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 I205 R1
|
220 |
17.5 |
961422 |
97.1% |
933540 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,717,969 |
T→C |
E237G (GAA→GGA) |
glyQ ← |
glycine‑‑tRNA ligase subunit alpha |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,717,969 | 0 | T | C | 100.0%
| 58.6
/ NA
| 18 | E237G (GAA→GGA) | glyQ | glycine‑‑tRNA ligase subunit alpha |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (9/9); total (9/9) |
TGGCTTTACGCGCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTTCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCCGCGTATTCGA > NZ_CP009273/3717889‑3718047
|
tGGCTTTACGCGCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCca > 1:109189/1‑90 (MQ=255)
gcATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCtgctgc < 2:119430/90‑1 (MQ=255)
cagcagGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGcttc < 2:84148/90‑1 (MQ=255)
cagcagGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGcttc < 2:84017/90‑1 (MQ=255)
cagcagGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGcttc < 2:126406/90‑1 (MQ=255)
ttGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCg > 1:294479/1‑90 (MQ=255)
gtgGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTc > 1:398847/1‑90 (MQ=255)
gtgGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTc > 1:271572/1‑90 (MQ=255)
gtgGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTc > 1:162266/1‑90 (MQ=255)
ggcggcTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGaa < 2:176007/90‑1 (MQ=255)
tttCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGt < 2:294479/90‑1 (MQ=255)
tACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGa < 2:83085/90‑1 (MQ=255)
cGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAg > 1:468293/1‑90 (MQ=255)
tCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTcc < 1:427578/90‑1 (MQ=255)
gTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCcac > 2:217202/1‑90 (MQ=255)
aGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACAt > 1:455328/1‑90 (MQ=255)
ggcagcggcagcGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCcgcg > 2:124568/1‑90 (MQ=255)
gcagcggATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCCGCGTATTCGa < 1:162862/90‑1 (MQ=255)
|
TGGCTTTACGCGCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTTCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCCGCGTATTCGA > NZ_CP009273/3717889‑3718047
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ 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
GACGCTCGGTGACGGAGATGGCTTTACGCGCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTTCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCCGCGTATTCGAAGTTGTAAGT > NZ_CP009273/3717871‑3718057
|
GACGCTCGGTGACGGAGATGGCTTTACGCGCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCC > SRR3722087.83857/1‑100 (MQ=60)
GTGACGGAGATGGCTTTACGCGCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCA > SRR3722087.110242/1‑100 (MQ=60)
ATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCG > SRR3722087.297481/1‑100 (MQ=60)
GGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTC > SRR3722087.163752/1‑100 (MQ=60)
GGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTC > SRR3722087.274242/1‑100 (MQ=60)
GGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTC > SRR3722087.403463/1‑100 (MQ=60)
TTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAG > SRR3722087.473741/1‑100 (MQ=60)
ATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACAT > SRR3722087.460633/1‑100 (MQ=60)
TCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCCGCGT < SRR3722087.432562/100‑1 (MQ=60)
GCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCCGCGTATTCGAAGTTGTAAGT < SRR3722087.164349/100‑1 (MQ=60)
|
GACGCTCGGTGACGGAGATGGCTTTACGCGCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTTCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCCGCGTATTCGAAGTTGTAAGT > NZ_CP009273/3717871‑3718057
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
