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 I208 R1
|
222 |
13.1 |
731276 |
96.6% |
706412 |
85.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,814,267 |
A→G |
A368A (GCT→GCC) |
alaS ← |
alanine‑‑tRNA ligase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,814,267 | 0 | A | G | 100.0%
| 50.0
/ NA
| 15 | A368A (GCT→GCC) | alaS | alanine‑‑tRNA ligase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (7/8); total (7/8) |
AAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGA > NZ_CP009273/2814185‑2814341
|
aaGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACt < 1:91950/90‑1 (MQ=255)
aCCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCttcttc < 1:62837/90‑1 (MQ=255)
aCCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCttcttc < 2:69213/90‑1 (MQ=255)
gCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTtcttcagtcttca > 2:120390/1‑90 (MQ=255)
aTCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCAc < 2:59080/90‑1 (MQ=255)
tCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCAcc > 1:10151/1‑90 (MQ=255)
aGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTc > 1:355549/1‑90 (MQ=255)
aGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTc > 1:8732/1‑90 (MQ=255)
gCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGt > 2:280536/1‑90 (MQ=255)
aaCGCCAGACCGCGCTCCAGAGTACGGGCAACCTGCTCTTCTGCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCt < 2:198403/90‑1 (MQ=255)
aaCGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCt < 2:355549/90‑1 (MQ=255)
gCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCa > 1:130954/1‑90 (MQ=255)
cgcgCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCag < 1:120390/90‑1 (MQ=255)
cgcgCTCCAGAGTACCGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCag < 1:245091/90‑1 (MQ=255)
gcgcTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCaga > 2:185125/1‑90 (MQ=255)
|
AAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGA > NZ_CP009273/2814185‑2814341
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ 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
AAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGTCG > NZ_CP009273/2814185‑2814354
|
AAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTC < SRR3722090.92948/100‑1 (MQ=60)
ACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGC < SRR3722090.63513/100‑1 (MQ=60)
ATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACC > SRR3722090.10263/1‑100 (MQ=60)
GCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTC > SRR3722090.360179/1‑100 (MQ=60)
GCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTC > SRR3722090.8826/1‑100 (MQ=60)
ATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCA > SRR3722090.132337/1‑100 (MQ=60)
CGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAAC < SRR3722090.121668/100‑1 (MQ=60)
CGCGCTCCAGAGTACCGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAAC < SRR3722090.248036/100‑1 (MQ=60)
CTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGTCG > SRR3722090.152108/1‑100 (MQ=60)
CTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGTCG > SRR3722090.259034/1‑100 (MQ=60)
|
AAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGTCG > NZ_CP009273/2814185‑2814354
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
