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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
879,010 |
T→C |
intergenic (‑166/‑119) |
ybjG ← / → mdfA |
undecaprenyl‑diphosphate phosphatase/multidrug efflux MFS transporter MdfA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 879,010 | 0 | T | C | 84.4%
| 80.5
/ 2.7
| 32 | intergenic (‑166/‑119) | ybjG/mdfA | undecaprenyl‑diphosphate phosphatase/multidrug efflux MFS transporter MdfA |
| Reads supporting (aligned to +/- strand): ref base T (3/2); new base C (14/13); total (17/15) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTA > NZ_CP009273/878923‑879094
|
aaGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAg > 1:29465/1‑90 (MQ=255)
aTCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACt < 1:579559/90‑1 (MQ=255)
gTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTCGt < 1:805160/90‑1 (MQ=255)
cTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCta > 2:227979/1‑81 (MQ=255)
cTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCta < 1:227979/81‑1 (MQ=255)
tCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGt < 2:610549/90‑1 (MQ=255)
cccTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTa > 2:97671/1‑90 (MQ=255)
ccTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTCGtaat < 2:189893/83‑1 (MQ=255)
ccTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTCGtaat > 1:189893/1‑83 (MQ=255)
tgggtgATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGttt > 1:51012/1‑90 (MQ=255)
ggtgATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCa > 2:368783/1‑90 (MQ=255)
gTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACaa > 1:404044/1‑90 (MQ=255)
aGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTtc < 2:29465/90‑1 (MQ=255)
ggTTAAATAAAACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTtct > 2:516973/1‑90 (MQ=255)
taaataaaACTTAAAGAAAGCGTAGCTATACTCGTAATAATTGTAAGaa > 2:912425/1‑49 (MQ=39)
taaataaaACTTAAAGAAAGCGTAGCTATACTCGTAATAATTGTAAGaa < 1:912425/49‑1 (MQ=39)
taaataaaACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGt < 2:250070/90‑1 (MQ=255)
aaataaaACTTAAAGAAAGCGTAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGtt > 1:338731/1‑90 (MQ=255)
aaataaaACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGaa < 2:210696/47‑1 (MQ=255)
aaataaaACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGaa > 1:210696/1‑47 (MQ=255)
aaataaaACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGtt > 2:58499/1‑90 (MQ=255)
aaattAAAGAAAGCGTAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGTTACAAAATTCGCTTTCTCGTTAGCTgc > 1:97381/4‑90 (MQ=255)
aaCTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTgc > 1:704474/1‑90 (MQ=255)
aCTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTgcg > 2:632359/1‑90 (MQ=255)
ttAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCt < 2:218794/90‑1 (MQ=255)
ttAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCt < 2:659020/90‑1 (MQ=255)
aaagaaagCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCttt < 2:266874/90‑1 (MQ=255)
aaagaaagCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCttt < 2:509264/90‑1 (MQ=255)
aaagaaagCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCttt < 1:632359/90‑1 (MQ=255)
aaagaaagCCTAGCTATACTCGTATTAA‑TGTAAGAATGTGCTTAAGCGTGGTTTCAGCTACAAAGTTCGCTTTCTAGTTAGCTGCGCttt < 2:97381/90‑1 (MQ=255)
aagCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTttatta > 1:812154/1‑90 (MQ=255)
aagCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTttatta > 1:462681/1‑90 (MQ=255)
|
AAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTA > NZ_CP009273/878923‑879094
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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
AAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTA > NZ_CP009273/878913‑879109
|
AAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAG > SRR3722072.29982/1‑100 (MQ=60)
GGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATAC < SRR3722072.720660/100‑1 (MQ=60)
GGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATAC < SRR3722072.168663/100‑1 (MQ=60)
GGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATAC < SRR3722072.898129/100‑1 (MQ=60)
TAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTC < SRR3722072.774404/100‑1 (MQ=60)
TAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTC < SRR3722072.889482/100‑1 (MQ=60)
CGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTCGTAAT < SRR3722072.231811/100‑1 (MQ=60)
ATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TG < SRR3722072.589909/100‑1 (MQ=60)
GTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAA > SRR3722072.193191/1‑100 (MQ=60)
GTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAA < SRR3722072.819205/100‑1 (MQ=60)
gagataatcggacgtctcgtgggctcggagatgtgtataagagacagGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGAATG < SRR3722072.849560/53‑1 (MQ=60)
tcgtgggctcggagatgtgtataagagacagGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGTAATAATTGTAAGAATGTGCTTAAC < SRR3722072.928106/69‑1 (MQ=60)
CTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTT > SRR3722072.51941/1‑100 (MQ=60)
GTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAA > SRR3722072.411332/1‑100 (MQ=60)
GGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTT > SRR3722072.344691/1‑100 (MQ=60)
GGCATAGGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCtgtctcttatacacatctccgagcccacgaga > SRR3722072.214288/1‑68 (MQ=60)
GGTTAAATAAAACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGC > SRR3722072.717041/1‑100 (MQ=60)
GGTTAAATAAAAATTAAAGAAAGCGTAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGTTACAAAATTCGCTTTCTCGTTAGCTGC > SRR3722072.99186/1‑100 (MQ=60)
AACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTA > SRR3722072.826302/1‑100 (MQ=60)
AACTTAAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTA > SRR3722072.471151/1‑100 (MQ=60)
AAAGAAAGCGCAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTC < SRR3722072.643656/100‑1 (MQ=60)
CAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTA < SRR3722072.59569/100‑1 (MQ=60)
CAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTA < SRR3722072.43412/100‑1 (MQ=60)
|
AAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGTAATAA‑TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTA > NZ_CP009273/878913‑879109
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
