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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
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%
| 68.7
/ NA
| 17 | 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 . (8/9); total (8/9) |
TTTGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATAAAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTC > NZ_CP009273/4180491‑4180658
|
tttGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATa > 1:24793/1‑90 (MQ=255)
ttGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATaa > 2:699661/1‑90 (MQ=255)
ttGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATaa > 1:595035/1‑90 (MQ=255)
tACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATaaaaaaca > 2:386086/1‑88 (MQ=255)
ggAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACaa < 2:359308/90‑1 (MQ=255)
ggAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACaa < 2:24559/90‑1 (MQ=255)
ttttAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCtt < 1:267131/90‑1 (MQ=255)
ttCGCCCTGGATAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCt > 1:194548/1‑90 (MQ=255)
ttCGCCCGGTACAACATTCCTGCTGACGGCACTACCCT‑AAAAACCCCAACCCTTTTAAAAACCTTGCGTTTTTCCTGTTCCGAAGCGGCt > 1:335133/1‑90 (MQ=255)
tCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTc < 2:270435/90‑1 (MQ=255)
tCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTc < 2:153881/90‑1 (MQ=255)
acaTTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTa > 1:218329/1‑90 (MQ=255)
caTTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTAc < 2:244742/90‑1 (MQ=255)
ttCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGt < 2:294304/90‑1 (MQ=255)
ccTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTc > 2:307505/1‑90 (MQ=255)
ccTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTc > 2:716281/1‑90 (MQ=255)
ccTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAAATTACGttt > 1:90384/1‑89 (MQ=255)
gACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTCCCGTAGCGGCTCGGAATAAATTTACGTTCTTACAt > 1:362295/1‑90 (MQ=255)
cGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTc < 2:334105/90‑1 (MQ=255)
cGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTc > 1:510626/1‑90 (MQ=255)
cGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTc < 1:351025/90‑1 (MQ=255)
|
TTTGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATAAAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTC > NZ_CP009273/4180491‑4180658
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 30 ≤ 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
ACTTTGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATAAAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGTCTCATAGTCTTTGCGAGGCGCGTC > NZ_CP009273/4180489‑4180685
|
ACTTTGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACAC < SRR3722112.381901/100‑1 (MQ=60)
gccgtcagcaggaatgttgtcCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTCCTGACTGCACTACCAT‑AAAAAACACAACGCTTT > SRR3722112.535058/22‑100 (MQ=60)
TTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCT < SRR3722112.270261/100‑1 (MQ=60)
GAAGAAGCTTTTCGCCCTGGATAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCT > SRR3722112.196927/1‑100 (MQ=60)
GAAGAAGCTTTTCGCCCGGTACAACATTCCTGCTGACGGCACTACCCT‑AAAAACCCCAACCCTTTTAAAAACCTTGCGTTTTTCCTGTTCCGAAGCGGCT > SRR3722112.339206/1‑100 (MQ=28)
GCCTTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTA > SRR3722112.220959/1‑100 (MQ=60)
GGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAAATTACGTTT > SRR3722112.91516/1‑100 (MQ=60)
CATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTCCCGTAGCGGCTCGGAATAAATTTACGTTCTTACAT > SRR3722112.366935/1‑100 (MQ=60)
TTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTC > SRR3722112.518083/1‑100 (MQ=60)
CGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGTCTCATAG < SRR3722112.355456/100‑1 (MQ=60)
CTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCtgtctcttatacac > SRR3722112.443909/1‑86 (MQ=60)
AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGTCTCATAGTCTTTGCGAGGC > SRR3722112.566301/1‑100 (MQ=60)
AAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGTCTCATAGTCTTTGCGAGGCGCC > SRR3722112.578320/1‑100 (MQ=60)
ACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGTCTCATAGTCTTTGCGAGGCGCGTC > SRR3722112.589678/1‑100 (MQ=60)
|
ACTTTGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATAAAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGTCTCATAGTCTTTGCGAGGCGCGTC > NZ_CP009273/4180489‑4180685
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
