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 F3 I122 R1
|
193 |
20.9 |
1228102 |
94.7% |
1163012 |
84.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,180,586 |
(A)7→6 |
intergenic (+333/+77) |
yjaZ → / ← thiH |
heat‑shock protein C/2‑iminoacetate synthase ThiH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,180,580 | 0 | A | . | 100.0%
| 74.4
/ NA
| 18 | intergenic (+327/+83) | yjaZ/thiH | heat‑shock protein C/2‑iminoacetate synthase ThiH |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (6/12); total (6/12) |
TTTGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATAAAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCG > NZ_CP009273/4180491‑4180660
|
tttGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATa > 2:387363/1‑90 (MQ=255)
tttGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATa > 2:321643/1‑90 (MQ=255)
ttGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATaa > 1:133215/1‑90 (MQ=255)
ttGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATaa > 1:183753/1‑90 (MQ=255)
ttGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATaa > 2:126558/1‑90 (MQ=255)
ttGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATaa > 1:548066/1‑90 (MQ=255)
ttACGGAATTTTTAAGAAAGGCAGGGCGAAACTAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATaaaaaac < 1:292142/90‑2 (MQ=255)
aTTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGc < 2:183753/90‑1 (MQ=255)
aTTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGc < 2:273031/90‑1 (MQ=255)
aTTTTAAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGc < 2:196044/90‑1 (MQ=255)
aaGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGc < 1:222898/80‑1 (MQ=255)
aaGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGc > 2:222898/1‑80 (MQ=255)
aaGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCaacaac > 1:18743/1‑90 (MQ=255)
aGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTcaac > 2:157547/1‑86 (MQ=255)
aGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTcaac < 1:157547/86‑1 (MQ=255)
aGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCt < 1:547348/90‑1 (MQ=255)
gCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGc < 1:511906/90‑1 (MQ=255)
tCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTc < 1:122549/90‑1 (MQ=255)
aacaTTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAAttt < 2:113673/90‑1 (MQ=255)
caTTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTAc < 1:321643/90‑1 (MQ=255)
ttCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGt < 2:164134/90‑1 (MQ=255)
ccTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTc > 2:69410/1‑90 (MQ=255)
tgACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTTCGTTCTTACa > 2:45407/1‑90 (MQ=255)
gACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACAt > 1:147796/1‑90 (MQ=255)
gCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCg < 2:133215/90‑1 (MQ=255)
|
TTTGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATAAAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCG > NZ_CP009273/4180491‑4180660
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATAAAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACAT > NZ_CP009273/4180497‑4180656
|
TTACGGAATTTTTAAGAAAGGCAGGGCGAAACTAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTT < SRR3721989.297551/100‑1 (MQ=60)
ATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAAC > SRR3721989.19066/1‑100 (MQ=60)
ATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAAC < SRR3721989.226924/100‑1 (MQ=60)
AGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGT < SRR3721989.160405/100‑1 (MQ=60)
AGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGG < SRR3721989.559167/100‑1 (MQ=60)
GCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAAT < SRR3721989.522832/100‑1 (MQ=60)
TCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATT < SRR3721989.124795/100‑1 (MQ=60)
CATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACAT > SRR3721989.150474/1‑100 (MQ=60)
CATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACAT < SRR3721989.327762/100‑1 (MQ=60)
|
TTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATAAAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACAT > NZ_CP009273/4180497‑4180656
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
