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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
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 | 92.9%
| 74.4
/ ‑0.4
| 28 | intergenic (‑6/+166) | mdtG/lpxL | multidrug efflux MFS transporter MdtG/kdo(2)‑lipid IV(A) lauroyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (1/1); new base C (16/10); total (17/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.38e-01 |
AGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCAATC > NZ_CP009273/1110880‑1111037
|
aGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCa > 1:98456/1‑90 (MQ=255)
cAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGt < 1:363344/90‑1 (MQ=255)
ggCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGa > 2:801466/1‑90 (MQ=255)
gCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGaa > 1:256540/1‑90 (MQ=255)
gCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGCGTCATTTTCCCAGGGAGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGaa > 1:1523410/1‑90 (MQ=255)
tttcgtttcCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGaaa < 1:878864/90‑1 (MQ=255)
tttcgtttcCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGaaa < 1:896046/90‑1 (MQ=255)
tttcCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATa < 1:21412/90‑1 (MQ=255)
ccAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGc > 2:265433/1‑90 (MQ=255)
aGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGcac < 2:728510/90‑1 (MQ=255)
aGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGcac < 2:1450781/90‑1 (MQ=255)
aGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGcac < 1:833795/90‑1 (MQ=255)
tttATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCacac < 1:1027260/90‑1 (MQ=255)
gtgtCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTg < 1:926476/41‑1 (MQ=255)
gtgtCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTg > 2:926476/1‑41 (MQ=255)
gtgtCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATgc > 2:1392772/1‑90 (MQ=255)
gtCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATgcgc > 1:587778/1‑90 (MQ=255)
gtCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATgcgc > 1:1276019/1‑90 (MQ=255)
gtCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATgcgc > 1:1220521/1‑90 (MQ=255)
cATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGccc > 2:225447/1‑90 (MQ=255)
cacaGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTc < 1:555917/90‑1 (MQ=255)
caGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCa > 1:876872/1‑90 (MQ=255)
gggTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAgg > 2:310536/1‑90 (MQ=255)
gCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCg > 2:128929/1‑71 (MQ=255)
gCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCg < 1:128929/71‑1 (MQ=255)
gCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGGCTTCCAGGGGGCGCAATc > 2:911885/1‑90 (MQ=255)
gCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCAATc > 2:419375/1‑90 (MQ=255)
gCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCAATc > 2:498256/1‑90 (MQ=255)
|
AGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCAATC > NZ_CP009273/1110880‑1111037
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ 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
CTGAAGGCGGCACCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCAATCCAGAGAGC > NZ_CP009273/1110855‑1111045
|
CTGAAGGCGGCACCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCC < SRR3722078.865371/100‑1 (MQ=60)
AGGCGGCACCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTG < SRR3722078.773853/100‑1 (MQ=60)
GTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCA > SRR3722078.99612/1‑100 (MQ=60)
ccgccatcgtcggcagcgtcagatgtgtataagagacagGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGC < SRR3722078.939204/61‑1 (MQ=60)
GCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAA > SRR3722078.259681/1‑100 (MQ=60)
GCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGCGTCATTTTCCCAGGGAGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAA > SRR3722078.1548244/1‑100 (MQ=60)
CAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGA < SRR3722078.367778/100‑1 (MQ=60)
TTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCAC < SRR3722078.908082/100‑1 (MQ=60)
TTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCAC < SRR3722078.890675/100‑1 (MQ=60)
TTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAA < SRR3722078.21685/100‑1 (MQ=60)
AGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATG < SRR3722078.844881/100‑1 (MQ=60)
TTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCG < SRR3722078.1042496/100‑1 (MQ=60)
TTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGC > SRR3722078.1239726/1‑100 (MQ=60)
TTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGC > SRR3722078.594618/1‑100 (MQ=60)
TTATAGGGGTGTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGC > SRR3722078.1296302/1‑100 (MQ=60)
GTCATTTTCACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCA > SRR3722078.888648/1‑100 (MQ=60)
aagagacagGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGG < SRR3722078.130418/91‑1 (MQ=60)
CACAGGGTGACATAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGC < SRR3722078.562475/100‑1 (MQ=60)
TAGCAACCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCAATCCAGAGAGC > SRR3722078.220363/1‑100 (MQ=60)
|
CTGAAGGCGGCACCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACATAGCAATCCGCTGTTGGTGCGCCAGGCGCGGTGAACATAAGAAGAAAAGATAAGCACACTAATTATGCGCCCGACTTCCAGGGGGCGCAATCCAGAGAGC > NZ_CP009273/1110855‑1111045
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
