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 F5 I102 R1
|
278 |
39.1 |
2251254 |
95.8% |
2156701 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
441,393 |
A→C |
F244V (TTC→GTC) |
yajR ← |
MFS transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 441,393 | 0 | A | C | 100.0%
| 116.3
/ NA
| 33 | F244V (TTC→GTC) | yajR | MFS transporter |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (20/13); total (20/13) |
CTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTC > NZ_CP009273/441306‑441478
|
cTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAcccc < 2:523240/91‑1 (MQ=255)
tCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTg > 2:156729/1‑91 (MQ=255)
cAGCGTAGATAAGGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGc > 1:1108044/1‑91 (MQ=255)
gCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCAt > 2:528713/1‑91 (MQ=255)
gATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGcc < 2:472434/91‑1 (MQ=255)
gATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGcc > 2:460454/1‑91 (MQ=255)
tAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAg < 1:1033493/91‑1 (MQ=255)
ataaaaGGCAGGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGCCCTTCCAGTGTTCAGCCGCCGGGACCCCTGGATCAGCCAGtt < 2:958495/88‑1 (MQ=255)
aTGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGtt > 2:892690/1‑91 (MQ=255)
aaaGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTc < 2:86196/91‑1 (MQ=255)
aGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCg > 1:572166/1‑91 (MQ=255)
ggCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCgg > 1:184585/1‑91 (MQ=255)
ggCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCgg > 1:907560/1‑91 (MQ=255)
ggCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCgg > 1:302972/1‑91 (MQ=255)
cACGCCCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCgggc < 2:725579/91‑1 (MQ=255)
cACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCgggc > 1:204501/1‑91 (MQ=255)
aCGTCCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAg < 1:772401/80‑1 (MQ=255)
aCGACCGAGCCAACGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAg > 2:772401/1‑80 (MQ=255)
gACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCgggcagg < 2:286324/91‑1 (MQ=255)
gAGCCAAAGGCGATTAGCATTGTCGCCAGATCGACCTTGCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCggacagggtac > 2:553433/1‑88 (MQ=255)
aaaGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAAc > 2:59188/1‑91 (MQ=255)
gATTAGCATTGTCGCCAGATGGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGAc > 2:734054/1‑91 (MQ=255)
aTTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCa > 1:146523/1‑91 (MQ=255)
ttGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCaa < 1:352544/91‑1 (MQ=255)
gTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAACCGTCGACATCCGCaaaa > 2:869845/1‑91 (MQ=255)
tCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAat < 1:460454/91‑1 (MQ=255)
cAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGc < 1:279312/91‑1 (MQ=255)
aTAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGa < 2:282557/91‑1 (MQ=255)
tAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGac < 2:865536/91‑1 (MQ=255)
gACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGacac > 1:632005/1‑91 (MQ=255)
cTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAACCGTCGACATCAGCAAAATATGCAGACACATa < 1:917/91‑1 (MQ=255)
tCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAAt > 2:1121943/1‑91 (MQ=255)
gccgGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGtt > 1:475479/1‑91 (MQ=255)
gccgGGACCCATGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGtt > 1:594180/1‑91 (MQ=255)
cgGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTc > 1:242847/1‑91 (MQ=255)
|
CTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTC > NZ_CP009273/441306‑441478
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ 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
CGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCC > NZ_CP009273/441299‑441493
|
CGCTTAACTTCAGCGTAGATAAGGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGC > SRR3722125.1133008/1‑101 (MQ=60)
AACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAG < SRR3722125.873370/101‑1 (MQ=60)
AGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCG > SRR3722125.584408/1‑101 (MQ=60)
GATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGG > SRR3722125.188168/1‑101 (MQ=60)
GATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGG > SRR3722125.309178/1‑101 (MQ=60)
GATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGG > SRR3722125.927666/1‑101 (MQ=60)
TAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGC > SRR3722125.208538/1‑101 (MQ=60)
TAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGC < SRR3722125.1056675/101‑1 (MQ=60)
AAATGAAAGGCACGTCCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGC < SRR3722125.789184/101‑1 (MQ=60)
AGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCtgtctcttatacacatctccgag > SRR3722125.220693/1‑78 (MQ=60)
GGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCA > SRR3722125.149316/1‑101 (MQ=60)
TTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGA < SRR3722125.359919/101‑1 (MQ=60)
TCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACAC < SRR3722125.470164/101‑1 (MQ=60)
TCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACAC > SRR3722125.645619/1‑101 (MQ=60)
CAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAA < SRR3722125.284968/101‑1 (MQ=60)
CTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAACCGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGT < SRR3722125.952/101‑1 (MQ=60)
GTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTT > SRR3722125.485504/1‑101 (MQ=60)
GTGTTCAGCCGCCGGGACCCATGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTT > SRR3722125.606957/1‑101 (MQ=60)
GTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTC > SRR3722125.247716/1‑101 (MQ=60)
CCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCC > SRR3722125.37594/1‑101 (MQ=60)
|
CGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCC > NZ_CP009273/441299‑441493
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
