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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
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 | 100.0%
| 67.1
/ NA
| 21 | S84P (TCA→CCA) | btuB | TonB‑dependent vitamin B12 receptor BtuB |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (7/14); total (7/14) |
ACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGG > NZ_CP009273/4153730‑4153894
|
aCCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCAt < 1:584517/90‑1 (MQ=255)
ggCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTAttt > 1:534374/1‑90 (MQ=255)
gTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTGAGGGCAAGGCCCAGCTAttttttt > 1:698463/1‑88 (MQ=255)
ccTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTcgcg < 2:264542/90‑1 (MQ=255)
gTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCCCCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACa < 1:195031/90‑1 (MQ=255)
tCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACaa < 2:74906/90‑1 (MQ=255)
atgatgTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTTAGGGGAGGCCCCATCTATTTTTTTTTGCGGGAaaaaag > 2:137799/1‑88 (MQ=255)
atgatgTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGGTCAGGTCAGCTCCCCCCTTTTTTTTTTTGCGGGACaaaac > 1:277650/1‑88 (MQ=255)
tgatgTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGc < 2:198545/90‑1 (MQ=255)
gatgTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGcc < 1:322018/90‑1 (MQ=255)
gtgCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGCTCCCATCTATTTTTATTCGCGGGACAAATGCCAGt > 2:422427/1‑90 (MQ=255)
gcgcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGATCAGGTCAGCTCCCCTCTATTTTTTTTCCCCGGACAAAAGCCAGGCAtgt > 2:519890/1‑90 (MQ=255)
gcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATgtgt < 1:510879/90‑1 (MQ=255)
cGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTg < 1:711168/90‑1 (MQ=255)
cTTCCGGGCGTCGATATCCCCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGgtg < 2:666125/90‑1 (MQ=255)
ttCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGgtgt < 1:130196/90‑1 (MQ=255)
gTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGAt < 2:247283/90‑1 (MQ=255)
tCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTAc < 2:534374/90‑1 (MQ=255)
tCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATCGATGGCGTAc < 2:402799/90‑1 (MQ=255)
tCACCCAAAACGGCGGTTCAGGGCAGCTCCCATCTATTTTTATTCGCGGTACAAAAGCCAGTCATGTGTTGGGGTTAATTGATGGCGTAc > 2:762033/1‑90 (MQ=255)
cAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCggggg < 2:356995/90‑1 (MQ=255)
|
ACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGG > NZ_CP009273/4153730‑4153894
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 19 ≤ 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
AGGATATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGGTTCTGCCGACCTT > NZ_CP009273/4153721‑4153914
|
AGGATATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATC < SRR3722073.134814/100‑1 (MQ=60)
ATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGGTCAGGTCCGCTCCCATCTATTT > SRR3722073.545525/1‑100 (MQ=60)
ACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTAT < SRR3722073.596724/100‑1 (MQ=60)
nnnnnnnnnnnnnnnnnnnaTCAATGATGTGCTGCGCCGTCTTCCGGTCGTCGATATAACCCAAAACGGCGGTTCTGGTCAGCTCCCATCTATTTTTATT < SRR3722073.275983/80‑1 (MQ=60)
GTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCCCCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTC < SRR3722073.198930/100‑1 (MQ=60)
ATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTTCGGGCAGCTCCCCTCTATTTTTTTTCGCGGTACAAAaggcaggcctgg > SRR3722073.373421/1‑88 (MQ=60)
gtataagagacagGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGT < SRR3722073.542538/87‑1 (MQ=60)
GATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGT < SRR3722073.328847/100‑1 (MQ=60)
GCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAAT < SRR3722073.521646/100‑1 (MQ=60)
CGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTG < SRR3722073.725538/100‑1 (MQ=60)
TTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGG < SRR3722073.132921/100‑1 (MQ=60)
TCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTTTTTTCGGGACAAAAGCCAGTCATGTGTTGGTGctgtctctttta > SRR3722073.607055/1‑88 (MQ=60)
GGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGGGAGTGGTTCTG > SRR3722073.10680/1‑100 (MQ=60)
GCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGGTTCTGCCGAC > SRR3722073.315693/1‑100 (MQ=60)
CCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCGGAATCTGGCGGGGGTGAGTGGTTCTGCCGACCTT > SRR3722073.437127/1‑100 (MQ=60)
|
AGGATATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGGTTCTGCCGACCTT > NZ_CP009273/4153721‑4153914
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
