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 I122 R1
|
193 |
20.9 |
1228102 |
94.7% |
1163012 |
84.0 |
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 | 94.7%
| 59.9
/ ‑4.1
| 19 | coding (250/1845 nt) | btuB | TonB‑dependent vitamin B12 receptor BtuB |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (8/10); minor base . (1/0); total (9/10) |
| Fisher's exact test for biased strand distribution p-value = 4.74e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGT > NZ_CP009273/4153744‑4153899
|
aCCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTcgc < 2:598736/90‑1 (MQ=255)
gtgCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTTAGGTCAGCTCCCCTCTTTTTTTTTTTGCGGGACAAAAGCCAgg > 1:130810/1‑89 (MQ=255)
gctgcGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCa < 1:598229/90‑1 (MQ=255)
ctgcGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGC‑‑‑‑‑TCTATTTTTTTTCGCGGTACAAAAGCCAGTCATGTGtt > 1:147919/1‑90 (MQ=255)
gcgcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTTTTCGCGGTACAAAAGCCAGTCAtgt > 1:169761/1‑90 (MQ=255)
gcgcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCAtgt > 2:493481/1‑90 (MQ=255)
cGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTg < 1:562706/90‑1 (MQ=255)
gTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAAAGCCAGTCATGTGTTgg > 2:130431/1‑90 (MQ=255)
ttCCGGGCGTCGATATCACACAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGgtgt < 1:104571/90‑1 (MQ=255)
gggCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAAt < 1:188135/90‑1 (MQ=255)
cGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCCTCTATTTTTTTTTGCGGGACAAAAGCCAGTCATGTGTTGGGGTTAAttta > 1:176267/1‑88 (MQ=255)
gTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTTTTCGCGGGACAAATGCCAGTCATGTGTTGGGGTTAATTGAt > 2:188135/1‑90 (MQ=255)
gTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGAt < 1:539755/90‑1 (MQ=255)
atCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTa < 1:176815/90‑1 (MQ=255)
cccAAAACGGCGGTTCAGGTCAGCTCCCCTCTATTTTTTTTTGCGGGACAAAAGCCAGTCATGGGTTGGGGTTTATTTATGGCGTACGcc > 1:257129/1‑90 (MQ=255)
gTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCgg < 1:493481/90‑1 (MQ=255)
cAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGt < 1:232498/90‑1 (MQ=255)
gCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATgtgt < 1:236602/44‑1 (MQ=255)
gCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATgtgt > 2:236602/1‑44 (MQ=255)
|
ACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGT > NZ_CP009273/4153744‑4153899
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 15 ≤ 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
CAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGGTTCTGCCG > NZ_CP009273/4153752‑4153909
|
CAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGC‑‑‑‑‑TCTATTTTTTTTCGCGGTACAAAAGCCAGTCATGTGTT > SRR3721989.150598/1‑100 (MQ=60)
ATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTTTTCGCGGTACAAAAGCCAGTCATGT > SRR3721989.172875/1‑100 (MQ=60)
ATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGCTCCCATCTATTTTTTTTTGCGGGACAAAAGCCAGTCATGC > SRR3721989.347202/1‑100 (MQ=60)
GCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTG < SRR3721989.611231/100‑1 (MQ=60)
acgtcgtcggcagcgtcagatgtgtataagagacaGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAAT < SRR3721989.240847/65‑1 (MQ=60)
CGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTG < SRR3721989.574908/100‑1 (MQ=60)
GTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCCTCTATTTTTTTTTGCGGGACAAAAGCCAGTCATGTGTTGGGGTTAATTTA > SRR3721989.179492/1‑100 (MQ=60)
TTCCGGGCGTCGATATCACACAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGG < SRR3721989.106486/100‑1 (MQ=60)
GGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTA < SRR3721989.191581/100‑1 (MQ=60)
GTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCCTCTATTTTTTTTTGCGGGACAAAAGCCAGTCATGGGTTGGGGTTTATTTATGGCGTACGCC > SRR3721989.261699/1‑100 (MQ=52)
GTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCC < SRR3721989.551378/100‑1 (MQ=60)
ATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATC < SRR3721989.180050/100‑1 (MQ=60)
GTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGG < SRR3721989.503932/100‑1 (MQ=60)
GGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGGTTCTG > SRR3721989.84359/1‑100 (MQ=60)
CAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGGTTCTGCCG < SRR3721989.236681/100‑1 (MQ=60)
|
CAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGGTTCTGCCG > NZ_CP009273/4153752‑4153909
|
| 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: ‑ |
