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 I217 R1
|
10 |
20.8 |
1414158 |
96.8% |
1368904 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,909,799 |
C→T |
intergenic (‑8/+89) |
proQ ← / ← msrC |
RNA chaperone ProQ/L‑methionine (R)‑S‑oxide reductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,909,799 | 0 | C | T | 77.8%
| 57.0
/ 13.1
| 27 | intergenic (‑8/+89) | proQ/msrC | RNA chaperone ProQ/L‑methionine (R)‑S‑oxide reductase |
| Reads supporting (aligned to +/- strand): ref base C (4/2); new base T (10/11); total (14/13) |
| Fisher's exact test for biased strand distribution p-value = 6.48e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.67e-01 |
GTGGGGAAAACGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTATCCG > NZ_CP009273/1909723‑1909883
|
gTGGGGAAAACGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACgg > 2:459301/1‑90 (MQ=255)
gTGGGGAAAACGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACgg > 2:307907/1‑90 (MQ=255)
ggggAAAACGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGAc > 2:578427/1‑90 (MQ=255)
ggAAAACGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGACGt > 2:677839/1‑90 (MQ=255)
tCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCcaacaa > 1:702587/1‑90 (MQ=255)
ccAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCCAACAAgcgc < 1:335905/90‑1 (MQ=255)
ccAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCCAACAAgcgc < 2:117666/90‑1 (MQ=255)
gAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCCAACAAGCGCAgg > 1:521733/1‑90 (MQ=255)
gcgATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGa > 2:674224/1‑90 (MQ=255)
cgATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGaa > 1:581513/1‑90 (MQ=255)
ttACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAg < 1:677839/90‑1 (MQ=255)
aCTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGc < 1:462767/90‑1 (MQ=255)
tcttTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCTAACAAGCGCAGGCATGAACAGGCGTc < 1:518082/90‑1 (MQ=255)
gCTATTCAACTTAGGTTGATTTTCCATGAAATTTCCTGATTACAACGGACGTAGCCAACAAGCGCATGCATGAACAGGCGTCATTATAAt > 2:186694/1‑90 (MQ=255)
tATTCAACTTAGGTTGATTTTCCATGAAATTTCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGa > 2:450364/1‑90 (MQ=255)
aTTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGAc > 2:26891/1‑90 (MQ=255)
aTTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGAc > 1:107524/1‑90 (MQ=255)
aTTCAACTTAGGTTGATTTTCCATGAAATTTCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGAc > 2:677512/1‑90 (MQ=255)
cTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGACTTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATc < 2:309212/90‑1 (MQ=255)
ggTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTa < 2:415361/90‑1 (MQ=255)
ggTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTa < 1:45232/90‑1 (MQ=255)
ggTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTa < 2:87167/90‑1 (MQ=255)
ggTTGATTTTCCATGAAATTTCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTa < 1:585586/90‑1 (MQ=255)
aTTTTCCATGAAATTTTCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGc > 2:317009/1‑90 (MQ=255)
aTGAAATTTCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTa < 2:581513/90‑1 (MQ=255)
gAAATTTTCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTATc < 1:674224/90‑1 (MQ=255)
aaTTTTCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTATCCg < 1:578427/90‑1 (MQ=255)
|
GTGGGGAAAACGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTATCCG > NZ_CP009273/1909723‑1909883
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ 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
CGCACTGAAACAGTGGGGAAAACGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTATCCGTTGATTATCCTGCGA > NZ_CP009273/1909711‑1909898
|
CGCACTGAAACAGTGGGGAAAACGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAAC < SRR3722100.507126/100‑1 (MQ=60)
GGGAAAACGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCCAACAA > SRR3722100.711168/1‑100 (MQ=60)
CGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCCAACAAGCGCAGG > SRR3722100.527899/1‑100 (MQ=60)
GCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAA > SRR3722100.588496/1‑100 (MQ=60)
CCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAAC < SRR3722100.339209/100‑1 (MQ=60)
TTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTAT < SRR3722100.686108/100‑1 (MQ=60)
ACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAA < SRR3722100.468013/100‑1 (MQ=60)
TCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCTAACAAGCGCAGGCATGAACAGGCGTCATTATAATGA < SRR3722100.524190/100‑1 (MQ=60)
CTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGAC > SRR3722100.108585/1‑100 (MQ=60)
GGTTGATTTTCCATGAAATTTTCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGT < SRR3722100.45663/100‑1 (MQ=60)
GGTTGATTTTCCATGAAATTTCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGT < SRR3722100.592631/100‑1 (MQ=60)
GAAATTTTCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTATCCGTTGATTAT < SRR3722100.682443/100‑1 (MQ=60)
AATTTTCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTATCCGTTGATTATCC < SRR3722100.585368/100‑1 (MQ=60)
TCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTATCCGTTGATTATCCTGCGA < SRR3722100.310757/100‑1 (MQ=60)
TCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTATCCGTTAATTATCCTGCGA < SRR3722100.215930/100‑1 (MQ=60)
|
CGCACTGAAACAGTGGGGAAAACGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTATCCGTTGATTATCCTGCGA > NZ_CP009273/1909711‑1909898
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
