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 I206 R1
|
206 |
23.7 |
1314362 |
96.8% |
1272302 |
86.2 |
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%
| 36.3
/ NA
| 13 | 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 (10/3); total (10/3) |
AATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGTACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATC > NZ_CP009273/1934481‑1934629
|
aatcTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGttaat > 1:141368/1‑90 (MQ=255)
gTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCa > 2:533430/1‑90 (MQ=255)
gTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCAAATGGATGTTAATTAATCa > 2:337507/1‑90 (MQ=255)
gtgtAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGt > 2:539109/1‑90 (MQ=255)
gcgcAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCgg > 1:606304/1‑90 (MQ=255)
gcAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGca > 1:395680/1‑90 (MQ=255)
gcAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGca > 1:454208/1‑90 (MQ=255)
gcAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGca > 2:278665/1‑90 (MQ=255)
gcAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTAACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGca > 2:448973/1‑90 (MQ=255)
ccAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCt < 1:473423/90‑1 (MQ=255)
ccAAATAAAAAAAGCCGGTACTAACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCt < 1:584206/90‑1 (MQ=255)
gactgCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATc > 1:1275/1‑90 (MQ=255)
gactgCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATc < 2:141368/90‑1 (MQ=255)
|
AATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGTACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATC > NZ_CP009273/1934481‑1934629
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CATGCTTTTCCAGTTTCGGATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGTACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGGAGCCGGTCAG > NZ_CP009273/1934448‑1934641
|
CATGCTTTTCCAGTTTCGGATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGC < SRR3722088.601960/100‑1 (MQ=60)
GGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAAT > SRR3722088.142817/1‑100 (MQ=60)
TAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGG > SRR3722088.613772/1‑100 (MQ=60)
GTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCA > SRR3722088.399946/1‑100 (MQ=60)
GTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCA > SRR3722088.459509/1‑100 (MQ=60)
CCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAA < SRR3722088.479026/100‑1 (MQ=60)
CCAAATAAAAAAAGCCGGTACTAACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAA < SRR3722088.591373/100‑1 (MQ=60)
AGCCNGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATC > SRR3722088.1293/1‑100 (MQ=60)
CTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGGAGCCGGTCAG > SRR3722088.32671/1‑100 (MQ=60)
|
CATGCTTTTCCAGTTTCGGATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGTACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGGAGCCGGTCAG > NZ_CP009273/1934448‑1934641
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
