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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,110,952 |
T→C |
intergenic (‑6/+166) |
mdtG ← / ← lpxL |
multidrug efflux MFS transporter MdtG/kdo(2)‑lipid IV(A) lauroyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,110,952 | 0 | T | C | 90.9%
| 24.4
/ ‑3.4
| 11 | intergenic (‑6/+166) | mdtG/lpxL | multidrug efflux MFS transporter MdtG/kdo(2)‑lipid IV(A) lauroyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (4/6); total (5/6) |
| Fisher's exact test for biased strand distribution p-value = 4.55e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGG > NZ_CP009273/1110879‑1111027
|
cAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGcc > 1:160773/1‑90 (MQ=255)
ggCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGa < 1:529362/90‑1 (MQ=255)
ggCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGa < 2:427608/90‑1 (MQ=255)
ttcCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATaa < 2:491817/90‑1 (MQ=255)
aGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGcac < 1:502080/90‑1 (MQ=255)
aGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGcac < 1:520246/90‑1 (MQ=255)
aGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCACCAGGCGCGGTGAACATAAGAAGAAAAGATAAGcac < 2:57540/90‑1 (MQ=255)
gtCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATgcgc > 1:510052/1‑90 (MQ=255)
gtCATTTTCACAGGGGGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATgcgc > 1:345583/1‑90 (MQ=255)
gggTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAgg > 1:455239/1‑90 (MQ=255)
gggTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAgg > 1:469739/1‑90 (MQ=255)
|
CAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGG > NZ_CP009273/1110879‑1111027
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ 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
GCGGCACCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGG > NZ_CP009273/1110861‑1111027
|
GCGGCACCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTT < SRR3722111.515691/100‑1 (MQ=60)
GGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCC > SRR3722111.162798/1‑100 (MQ=60)
GGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAG < SRR3722111.537672/100‑1 (MQ=60)
ctacacattgacattcgtcggcagcgtcagatgtgtataagagacaGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGA < SRR3722111.220096/54‑1 (MQ=60)
AGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATG < SRR3722111.509825/100‑1 (MQ=60)
AGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATG < SRR3722111.528376/100‑1 (MQ=60)
TTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGC > SRR3722111.517953/1‑100 (MQ=60)
TTATAGGGGTGTCATTTTCACAGGGGGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGC > SRR3722111.350227/1‑100 (MQ=60)
CATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGG > SRR3722111.462146/1‑100 (MQ=60)
CATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGG > SRR3722111.476902/1‑100 (MQ=60)
|
GCGGCACCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGG > NZ_CP009273/1110861‑1111027
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
