑100 (MQ=60)
ACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAAT < SRR3722236.867436/100‑1 (MQ=60)
ACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAAT < SRR3722236.92237/100‑1 (MQ=60)
TGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAG < SRR3722236.281505/100‑1 (MQ=60)
GAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGA > SRR3722236.265312/1‑100 (MQ=60)
TACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATAC < SRR3722236.431964/100‑1 (MQ=60)
CTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCT < SRR3722236.375180/100‑1 (MQ=60)
AGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCT > SRR3722236.630711/1‑100 (MQ=60)
AGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCT > SRR3722236.835113/1‑100 (MQ=60)
GAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTT > SRR3722236.751/1‑100 (MQ=60)
|
CTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTT > NZ_CP009273/1649408‑1649575
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
