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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
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%
| 77.0
/ NA
| 24 | 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 (13/11); total (13/11) |
GTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGC > NZ_CP009273/1110870‑1111033
|
gTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGt < 2:47219/90‑1 (MQ=255)
aaCAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGGGTCATTTTCACAGGGGGACATAGCAACCCGCTGTTGGGgcg > 2:416184/1‑90 (MQ=255)
aGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCa > 1:106281/1‑90 (MQ=255)
aGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCa > 2:35479/1‑90 (MQ=255)
aGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGgcgc > 2:368129/1‑90 (MQ=255)
ccAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCgg < 2:34043/90‑1 (MQ=255)
ggCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGa > 2:377185/1‑90 (MQ=255)
cgaTCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATa > 2:485457/1‑90 (MQ=255)
ccAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGc > 2:236320/1‑90 (MQ=255)
ccAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGc < 2:335950/90‑1 (MQ=255)
aGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGcac < 2:320224/90‑1 (MQ=255)
gtgtCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATaa < 2:265310/75‑1 (MQ=255)
gtgtCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATaa > 1:265310/1‑75 (MQ=255)
gtgtCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATgc > 2:32540/1‑90 (MQ=255)
gtgtCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATgc > 1:266398/1‑90 (MQ=255)
gtCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATgcgc > 1:342005/1‑90 (MQ=255)
gtCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATgcgc > 2:371261/1‑90 (MQ=255)
aTTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCg < 1:145319/90‑1 (MQ=255)
tttCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGAc > 2:425323/1‑90 (MQ=255)
aCATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGgcg < 1:35479/90‑1 (MQ=255)
cATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGgcgc < 2:266398/90‑1 (MQ=255)
cATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGgcgc < 1:371261/90‑1 (MQ=255)
cATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGgcgc < 1:236320/90‑1 (MQ=255)
cATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGgcgc < 2:66064/90‑1 (MQ=255)
|
GTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGC > NZ_CP009273/1110870‑1111033
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ 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
GAAGGCGGCACCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCAATCCAGAGAGCTTTTAT > NZ_CP009273/1110857‑1111051
|
GAAGGCGGCACCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGC < SRR3722094.145086/100‑1 (MQ=60)
GTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCA > SRR3722094.107806/1‑100 (MQ=60)
ggtcgtcggcagcgtcagatgtgtataagagacagTAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTA < SRR3722094.259955/65‑1 (MQ=60)
GTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATctgtc > SRR3722094.269262/1‑95 (MQ=60)
GTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGC > SRR3722094.270369/1‑100 (MQ=60)
TTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGC > SRR3722094.347648/1‑100 (MQ=60)
ATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGG < SRR3722094.147356/100‑1 (MQ=60)
ACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCAATCCAGAG < SRR3722094.35982/100‑1 (MQ=60)
CATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCAATCCAGAGA < SRR3722094.239665/100‑1 (MQ=60)
CATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCAATCCAGAGA < SRR3722094.377538/100‑1 (MQ=60)
CCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCAATCCAGAGAGCTTTTAT < SRR3722094.107496/100‑1 (MQ=60)
|
GAAGGCGGCACCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCAATCCAGAGAGCTTTTAT > NZ_CP009273/1110857‑1111051
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
