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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
950,036 |
(T)5→4 |
intergenic (‑114/+292) |
focA ← / ← ycaO |
formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 950,032 | 0 | T | . | 100.0%
| 48.7
/ NA
| 13 | intergenic (‑110/+296) | focA/ycaO | formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (4/9); total (4/9) |
GGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAG > NZ_CP009273/949946‑950101
|
ggCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGtttt < 2:480921/90‑1 (MQ=255)
tACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATAc < 1:539113/90‑1 (MQ=255)
cTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACgg < 1:524132/90‑1 (MQ=255)
cAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTa < 1:143140/90‑1 (MQ=255)
cAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTa < 1:187738/90‑1 (MQ=255)
cAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTa < 1:289400/90‑1 (MQ=255)
cAAAACATTATAGATAAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTa < 2:661296/90‑1 (MQ=255)
aTTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACgg > 1:732687/1‑80 (MQ=255)
aTTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACgg < 2:732687/80‑1 (MQ=255)
taGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGAt < 1:757154/90‑1 (MQ=255)
taGATGAGAAATTGATATAGATCACATCTCTCCTGGCTTATAGGCCCGTAACGCGCATGG‑TTTTATGCAAATACGGAGTAAATCTTTTAt < 2:433800/90‑1 (MQ=255)
gagaAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATcc > 1:600462/1‑90 (MQ=255)
gCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTa > 1:808745/1‑90 (MQ=255)
ataGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAg > 2:634289/1‑90 (MQ=255)
|
GGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAG > NZ_CP009273/949946‑950101
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 27 ≤ 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
TAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAATTTTTTCCGCATCCTCCGCTAAAAC > NZ_CP009273/949940‑950131
|
atcggacgtctcgtgggctcggagatgtgtataagagacagAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGC < SRR3722072.810390/59‑1 (MQ=60)
acggcatacgagataatcggacgtctcgtgggctcggagatgtgtataagagacagTATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGC < SRR3722072.701045/44‑1 (MQ=60)
TAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGC < SRR3722072.185349/100‑1 (MQ=60)
TAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGC < SRR3722072.250268/100‑1 (MQ=60)
TACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATA < SRR3722072.548815/100‑1 (MQ=60)
CTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATT < SRR3722072.533559/100‑1 (MQ=60)
CTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATT > SRR3722072.745681/1‑100 (MQ=60)
CAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGAT < SRR3722072.145700/100‑1 (MQ=60)
CAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGAT < SRR3722072.191000/100‑1 (MQ=60)
CAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGAT < SRR3722072.294396/100‑1 (MQ=60)
CATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCC > SRR3722072.611177/1‑100 (MQ=60)
TAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATA < SRR3722072.770512/100‑1 (MQ=60)
ATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTA > SRR3722072.822846/1‑100 (MQ=60)
GGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATActgtctcttatacacatctccgagcccacgagacgtccgattatctcgta > SRR3722072.352107/1‑50 (MQ=60)
GTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAATTTTTTCCGCATCCTCCGCTAAAAC > SRR3722072.223453/1‑100 (MQ=60)
|
TAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAATTTTTTCCGCATCCTCCGCTAAAAC > NZ_CP009273/949940‑950131
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
