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 F2 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
354,025 |
T→C |
E126G (GAA→GGA) |
cynR ← |
transcriptional regulator CynR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 354,025 | 0 | T | C | 87.9%
| 81.7
/ 3.2
| 33 | E126G (GAA→GGA) | cynR | transcriptional regulator CynR |
| Reads supporting (aligned to +/- strand): ref base T (3/1); new base C (10/19); total (13/20) |
| Fisher's exact test for biased strand distribution p-value = 2.76e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.44e-01 |
GGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTG > NZ_CP009273/353944‑354111
|
ggCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGc > 1:345499/1‑90 (MQ=255)
ggCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGc > 2:432148/1‑90 (MQ=255)
cGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTg < 2:471352/90‑1 (MQ=255)
cacaGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGt < 1:227424/90‑1 (MQ=255)
acaGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTg < 2:72728/90‑1 (MQ=255)
acaGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTg < 2:444876/90‑1 (MQ=255)
acaGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTg < 1:498869/90‑1 (MQ=255)
acaGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTg < 2:315384/90‑1 (MQ=255)
aGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGAt < 2:310613/90‑1 (MQ=255)
gcgcGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGc < 1:432148/90‑1 (MQ=255)
gcgcGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGc < 2:203214/90‑1 (MQ=255)
cAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAgc > 1:173606/1‑90 (MQ=255)
cAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAgc > 2:63724/1‑90 (MQ=255)
cAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAgc > 2:311565/1‑90 (MQ=255)
aTCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAg > 1:200862/1‑71 (MQ=255)
aTCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAg < 2:200862/71‑1 (MQ=255)
aTCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTg > 1:682906/1‑75 (MQ=255)
aTCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTg < 2:682906/75‑1 (MQ=255)
aTCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAgcgc > 2:117709/1‑90 (MQ=255)
aCGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAg > 1:395381/1‑90 (MQ=255)
aaCCCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATcc < 1:441416/90‑1 (MQ=255)
cgtcgCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCa > 1:292305/1‑90 (MQ=255)
gCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAggg < 1:647697/90‑1 (MQ=255)
aaGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCGGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGcc < 1:443019/90‑1 (MQ=255)
tatCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGTTAGCGCGCATAGAAATCCGCCATTAAgggg < 1:581911/83‑1 (MQ=255)
tatCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAgggg > 2:581911/1‑83 (MQ=255)
tatCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATaa > 2:432689/1‑90 (MQ=255)
tCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAg < 2:292305/90‑1 (MQ=255)
tctcCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTaa < 2:489694/90‑1 (MQ=255)
tGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTg < 1:642799/90‑1 (MQ=255)
gCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTgg > 1:406139/1‑90 (MQ=255)
gCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTgg < 2:387880/90‑1 (MQ=255)
aTTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTg < 1:616940/90‑1 (MQ=255)
|
GGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTG > NZ_CP009273/353944‑354111
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 30 ≤ 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
GGAATTGCCTCCAGCTCCGGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTGACGGCGATACGCA > NZ_CP009273/353926‑354124
|
GGAATTGCCTCCAGCTCCGGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTC > SRR3722112.319022/1‑100 (MQ=60)
CCTCCAGCTCCGGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAG < SRR3722112.58379/100‑1 (MQ=60)
CTCCAGCTCCGGCGAATGCAGAGGCGCGAAGGCAACCCCAACGTCCAGCTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGC < SRR3722112.630847/100‑1 (MQ=60)
CTCCAGCTCCGGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGC > SRR3722112.349814/1‑100 (MQ=60)
CACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGA < SRR3722112.230159/100‑1 (MQ=60)
ACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGAT < SRR3722112.506099/100‑1 (MQ=60)
GGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGC > SRR3722112.175733/1‑100 (MQ=60)
GCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCG < SRR3722112.438031/100‑1 (MQ=60)
CGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGctgtctctt > SRR3722112.203302/1‑91 (MQ=60)
CGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATctgtc > SRR3722112.693593/1‑95 (MQ=60)
GGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAG > SRR3722112.400561/1‑100 (MQ=60)
ACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCA > SRR3722112.295685/1‑100 (MQ=60)
AACCCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGG < SRR3722112.447526/100‑1 (MQ=60)
GCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAG < SRR3722112.657790/100‑1 (MQ=60)
CAAAGCATATCCTCGATTTTCCCCTGCGACATTTCCTGTAGCGGGAGCGTGATGCTGGGTTAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGT < SRR3722112.590796/100‑1 (MQ=60)
AAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCGGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAG < SRR3722112.449159/100‑1 (MQ=60)
ATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGG > SRR3722112.411506/1‑100 (MQ=60)
TGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTGACGG < SRR3722112.652797/100‑1 (MQ=60)
ATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTGACGGCGATAC < SRR3722112.626454/100‑1 (MQ=60)
CCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTGACGGCGATACGCA > SRR3722112.82459/1‑100 (MQ=60)
|
GGAATTGCCTCCAGCTCCGGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTGACGGCGATACGCA > NZ_CP009273/353926‑354124
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
