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 |
1,110,952 |
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 | 100.0%
| 34.9
/ NA
| 12 | intergenic (‑6/+166) | mdtG/lpxL | multidrug efflux MFS transporter MdtG/kdo(2)‑lipid IV(A) lauroyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (5/7); total (5/7) |
CACCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCAATC > NZ_CP009273/1110865‑1111037
|
cACCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAAccc < 1:192006/90‑1 (MQ=255)
ggTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTg > 2:622648/1‑90 (MQ=255)
cAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGcc < 1:197633/90‑1 (MQ=255)
ccAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGc < 2:517582/90‑1 (MQ=255)
ccAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGc < 2:83888/90‑1 (MQ=255)
gtgtCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGc > 1:716298/1‑77 (MQ=255)
gtgtCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGc < 2:716298/77‑1 (MQ=255)
gtCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATgcgc > 1:354925/1‑90 (MQ=255)
aTTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCg < 1:129155/90‑1 (MQ=255)
caGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCa > 2:675496/1‑90 (MQ=255)
ggTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAggg < 2:512869/90‑1 (MQ=255)
tAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCaa < 1:87587/90‑1 (MQ=255)
gCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCAATc > 2:164822/1‑90 (MQ=255)
|
CACCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCAATC > NZ_CP009273/1110865‑1111037
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ 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
CACCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCAATCCAGAGAGC > NZ_CP009273/1110865‑1111045
|
CACCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTG < SRR3722112.194356/100‑1 (MQ=60)
CAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTG < SRR3722112.200040/100‑1 (MQ=60)
GTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTActg > SRR3722112.727481/1‑97 (MQ=60)
TTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGTTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGNNNNNCACACNNATTnnnctc > SRR3722112.284121/1‑94 (MQ=60)
TTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGC > SRR3722112.359433/1‑100 (MQ=60)
ATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGG < SRR3722112.130761/100‑1 (MQ=60)
TAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCAATCCAGAGAGC < SRR3722112.88674/100‑1 (MQ=60)
|
CACCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCAATCCAGAGAGC > NZ_CP009273/1110865‑1111045
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
