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 I197 R1
|
189 |
12.7 |
697584 |
97.1% |
677354 |
86.2 |
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 | 93.3%
| 37.5
/ ‑3.1
| 15 | 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 (4/10); total (5/10) |
| Fisher's exact test for biased strand distribution p-value = 3.33e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.86e-01 |
GGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGG > NZ_CP009273/1110869‑1111027
|
ggTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAAccc < 2:133668/86‑1 (MQ=255)
ggTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAAccc > 1:133668/1‑86 (MQ=255)
cAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGcc > 1:126690/1‑90 (MQ=255)
aGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGgcgc < 2:62894/90‑1 (MQ=255)
ccAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCgg < 2:69664/90‑1 (MQ=255)
ccAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGc < 2:64197/90‑1 (MQ=255)
aGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGcac < 1:119354/90‑1 (MQ=255)
gtgtCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATgc < 1:203395/90‑1 (MQ=255)
gtCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGaaa < 1:62144/67‑1 (MQ=255)
gtCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGaaa > 2:62144/1‑67 (MQ=255)
gtCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATgcgc > 2:333834/1‑90 (MQ=255)
tCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGcc < 2:347603/90‑1 (MQ=255)
cATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGccc > 2:235784/1‑90 (MQ=255)
aTTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCg < 1:184698/90‑1 (MQ=255)
aTTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCg < 1:271721/90‑1 (MQ=255)
aTTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCg < 2:16874/90‑1 (MQ=255)
gggTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAgg > 1:24739/1‑90 (MQ=255)
|
GGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGG > NZ_CP009273/1110869‑1111027
|
| 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
AGGCGGCACCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGG > NZ_CP009273/1110859‑1111028
|
AGGCGGCACCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTG > SRR3722076.135227/1‑100 (MQ=60)
GGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCC > SRR3722076.128175/1‑100 (MQ=60)
gtataagagacagTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCAC < SRR3722076.62914/87‑1 (MQ=60)
AGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATG < SRR3722076.120776/100‑1 (MQ=60)
GTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTC < SRR3722076.206005/100‑1 (MQ=60)
CATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGG > SRR3722076.25035/1‑100 (MQ=60)
ATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGG < SRR3722076.187062/100‑1 (MQ=60)
ATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGG < SRR3722076.275709/100‑1 (MQ=60)
|
AGGCGGCACCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGG > NZ_CP009273/1110859‑1111028
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
