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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
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%
| 68.4
/ 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 . (7/10); total (7/10) |
TTGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATAAAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCG > NZ_CP009273/4180492‑4180660
|
ttGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATaa > 2:158006/1‑90 (MQ=255)
aCGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATaaaaaacac > 1:333678/1‑87 (MQ=255)
ggAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACaa < 2:333678/90‑1 (MQ=255)
aTTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGc < 2:37467/90‑1 (MQ=255)
aaaCGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGc > 1:348608/1‑69 (MQ=255)
aaaCGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGc < 2:348608/69‑1 (MQ=255)
aaaCGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTcaac < 1:315431/76‑1 (MQ=255)
aaaCGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTcaac > 2:315431/1‑76 (MQ=255)
aaaCGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGttttt > 1:50436/1‑90 (MQ=255)
aCGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCa < 2:164667/90‑1 (MQ=255)
aGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCt > 2:129332/1‑90 (MQ=255)
gaagCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGc < 1:113596/74‑1 (MQ=255)
gaagCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGc > 2:113596/1‑74 (MQ=255)
cTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAAt > 1:227161/1‑90 (MQ=255)
caTTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTAc < 2:50436/90‑1 (MQ=255)
ttCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGt < 2:397698/90‑1 (MQ=255)
ccTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTc > 2:333464/1‑90 (MQ=255)
gACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACAt < 1:247209/90‑1 (MQ=255)
gCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCg < 2:24556/90‑1 (MQ=255)
|
TTGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATAAAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCG > NZ_CP009273/4180492‑4180660
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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
ACTTTGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATAAAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGTCTCATAGTCTTTGCGAGGC > NZ_CP009273/4180489‑4180680
|
ACTTTGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACAC > SRR3722092.339574/1‑100 (MQ=60)
acaggtcCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGT < SRR3722092.321011/93‑1 (MQ=60)
AGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTgtctcttat > SRR3722092.354900/1‑91 (MQ=60)
AGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTT > SRR3722092.51287/1‑100 (MQ=60)
agacaGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATC < SRR3722092.115523/95‑1 (MQ=60)
GCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAAT > SRR3722092.230879/1‑100 (MQ=60)
GACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGTCTCAT < SRR3722092.251219/100‑1 (MQ=60)
CGGCACTACCAT‑AAAAAACACAACGCCTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGTCTCATAG > SRR3722092.469199/1‑100 (MQ=60)
AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGTCTCATAGTCTTTGCGAGGC > SRR3722092.138827/1‑100 (MQ=60)
AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGTCTCATAGTCTTTGCGAGGC > SRR3722092.198383/1‑100 (MQ=60)
|
ACTTTGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATAAAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGTCTCATAGTCTTTGCGAGGC > NZ_CP009273/4180489‑4180680
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
