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 F3 I96 R1
|
172 |
34.7 |
2005794 |
96.2% |
1929573 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,153,816 |
T→C |
S84P (TCA→CCA) |
btuB → |
TonB‑dependent vitamin B12 receptor BtuB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,153,816 | 0 | T | C | 100.0%
| 97.0
/ NA
| 30 | S84P (TCA→CCA) | btuB | TonB‑dependent vitamin B12 receptor BtuB |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (13/17); total (13/17) |
GATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGG > NZ_CP009273/4153756‑4153901
|
gatgTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGcc < 2:663136/90‑1 (MQ=255)
gatgTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGcc < 1:101850/90‑1 (MQ=255)
gtgCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTTTTTGCGGTACAAATGCCAGt > 2:828546/1‑90 (MQ=255)
tgctgcGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTTAGGGCAGCTCCCATCTATTTTTTTTTTCGGGACAAATGCCAATc > 2:970458/1‑90 (MQ=255)
gctgcGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCa < 2:820730/90‑1 (MQ=255)
gctgcGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCa < 2:408482/90‑1 (MQ=255)
gcgcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCCTCTATTTTTTTTTGCGGTACAAAAGCCCGTCAtgt > 1:388492/1‑90 (MQ=255)
gcgcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCCTCTATTTTTTTTTGCGGTACAAAAGCCAGTCAtgt > 1:930855/1‑90 (MQ=255)
gcgcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCAtgt > 2:437920/1‑90 (MQ=255)
gcgcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGGTCAGGTCCCCCCCCCTCGATTTTTATTCCCGGGACAAATGCCAGTctagt > 1:739393/1‑86 (MQ=255)
ccGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGtt < 1:437920/90‑1 (MQ=255)
gTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGAt < 2:534471/90‑1 (MQ=255)
gTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGAt < 1:815826/90‑1 (MQ=255)
atCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGAt < 2:268961/89‑1 (MQ=255)
tatCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGt < 1:621006/90‑1 (MQ=255)
tatCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGt < 1:420492/90‑1 (MQ=255)
tCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTAc < 2:478728/90‑1 (MQ=255)
tCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTAc < 1:370950/90‑1 (MQ=255)
aaaCGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGaa > 2:275645/1‑90 (MQ=255)
aaaCGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGGACAAAAGCCCGTCATGTGTTGGGGTTAATTTATGGGGTACGCCTGaa > 1:165512/1‑90 (MQ=255)
aaaCGGCGGGTCAGGTCCGCTCCCATCTATTTTTATTCGCGGTACAAAAACCCGTCATTGGTTGGGGTTGATTGATGGCGGACGCCTGaa > 1:762364/1‑90 (MQ=255)
aCGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATc < 2:182679/90‑1 (MQ=255)
aCGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATc < 2:90887/90‑1 (MQ=255)
gcggTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTgg > 2:399067/1‑90 (MQ=255)
cggTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGc > 2:940341/1‑90 (MQ=255)
cggTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGc < 1:161080/90‑1 (MQ=255)
cAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGt < 1:275645/90‑1 (MQ=255)
gCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCa < 1:84412/39‑1 (MQ=39)
gCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCa > 2:84412/1‑39 (MQ=39)
gCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTgg > 2:328958/1‑90 (MQ=255)
|
GATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGG > NZ_CP009273/4153756‑4153901
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CGTCAGGATATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGGTTCTGCCG > NZ_CP009273/4153717‑4153909
|
CGTCAGGATATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGCTCC > SRR3722236.78999/1‑100 (MQ=60)
CGTCAGGATATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGCTCC > SRR3722236.414191/1‑100 (MQ=60)
agccttcgtcggcagcgtcagatgtgtataagagacagGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATC < SRR3722236.262553/62‑1 (MQ=60)
GGATATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCT < SRR3722236.298620/100‑1 (MQ=60)
ATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCCTCTATTTTTTTTTGCGGTACAAAAGCCCGTCATGT > SRR3722236.393938/1‑100 (MQ=60)
ATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCCTCTATTTTTTTTTGCGGTACAAAAGCCAGTCATGT > SRR3722236.947289/1‑100 (MQ=60)
ATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGCTCCCATCTATTTTTTTTTGCGGGACAAAAGCCCGTCATGT > SRR3722236.279055/1‑100 (MQ=60)
GATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTTTTTGCGGGACAAAAGCCAGTCATGTGT > SRR3722236.268018/1‑100 (MQ=60)
GATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGT < SRR3722236.103270/100‑1 (MQ=60)
ctaagccttcgtcggcagcgtcagatgtgtataagagacaGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTG < SRR3722236.85578/60‑1 (MQ=60)
CCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATT < SRR3722236.444129/100‑1 (MQ=60)
GTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCC < SRR3722236.830033/100‑1 (MQ=60)
ATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGGACAAAAGCCCGTCATGTGTTGGGGTTAATTTATGGGGTACGCCTGAA > SRR3722236.167939/1‑100 (MQ=60)
ATATCACCCAAAACGGCGGGTCAGGTCCGCTCCCATCTATTTTTATTCGCGGTACAAAAACCCGTCATTGGTTGGGGTTGATTGATGGCGGACGCCTGAA > SRR3722236.775473/1‑100 (MQ=42)
TATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAAT < SRR3722236.426357/100‑1 (MQ=60)
TATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAAT < SRR3722236.631035/100‑1 (MQ=60)
TCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCT < SRR3722236.376174/100‑1 (MQ=60)
CGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGT < SRR3722236.163444/100‑1 (MQ=60)
CAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGGTTCTGCCG < SRR3722236.279658/100‑1 (MQ=60)
|
CGTCAGGATATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGGTTCTGCCG > NZ_CP009273/4153717‑4153909
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
