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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
502,414 |
T→C |
D42G (GAT→GGT) |
ybaK ← |
Cys‑tRNA(Pro)/Cys‑tRNA(Cys) deacylase YbaK |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 502,414 | 0 | T | C | 100.0%
| 101.7
/ NA
| 32 | D42G (GAT→GGT) | ybaK | Cys‑tRNA(Pro)/Cys‑tRNA(Cys) deacylase YbaK |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (26/6); total (26/6) |
TCCAGTTGACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGATCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACG > NZ_CP009273/502327‑502498
|
tCCAGTTGACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGAccc < 1:1226777/90‑1 (MQ=255)
ccTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCaaa > 1:239899/1‑90 (MQ=255)
ccTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCaaa > 2:522366/1‑90 (MQ=255)
gCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCt > 2:772887/1‑90 (MQ=255)
cGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAAttt > 2:774475/1‑90 (MQ=255)
ggTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCaa < 2:1318591/90‑1 (MQ=255)
tttCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAAtt > 1:1447340/1‑90 (MQ=255)
tataaCCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGttt > 2:1433/5‑90 (MQ=255)
tCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGtt > 1:1138865/1‑87 (MQ=255)
tCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGtt < 2:1138865/87‑1 (MQ=255)
tCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGtt < 2:1540883/87‑1 (MQ=255)
tCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGtt > 1:1540883/1‑87 (MQ=255)
tCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCa > 2:747431/1‑90 (MQ=255)
tCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCa > 1:1209239/1‑90 (MQ=255)
aCCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGc > 2:221773/1‑90 (MQ=255)
aCCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGc > 1:699456/1‑90 (MQ=255)
gTTCACTGCCACCAGCAGCGTTTTGTAGACCTGAccc > 1:782081/1‑37 (MQ=255)
gTTCACTGCCACCAGCAGCGTTTTGTAGACCTGAccc < 2:782081/37‑1 (MQ=255)
gTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCgg > 1:459546/1‑90 (MQ=255)
gTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCgg > 2:44559/1‑90 (MQ=255)
gTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCgg > 2:1290138/1‑90 (MQ=255)
ttCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGa > 2:806569/1‑90 (MQ=255)
cTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGt > 1:516868/1‑90 (MQ=255)
cTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGt > 1:268054/1‑90 (MQ=255)
caccaGCAGCGTTTTGTAGACCTGACCCGGATTTAAACCTAATTTTTTGACGACTCCACAGCCAAAATTGGTTTCAGCCGGATCGTGCTc < 2:1271536/90‑1 (MQ=255)
accaGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCg > 2:1024398/1‑90 (MQ=255)
accaGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCg > 1:1201922/1‑90 (MQ=255)
accaGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCg > 1:118342/1‑90 (MQ=255)
cagcagCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTa < 1:1127309/90‑1 (MQ=255)
cagcGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGt > 2:1505495/1‑90 (MQ=255)
cagcGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGt > 1:292929/1‑90 (MQ=255)
gACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGaaa > 2:106814/1‑90 (MQ=255)
ccTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAAc < 1:677505/89‑1 (MQ=255)
ccTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAAc > 2:677505/1‑89 (MQ=255)
ccTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACg > 1:404327/1‑90 (MQ=255)
|
TCCAGTTGACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGATCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACG > NZ_CP009273/502327‑502498
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATCCAGTTGACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGATCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACGAAATCTTGT > NZ_CP009273/502326‑502507
|
ATCCAGTTGACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAA > SRR3722078.242829/1‑100 (MQ=60)
TCCAGTTGACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAAC < SRR3722078.1246102/100‑1 (MQ=60)
CGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATT > SRR3722078.1470931/1‑100 (MQ=60)
GTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCA > SRR3722078.1156356/1‑100 (MQ=60)
GTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCA > SRR3722078.1566002/1‑100 (MQ=60)
GTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCA > SRR3722078.1228239/1‑100 (MQ=60)
GTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGC > SRR3722078.707875/1‑100 (MQ=60)
TCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTgtctcttatacacatctgacgctgccgacgatggcgggcgt > SRR3722078.792260/1‑59 (MQ=60)
TCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGG > SRR3722078.465038/1‑100 (MQ=60)
TCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGT > SRR3722078.271328/1‑100 (MQ=60)
TCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGT > SRR3722078.522984/1‑100 (MQ=60)
GTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCG > SRR3722078.1220771/1‑100 (MQ=60)
GTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCG > SRR3722078.119726/1‑100 (MQ=60)
CTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGT > SRR3722078.296498/1‑100 (MQ=60)
CAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATT < SRR3722078.1144549/100‑1 (MQ=60)
GTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACG > SRR3722078.409230/1‑100 (MQ=60)
TTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACGAA > SRR3722078.1003136/1‑100 (MQ=60)
ACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACGAAATCTTGT < SRR3722078.685332/100‑1 (MQ=60)
|
ATCCAGTTGACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGATCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACGAAATCTTGT > NZ_CP009273/502326‑502507
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
