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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
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%
| 37.3
/ NA
| 13 | S84P (TCA→CCA) | btuB | TonB‑dependent vitamin B12 receptor BtuB |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (7/6); total (7/6) |
GACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGG > NZ_CP009273/4153729‑4153901
|
gACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCa > 2:294773/1‑90 (MQ=255)
cGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTc < 1:294773/90‑1 (MQ=255)
cGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTc < 2:270279/90‑1 (MQ=255)
gTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGGTCAGGGCAGCTCCCATCTATTTTTTTTTGGGGGACa > 2:113474/1‑90 (MQ=255)
tgtgCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCTGGTCAGCTCCCATCTATTTTTTTTCGCGGTACAAATGCCAg > 2:310971/1‑90 (MQ=255)
gctgcGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCa < 1:292653/90‑1 (MQ=255)
gcgcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTTTTCGCGGGACAAATGCCAGGCAtgt > 2:341630/1‑90 (MQ=255)
gcgcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCAtgt > 2:291096/1‑90 (MQ=255)
ttCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGgtgt < 1:197880/90‑1 (MQ=255)
gTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGAt < 1:291096/90‑1 (MQ=255)
cGATATCACCCAAAACGGCGGTCCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATgg > 2:301050/1‑90 (MQ=255)
tCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTAc < 1:329727/90‑1 (MQ=255)
gCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTgg > 2:23134/1‑90 (MQ=255)
|
GACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGG > NZ_CP009273/4153729‑4153901
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCT > NZ_CP009273/4153724‑4153886
|
ATATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTAT < SRR3722092.415635/100‑1 (MQ=60)
CGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAA < SRR3722092.299924/100‑1 (MQ=60)
GTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCCTCTATTTTTTTTTGCGGGACAAAAGCCAGTCATGTGTTGG > SRR3722092.34021/1‑100 (MQ=60)
GCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTG < SRR3722092.297741/100‑1 (MQ=60)
TTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGG < SRR3722092.201153/100‑1 (MQ=60)
GTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCC < SRR3722092.296154/100‑1 (MQ=60)
TCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCT < SRR3722092.335573/100‑1 (MQ=60)
|
ATATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCT > NZ_CP009273/4153724‑4153886
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
