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 |
3,715,736 |
T→C |
K674K (AAA→AAG) |
glyS ← |
glycine‑‑tRNA ligase subunit beta |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,715,736 | 0 | T | C | 100.0%
| 144.7
/ NA
| 39 | K674K (AAA→AAG) | glyS | glycine‑‑tRNA ligase subunit beta |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (22/17); total (22/17) |
CCTGCCAGATGGCAGGCTATTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGTTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACTTTATCGAAGAAAGCATCAACCGG > NZ_CP009273/3715653‑3715819
|
ccTGCCAGATGGCAGGCTATTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTcc > 1:291202/1‑90 (MQ=255)
tGGCAGGCTATTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTc < 1:125480/90‑1 (MQ=255)
tGGCAGGCTATTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTc < 2:217808/90‑1 (MQ=255)
cAGGCTATTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCCTCTCCAGCATGGTCAGa < 2:174647/90‑1 (MQ=255)
ggCTATTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACg < 1:110282/90‑1 (MQ=255)
ggCTATTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACg > 2:150466/1‑90 (MQ=255)
tttAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGa < 2:470875/90‑1 (MQ=255)
tttAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGa < 1:311300/90‑1 (MQ=255)
aCGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGa < 2:173798/76‑1 (MQ=255)
aCGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGa > 1:173798/1‑76 (MQ=255)
aCGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCaa > 1:444107/1‑90 (MQ=255)
aCGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCaa > 2:164543/1‑90 (MQ=255)
ggCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGa > 2:593667/1‑74 (MQ=255)
ggCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGa < 1:593667/74‑1 (MQ=255)
ggCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAAtt > 1:460491/1‑90 (MQ=255)
ggCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAAtt > 2:589694/1‑90 (MQ=255)
attGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGtcat > 1:448980/1‑90 (MQ=255)
ttGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGtcatc < 1:553317/90‑1 (MQ=255)
ttGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGtcatc < 1:594640/90‑1 (MQ=255)
ttGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGtcatc < 1:164543/90‑1 (MQ=255)
tGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGtcatca > 2:367075/1‑90 (MQ=255)
cAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCAt < 1:199662/90‑1 (MQ=255)
gAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGAcc > 2:303055/1‑90 (MQ=255)
gAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGAcc < 2:192432/90‑1 (MQ=255)
gAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGAcc > 1:192432/1‑90 (MQ=255)
aGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACTTTATCGAAGAAAGCATCa > 1:311871/1‑90 (MQ=255)
gTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACTTTATCGAAGAAAGCATCaa > 2:263754/1‑90 (MQ=255)
gTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACTTTATCGAAGAAAGCATCaa > 1:577079/1‑90 (MQ=255)
gTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACTTTATCGAAGAAAGCATCaa > 2:325527/1‑90 (MQ=255)
gTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACTTTATCGAAGAAAGCATCaa > 2:359682/1‑90 (MQ=255)
gTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACTTTATCGAAGAAAGCATCaa > 2:495150/1‑90 (MQ=255)
gTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACTTTATCGAAGAAAGCATCaa > 2:526004/1‑90 (MQ=255)
ttCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACTTTATCGAAGAAAGCATCAAc < 2:291202/90‑1 (MQ=255)
ttCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACTTTATCGAAGAAAGCATCAAc < 2:444107/90‑1 (MQ=255)
ttCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACTTTATCGAAGAAAGCATCAAc < 2:524955/90‑1 (MQ=255)
tCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGc > 2:180009/1‑39 (MQ=37)
tCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGc < 1:180009/39‑1 (MQ=255)
tCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACTTTATCGAAGAAAGCATCAAcc > 2:384460/1‑90 (MQ=255)
gcgcAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACTTTATCGAAGAAAGCATCAACCgg > 2:458421/1‑90 (MQ=255)
|
CCTGCCAGATGGCAGGCTATTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGTTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACTTTATCGAAGAAAGCATCAACCGG > NZ_CP009273/3715653‑3715819
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATAAAAAAAGCCTGCCAGATGGCAGGCTATTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGTTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACTTTATCGAAGAAAGCATCAACCGGTTCA > NZ_CP009273/3715643‑3715823
|
ATAAAAAAAGCCTGCCAGATGGCAGGCTATTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCC < SRR3721989.508983/100‑1 (MQ=60)
ATAAAAAAAGCCTGCCAGATGGCAGGCTATTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCC > SRR3721989.296582/1‑100 (MQ=60)
AAAAAAGCCTGCCAGATGGCAGGCTATTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGC < SRR3721989.489475/100‑1 (MQ=60)
TGGCAGGCTATTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGA < SRR3721989.127788/100‑1 (MQ=60)
agacagATTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATAT < SRR3721989.606576/94‑1 (MQ=60)
GGCTATTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGC < SRR3721989.112292/100‑1 (MQ=60)
CTATTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACctgt > SRR3721989.176988/1‑96 (MQ=60)
CTATTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAA > SRR3721989.453366/1‑100 (MQ=60)
ATTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATT > SRR3721989.470144/1‑100 (MQ=60)
TTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTC < SRR3721989.317191/100‑1 (MQ=60)
tccttacgtcgtcggcagcgtcagatgtgtataagagacaGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGT < SRR3721989.183309/60‑1 (MQ=60)
CGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCAT > SRR3721989.458349/1‑100 (MQ=60)
TTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACC > SRR3721989.195949/1‑100 (MQ=60)
TTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACC < SRR3721989.565307/100‑1 (MQ=60)
TTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACC < SRR3721989.167544/100‑1 (MQ=60)
TTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACC < SRR3721989.607565/100‑1 (MQ=60)
CAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACT < SRR3721989.203303/100‑1 (MQ=60)
GCGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACTTTATCGAAGAAAGCATCA > SRR3721989.317779/1‑100 (MQ=60)
CGCAGGAACAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACTTTATCGAAGAAAGCATCAA > SRR3721989.589603/1‑100 (MQ=60)
CAGTTCGCGCAGCTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACctgtctcttatacacatctgacgctgcc > SRR3721989.600792/1‑72 (MQ=60)
|
ATAAAAAAAGCCTGCCAGATGGCAGGCTATTTAATAACGGCGTTATTATTGCAACAGCGAAATATCCGCAACGCGCAGGAACAGTTCGCGCAGTTTCTCCAGCATGGTCAGACGGTTGATACGCAATTCTTTGTCATCAACCATGACCATCACTTTATCGAAGAAAGCATCAACCGGTTCA > NZ_CP009273/3715643‑3715823
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
