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 |
737,899 |
A→G |
N38N (AAT→AAC) |
dtpD ← |
dipeptide permease DtpD |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 737,899 | 0 | A | G | 100.0%
| 130.5
/ NA
| 35 | N38N (AAT→AAC) | dtpD | dipeptide permease DtpD |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (13/22); total (13/22) |
AAAAGCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATA > NZ_CP009273/737811‑737976
|
aaaaGCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGtt < 2:857123/91‑1 (MQ=255)
aaaaGCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGtt < 1:765035/91‑1 (MQ=255)
gCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTg < 2:1117277/91‑1 (MQ=255)
gCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTg < 1:937295/91‑1 (MQ=255)
cGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATa < 1:818298/91‑1 (MQ=255)
aGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATaga < 1:699754/91‑1 (MQ=255)
aGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATaga < 1:849408/91‑1 (MQ=255)
cGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATcagc < 2:38645/91‑1 (MQ=255)
cGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATcagc < 1:532546/91‑1 (MQ=255)
gACATACACCAGCGAACAGTAGGGGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAgg > 1:220481/1‑91 (MQ=255)
gACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAgg > 1:960774/1‑91 (MQ=255)
acacCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATa < 1:169465/73‑1 (MQ=255)
acacCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATa > 2:169465/1‑73 (MQ=255)
cAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATg < 2:809066/91‑1 (MQ=255)
aCAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTGTTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTaa < 1:519645/91‑1 (MQ=255)
cAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTaaa > 1:1091595/1‑91 (MQ=255)
gTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTaaaac > 2:81277/1‑90 (MQ=255)
aGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCt > 2:727027/1‑91 (MQ=255)
aGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCt > 2:827720/1‑91 (MQ=255)
ggCGCTAAATAACGCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTa < 2:502667/91‑1 (MQ=255)
aaCTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTccc < 1:827720/91‑1 (MQ=255)
aaCTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTccc < 2:543699/91‑1 (MQ=255)
aCTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCa > 2:767145/1‑91 (MQ=255)
cGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGAt > 1:1093695/1‑91 (MQ=255)
tAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGAttt > 2:469/1‑91 (MQ=255)
tGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAgcg > 1:984169/1‑91 (MQ=255)
gAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAgcgc > 1:374451/1‑91 (MQ=255)
tATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAAc < 2:464164/91‑1 (MQ=255)
tATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAAc < 1:911643/91‑1 (MQ=255)
tCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGa < 2:1091595/91‑1 (MQ=255)
gtgttATTTTAGTTGGTTGGTGAGATAGAGAATCAGCGGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACa < 2:833178/87‑1 (MQ=37)
gTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACa < 2:262771/91‑1 (MQ=255)
gTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACa < 1:745940/91‑1 (MQ=255)
gTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACa < 1:371016/91‑1 (MQ=255)
tGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATa > 2:308228/1‑91 (MQ=255)
|
AAAAGCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATA > NZ_CP009273/737811‑737976
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 31 ≤ 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
GCCAAAAAGCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTAAATAGCGCGCGGCTGTGATG > NZ_CP009273/737807‑737999
|
GCCAAAAAGCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGTTTGGTGAG < SRR3722125.1022069/101‑1 (MQ=60)
AAAAGCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAG < SRR3722125.781631/101‑1 (MQ=60)
catacgagatcatgcctagtctcgtgggctcggagatgtgtataagagacagTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAA < SRR3722125.590201/49‑1 (MQ=60)
GCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAA < SRR3722125.958100/101‑1 (MQ=60)
agagacagGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGC < SRR3722125.172733/93‑1 (MQ=60)
CGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGC < SRR3722125.836231/101‑1 (MQ=60)
AGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAG < SRR3722125.868111/101‑1 (MQ=60)
AGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAG < SRR3722125.714832/101‑1 (MQ=60)
GGATTGGCGTGACATACACCAGCGAACAGTAGGGGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGG > SRR3722125.224845/1‑101 (MQ=60)
GGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGG > SRR3722125.982188/1‑101 (MQ=60)
CGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCA < SRR3722125.543905/101‑1 (MQ=60)
CACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAA > SRR3722125.1116156/1‑101 (MQ=60)
ACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTGTTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAAT < SRR3722125.530698/101‑1 (MQ=60)
CTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGAT > SRR3722125.1118306/1‑101 (MQ=60)
AACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAG < SRR3722125.845902/101‑1 (MQ=60)
CTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCG > SRR3722125.1006147/1‑101 (MQ=60)
TCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGC > SRR3722125.382292/1‑101 (MQ=60)
TATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTAA < SRR3722125.931843/101‑1 (MQ=60)
cagGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTAAATAG < SRR3722125.679369/98‑1 (MQ=60)
cagGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTAAATAG < SRR3722125.832343/98‑1 (MQ=60)
GTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTAAATAG < SRR3722125.762028/101‑1 (MQ=60)
GTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTAAATAG < SRR3722125.378786/101‑1 (MQ=60)
ATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTAAATAGCGCGC > SRR3722125.481141/1‑101 (MQ=60)
GTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTAAATAGCGCGCGGCTGTGATG < SRR3722125.1080297/101‑1 (MQ=60)
|
GCCAAAAAGCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTAAATAGCGCGCGGCTGTGATG > NZ_CP009273/737807‑737999
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
