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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,909,798 |
T→C |
intergenic (‑7/+90) |
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 | 1,909,798 | 0 | T | C | 92.0%
| 72.4
/ ‑0.9
| 25 | intergenic (‑7/+90) | proQ/msrC | RNA chaperone ProQ/L‑methionine (R)‑S‑oxide reductase |
| Reads supporting (aligned to +/- strand): ref base T (0/2); new base C (12/11); total (12/13) |
| Fisher's exact test for biased strand distribution p-value = 4.80e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01 |
CAGTGGGGAAAACGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTATCCG > NZ_CP009273/1909721‑1909883
|
cAGTGGGGAAAACGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAAc < 1:30472/90‑1 (MQ=255)
tGGGGAAAACGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGa > 1:713676/1‑90 (MQ=255)
ggggAAAACGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGAc > 2:280042/1‑90 (MQ=255)
ttCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCcaaca > 2:470915/1‑90 (MQ=255)
gAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTccc < 2:343586/58‑1 (MQ=255)
gAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTccc > 1:343586/1‑58 (MQ=255)
cgATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGaa > 1:674143/1‑90 (MQ=255)
gATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAAc < 1:420283/90‑1 (MQ=255)
cttcttTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCg < 2:32251/90‑1 (MQ=255)
tttACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCAt > 2:619087/1‑90 (MQ=255)
tGCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATaa < 1:311940/90‑1 (MQ=255)
gCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAg > 1:918135/1‑77 (MQ=255)
gCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAg < 2:918135/77‑1 (MQ=255)
gCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAAt > 1:370902/1‑90 (MQ=255)
gCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAAt > 1:777294/1‑90 (MQ=255)
gCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAAt > 2:829979/1‑90 (MQ=255)
tCAACTTAGGTTGATTTTCCATGAAATTTCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGc < 1:353475/90‑1 (MQ=255)
aCTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTAt > 2:92062/1‑90 (MQ=255)
aCTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTAt < 2:313194/90‑1 (MQ=255)
aCTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTAt > 1:155255/1‑90 (MQ=255)
tAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAg > 2:367222/1‑90 (MQ=255)
ggTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTa < 1:367222/90‑1 (MQ=255)
aTTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGc < 2:155255/90‑1 (MQ=255)
aTTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGc < 2:713676/90‑1 (MQ=255)
tttCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTa < 1:131542/90‑1 (MQ=255)
aTGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTa < 2:854259/90‑1 (MQ=255)
aaTTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTATCCg < 1:491462/90‑1 (MQ=255)
|
CAGTGGGGAAAACGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTATCCG > NZ_CP009273/1909721‑1909883
|
| 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
ACTGAAACAGTGGGGAAAACGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTATCCGTTGATTATCC > NZ_CP009273/1909714‑1909893
|
CCTGAAACAGTGGGGAAAACGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGA > SRR3722072.726394/1‑100 (MQ=60)
CAGTGGGGAAAACGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCC < SRR3722072.31014/100‑1 (MQ=60)
CGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACctgtctcttatacacatctccg > SRR3722072.349647/1‑78 (MQ=60)
GCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAA > SRR3722072.686215/1‑100 (MQ=60)
GATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATT < SRR3722072.427900/100‑1 (MQ=60)
CTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATctg > SRR3722072.933907/1‑97 (MQ=60)
CTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAAT > SRR3722072.377490/1‑100 (MQ=60)
CTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAAT > SRR3722072.790951/1‑100 (MQ=60)
CTGCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTAT > SRR3722072.157984/1‑100 (MQ=60)
TGCTATTCAACTTAGGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATC < SRR3722072.317378/100‑1 (MQ=60)
TCAACTTAGGTTGATTTTCCATGAAATTTCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAA < SRR3722072.359728/100‑1 (MQ=60)
GGTTGATTTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGT < SRR3722072.373748/100‑1 (MQ=60)
TTTCCATGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTATCCGT < SRR3722072.133905/100‑1 (MQ=60)
TGAAATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTATCCGTTGATTA > SRR3722072.906433/1‑100 (MQ=60)
AATTCCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTATCCGTTGATTATCC < SRR3722072.500341/100‑1 (MQ=60)
|
ACTGAAACAGTGGGGAAAACGTTCGGCCAGAAACGCGATTACTTCTTTACTGCTATTCAACTTAGGTTGATTTTCCATGAAATTTCCTGATTACAACGGACGTAGCCAACAAGCGCAGGCATGAACAGGCGTCATTATAATGACGCTATCAGTAAATGCTACGTTATCCGTTGATTATCC > NZ_CP009273/1909714‑1909893
|
| 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: ‑ |
