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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,934,547 |
T→C |
intergenic (‑97/+23) |
lpxM ← / ← mepM |
lauroyl‑Kdo(2)‑lipid IV(A) myristoyltransferase/murein DD‑endopeptidase MepM |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,934,547 | 0 | T | C | 100.0%
| 45.5
/ NA
| 15 | intergenic (‑97/+23) | lpxM/mepM | lauroyl‑Kdo(2)‑lipid IV(A) myristoyltransferase/murein DD‑endopeptidase MepM |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (10/5); total (10/5) |
CGGATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGTACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGA > NZ_CP009273/1934464‑1934624
|
cGGATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGc < 2:6240/90‑1 (MQ=255)
gCAAAAATCAACCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATg < 1:264910/90‑1 (MQ=255)
tAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGc > 1:278674/1‑90 (MQ=255)
tAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGc > 1:345125/1‑90 (MQ=255)
tAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGc > 2:440706/1‑90 (MQ=255)
aGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCt > 2:79789/1‑90 (MQ=255)
cggcgCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGc < 2:278674/90‑1 (MQ=255)
gcAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGca > 1:47321/1‑90 (MQ=255)
gcAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGca > 2:151619/1‑90 (MQ=255)
gcAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGca > 2:431936/1‑90 (MQ=255)
cTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAAt < 2:263399/90‑1 (MQ=255)
gCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTgg > 1:134520/1‑90 (MQ=255)
cACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGc > 1:441466/1‑90 (MQ=255)
aGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAAtt > 1:463713/1‑90 (MQ=255)
gTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGcga < 2:144433/90‑1 (MQ=255)
|
CGGATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGTACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGA > NZ_CP009273/1934464‑1934624
|
| 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
GCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGTACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGGAGCCGGTCAGCCC > NZ_CP009273/1934472‑1934644
|
GCAAAAATCAACCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATT < SRR3722111.268077/100‑1 (MQ=60)
GGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGC > SRR3722111.282165/1‑100 (MQ=60)
GGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGC > SRR3722111.349762/1‑100 (MQ=60)
GTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCA > SRR3722111.47899/1‑100 (MQ=60)
AACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGG > SRR3722111.136219/1‑100 (MQ=60)
ACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGC > SRR3722111.448108/1‑100 (MQ=60)
AAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATT > SRR3722111.470777/1‑100 (MQ=60)
GGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGGAG > SRR3722111.81543/1‑100 (MQ=60)
GACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGGAGCCGGTC > SRR3722111.148918/1‑100 (MQ=60)
CTGCGTACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGGAGCCGGTCAG > SRR3722111.230354/1‑100 (MQ=60)
CGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGGAGCCGGTCAGCCC < SRR3722111.1763/100‑1 (MQ=60)
|
GCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGTACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGGAGCCGGTCAGCCC > NZ_CP009273/1934472‑1934644
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
