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 I209 R1
|
216 |
14.4 |
815930 |
96.1% |
784108 |
85.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,527,151 |
T→C |
Q87Q (CAA→CAG) |
nanS ← |
9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,527,151 | 0 | T | C | 100.0%
| 55.6
/ NA
| 18 | Q87Q (CAA→CAG) | nanS | 9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (13/5); total (13/5) |
TGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTTTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAA > NZ_CP009273/4527079‑4527236
|
tGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCag < 2:352652/90‑1 (MQ=255)
ttATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGa < 2:371634/90‑1 (MQ=255)
aTCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATg < 2:201007/90‑1 (MQ=255)
gAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGAt > 2:182152/1‑90 (MQ=255)
aaGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAAccc < 1:336049/90‑1 (MQ=255)
aaGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAAccc > 2:172987/1‑90 (MQ=255)
aGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCt < 1:26193/90‑1 (MQ=255)
gCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCa > 1:270622/1‑90 (MQ=255)
ttCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGa > 1:88173/1‑90 (MQ=255)
cAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCa > 2:43768/1‑90 (MQ=255)
tGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTc > 1:96729/1‑90 (MQ=255)
gCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAg > 1:343108/1‑90 (MQ=255)
aCTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCATGTGGGCAGTGAGTCAGTGGAATAATGTCGt > 1:126519/1‑90 (MQ=255)
gtgtCTGATGATTCGTTGCCAGAGGCTGGTGATAACCCTGCATATCCTGTACATCGGGTGGGCAGTGAGTCAGTGGAATAATGTCGTTaa > 1:180954/1‑90 (MQ=255)
gtgtCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTaa > 1:8429/1‑90 (MQ=255)
gtgtCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTaa > 2:219817/1‑90 (MQ=255)
gtgtCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTaa > 2:270185/1‑90 (MQ=255)
gtgtCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTaa > 2:300981/1‑90 (MQ=255)
|
TGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTTTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAA > NZ_CP009273/4527079‑4527236
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ 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
ACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTTTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAAAGTGACATGG > NZ_CP009273/4527052‑4527246
|
GCGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTC > SRR3722091.275953/1‑100 (MQ=60)
gatctacactaagatggtcgtcggcagcgtcagatgtgtataagagacagGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGA < SRR3722091.314982/50‑1 (MQ=60)
GGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCA > SRR3722091.275050/1‑100 (MQ=60)
AAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCC < SRR3722091.341917/100‑1 (MQ=60)
AGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTG < SRR3722091.26558/100‑1 (MQ=60)
GGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGA > SRR3722091.89533/1‑100 (MQ=60)
ATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTC > SRR3722091.98226/1‑100 (MQ=60)
GCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAG > SRR3722091.349122/1‑100 (MQ=60)
ACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCATGTGGGCAGTGAGTCAGTGGAATAATGTCGT > SRR3722091.128427/1‑100 (MQ=60)
GTGCCGTAGTGTGTCTGATGATTCGTTGCCAGAGGCTGGTGATAACCCTGCATATCCTGTACATCGGGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAA > SRR3722091.183559/1‑100 (MQ=60)
GTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAA > SRR3722091.8551/1‑100 (MQ=60)
GTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATATCGTTAAAGTGA > SRR3722091.106186/1‑100 (MQ=60)
GTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAAAGTGACATGG > SRR3722091.138809/1‑100 (MQ=60)
|
ACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTTTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAAAGTGACATGG > NZ_CP009273/4527052‑4527246
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
