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 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
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%
| 27.7
/ NA
| 8 | 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 . (6/2); total (6/2) |
GGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAAT > NZ_CP009273/949946‑950107
|
ggCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGtttt > 1:457572/1‑90 (MQ=255)
cAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTa < 1:560731/90‑1 (MQ=255)
gCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGttttat > 1:570747/1‑70 (MQ=255)
gCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGttttat < 2:570747/72‑3 (MQ=255)
cATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAatat < 1:185507/90‑1 (MQ=255)
cATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAAtttt > 1:4260/1‑90 (MQ=255)
atatCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTa > 2:452771/1‑90 (MQ=255)
cGCCTGGCTTATAGGCCCGTAACTCGCATGGtttt > 1:582762/1‑35 (MQ=255)
cGCCTGGCTTATAGGCCCGTAACTCGCATGGtttt < 2:582762/35‑1 (MQ=255)
gCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTa > 1:183126/1‑90 (MQ=255)
ataGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAg > 1:266865/1‑90 (MQ=255)
cccGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGaa > 1:338104/1‑90 (MQ=255)
ccGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAAt > 1:461238/1‑90 (MQ=255)
|
GGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAAT > NZ_CP009273/949946‑950107
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ 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
TAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAAT > NZ_CP009273/949940‑950107
|
TAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGC < SRR3722109.75699/100‑1 (MQ=60)
TACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGctgtctct > SRR3722109.579401/1‑92 (MQ=60)
CAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGAT < SRR3722109.569239/100‑1 (MQ=60)
CATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCC < SRR3722109.187791/100‑1 (MQ=60)
TGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTT > SRR3722109.4329/1‑100 (MQ=60)
GATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACctgtctcttatacacatctgacgctgccgacgaatgtcaatgtgt > SRR3722109.591581/1‑55 (MQ=60)
ATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTA > SRR3722109.185379/1‑100 (MQ=60)
CGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAG > SRR3722109.270163/1‑100 (MQ=60)
GGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAA > SRR3722109.342590/1‑100 (MQ=60)
GCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAAT > SRR3722109.468159/1‑100 (MQ=60)
|
TAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAAT > NZ_CP009273/949940‑950107
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
