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 |
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 | 97.1%
| 91.2
/ ‑3.4
| 34 | K287E (AAG→GAG) | ydgH | DUF1471 family protein YdgH |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (11/22); total (11/23) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.61e-01 |
ATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATC > NZ_CP009273/1673458‑1673617
|
atgGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGaaa < 2:449865/90‑1 (MQ=255)
tgGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAg < 2:554275/90‑1 (MQ=255)
ggTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAg < 2:47049/89‑1 (MQ=255)
ggTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAg > 1:47049/1‑89 (MQ=255)
tCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTg > 1:96393/1‑90 (MQ=255)
cccGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGc < 1:215090/90‑1 (MQ=255)
cccGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGc < 1:87698/90‑1 (MQ=255)
cccGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGc < 1:46377/90‑1 (MQ=255)
ccGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCt < 2:318575/90‑1 (MQ=255)
ccGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCt < 1:128722/90‑1 (MQ=255)
cGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTa < 2:331967/90‑1 (MQ=255)
gTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGaaa > 2:76687/1‑82 (MQ=255)
gTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGaaa < 1:76687/82‑1 (MQ=255)
gTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTaa < 1:551894/90‑1 (MQ=255)
gTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTaa < 2:77144/90‑1 (MQ=255)
aTCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACcac < 1:274271/90‑1 (MQ=255)
aTCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACcac < 1:299281/90‑1 (MQ=255)
aTTCTCTGGCAACCACGGAAACATGACCAAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAAAAGGGTGCAAAGTTTTACCACATCAc < 1:690412/90‑1 (MQ=255)
ctGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGcc > 2:560530/1‑90 (MQ=255)
gCAACATGACCGAAGTCTCCTATCAGGTTGCAAAACGTGCCGCGGAAAAAGGTGCTAAGTATTCCCACATCCCCCGCCAGTGGCAGGAAc < 2:57823/90‑1 (MQ=255)
aaCATGCCCGAATTCTCCTATCAGGTTGGGAAACGGGCCGGGGAAAAAGGTGCTAATTATTACCACATCCCCCGCCAGTGGCAGGAACGt < 1:600179/90‑1 (MQ=255)
aCATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTg > 2:114354/1‑90 (MQ=255)
aTGACCGAGGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGt > 2:480128/1‑90 (MQ=255)
gcccGAATTCTCTTGTCAGGTTGCAAAAGGGGCCGGGGAGAAAGGTTTAAAGTTTTCCCACATCCCCCGCCAGTGGCAGGAACGTGGtaa < 1:368020/88‑1 (MQ=255)
aCCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGaaa < 1:46266/42‑1 (MQ=255)
aCCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGaaa > 2:46266/1‑42 (MQ=255)
ccTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCg > 2:485420/1‑90 (MQ=255)
ggTTGCAAAACGTGCCGAGGAAAAAGGTGCAAATTATTCCCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAgcgc < 1:709069/90‑1 (MQ=255)
tGCGAAACGTGCCGGGGAGAAAGGTGCTAAGTATTACCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGa < 2:25313/90‑1 (MQ=255)
tGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGa > 2:199762/1‑90 (MQ=255)
tGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGGGGGAATAACCTGACCGTCAGCGCAGa > 1:325610/1‑90 (MQ=255)
tGCAAAAGGGGCCGGGGAAAAGGGTGATAAGTATTCCCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGa < 1:560530/90‑1 (MQ=255)
gCGAAACGTGCCGCGGAGAAAGGTGCTAAGTGTTACCACATCACCCGCCAGTGGCAGGAACGTGGGAAAAACCTGACCGTCAGCGCCGAt > 1:634767/1‑90 (MQ=255)
caaaaCGTGCCGGGGAAAAAGGTGCTAATTATTACCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATc < 2:604198/88‑1 (MQ=255)
|
ATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATC > NZ_CP009273/1673458‑1673617
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 13 ≤ 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
CAGCGATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGTTAC > NZ_CP009273/1673450‑1673640
|
CAGCGATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGG > SRR3722112.47626/1‑100 (MQ=60)
GCGATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTG > SRR3722112.97597/1‑100 (MQ=60)
gacattcgtcggcagcgtcagatgtgtataagagacagCGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGT < SRR3722112.46831/62‑1 (MQ=60)
ATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGT < SRR3722112.77616/100‑1 (MQ=60)
CCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTAC < SRR3722112.217681/100‑1 (MQ=60)
CCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTAC < SRR3722112.88788/100‑1 (MQ=60)
CCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTAC < SRR3722112.46945/100‑1 (MQ=60)
CCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACC < SRR3722112.130320/100‑1 (MQ=60)
GTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCAC < SRR3722112.560236/100‑1 (MQ=60)
ATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCC < SRR3722112.302732/100‑1 (MQ=60)
ATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCC < SRR3722112.277473/100‑1 (MQ=60)
ATTCTCTGGCAACCACGGAAACATGACCAAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAAAAGGGTGCAAAGTTTTACCACATCACCCGCCAGTGG < SRR3722112.701196/100‑1 (MQ=60)
TCGGGCAACTACGGCAACATGCCCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGGGGAGAAAGGTGCTAAGTATTACCACATCCCCCGCCAGTGGCAGG < SRR3722112.532704/100‑1 (MQ=60)
AACATGCCCGAATTCTCCTATCAGGTTGGGAAACGGGCCGGGGAAAAAGGTGCTAATTATTACCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACC < SRR3722112.609376/100‑1 (MQ=60)
CCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGGGGGAATAACCTGACCGTCAGCGCAGA > SRR3722112.329483/1‑100 (MQ=60)
CTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTGTTACCACATCACCCGCCAGTGGCAGGAACGTGGGAAAAACCTGACCGTCAGCGCCGAT > SRR3722112.644616/1‑100 (MQ=60)
GGTTGCAAAACGTGCCGAGGAAAAAGGTGCAAATTATTCCCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTAT < SRR3722112.720155/100‑1 (MQ=60)
GGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTTAGTTAC > SRR3722112.92963/1‑100 (MQ=60)
|
CAGCGATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGTTAC > NZ_CP009273/1673450‑1673640
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
