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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,673,542 |
A→G |
K287E (AAG→GAG) |
ydgH → |
DUF1471 family protein YdgH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,673,542 | 0 | A | G | 91.7%
| 52.5
/ ‑0.2
| 24 | K287E (AAG→GAG) | ydgH | DUF1471 family protein YdgH |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base G (8/14); total (9/15) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.27e-01 |
CGATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATA > NZ_CP009273/1673453‑1673627
|
cGATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCga < 1:512104/90‑1 (MQ=255)
atgGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGaaa < 1:813013/90‑1 (MQ=255)
ccGTTCGATAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCt < 1:376979/90‑1 (MQ=255)
ccGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCt < 2:437584/90‑1 (MQ=255)
cGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTa < 2:636089/90‑1 (MQ=255)
cGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTa < 2:280873/90‑1 (MQ=255)
cGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTa > 2:288197/1‑90 (MQ=255)
cGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTa < 1:268824/90‑1 (MQ=255)
gTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTaa > 2:175466/1‑90 (MQ=255)
tCGCCAGTATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGt < 2:781686/90‑1 (MQ=255)
tCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGt < 2:276985/90‑1 (MQ=255)
tctcTGGAAACTCCGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCcccc < 2:188804/90‑1 (MQ=255)
ctGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGcc > 1:469030/1‑90 (MQ=255)
gCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCCCCCGCCAGTGGCAGGAAc < 1:288197/90‑1 (MQ=255)
aaCATGACCGAAGTCTCCTATCAGGTTGCGAACCGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCCCCCGCCAGTGGCAGGAACGt < 1:175466/90‑1 (MQ=255)
aaCATGACCGAAGTCCCCTATCAGGTTGCGAAACGTCCCGCGGAAAAAGGTGCTAAGTATTCCCACATCACCCGCCAGTGGCAGGAACGt < 1:596917/90‑1 (MQ=255)
aCCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGtaat > 1:518116/1‑90 (MQ=255)
tctcCTATAAGGTTGCGAAGCGTCCCGGGGAGAAAGGTGATAAATTTTACCACACCGCCCGCCAGTGGCAGGAACGTGGTAATAACCTGa < 1:446833/90‑1 (MQ=255)
ggTTGCAAACCGTGCGGGGGAGAAGGGTGCTAATTTTTCCCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAgcgc < 2:13053/90‑1 (MQ=255)
gTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCa > 1:566161/1‑90 (MQ=255)
tGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGa > 1:204948/1‑90 (MQ=255)
tGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGGGGCAGGAAAGGGGGAATAACGTTTCCGGCCGCGCAGa > 2:546883/1‑90 (MQ=255)
gAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCt > 2:246447/1‑90 (MQ=255)
gTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGGAATAACCTGACCGTCAGCGCAGATCTGtata > 2:201364/1‑90 (MQ=255)
cgcgGAAAAGGGTGTTAATTTTTCCCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTataaata < 2:51633/90‑1 (MQ=255)
|
CGATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATA > NZ_CP009273/1673453‑1673627
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CGATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATT > NZ_CP009273/1673453‑1673633
|
CGATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGC < SRR3722079.393615/100‑1 (MQ=60)
CGATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGC < SRR3722079.516776/100‑1 (MQ=60)
ATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGT < SRR3722079.821731/100‑1 (MQ=60)
CCGTTCGATAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACC < SRR3722079.380038/100‑1 (MQ=60)
CGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCA < SRR3722079.271076/100‑1 (MQ=60)
ATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCC > SRR3722079.473131/1‑100 (MQ=60)
CGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAAT > SRR3722079.522885/1‑100 (MQ=60)
GCAACATGCCCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGGGGAGAAAGGTGCTAAGTATTACCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAA < SRR3722079.290578/100‑1 (MQ=60)
AACATGCCCGAAGTCTCCTATCAGGTTGCGAACCGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACC < SRR3722079.176995/100‑1 (MQ=60)
AACATGACCGAAGTCCCCTATCAGGTTGCGAAACGTCCCGCGGAAAAAGGTGCTAAGTATTCCCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACC < SRR3722079.602907/100‑1 (MQ=60)
TCTCCTATAAGGTTGCGAAGCGTCCCGGGGAGAAAGGTGATAAATTTTACCACACCGCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGC < SRR3722079.450738/100‑1 (MQ=52)
CTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCA > SRR3722079.571691/1‑100 (MQ=60)
CCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGA > SRR3722079.206716/1‑100 (MQ=60)
GTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATctgtctcttat > SRR3722079.576992/1‑89 (MQ=60)
|
CGATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATT > NZ_CP009273/1673453‑1673633
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
