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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
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%
| 46.8
/ NA
| 12 | 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 . (8/4); total (8/4) |
TCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAATTTTTTCCGC > NZ_CP009273/949944‑950116
|
tCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGtt > 1:1100486/1‑90 (MQ=255)
cgacgaGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGttttat < 1:935917/90‑3 (MQ=255)
tACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATAc < 2:855700/90‑1 (MQ=255)
aCTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACg < 1:840143/90‑1 (MQ=255)
cTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACgg < 2:159019/90‑1 (MQ=255)
gaAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCaa > 1:782782/1‑90 (MQ=255)
aaTTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCaaat > 2:501544/1‑90 (MQ=255)
cGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAAtt > 1:984906/1‑90 (MQ=255)
ccTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTaa > 2:334188/1‑90 (MQ=255)
cccGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGaa > 2:430662/1‑90 (MQ=255)
ccGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAAt > 2:1180749/1‑90 (MQ=255)
ccGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAAt > 2:19928/1‑90 (MQ=255)
ccGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAAt > 2:560878/1‑90 (MQ=255)
gCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAATTTTTTCCGc < 1:844882/90‑1 (MQ=255)
|
TCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAATTTTTTCCGC > NZ_CP009273/949944‑950116
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ 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
|
TAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGTTTATAGGCCCGTAACTCGCATGG‑TTTTATGC < SRR3722089.176529/100‑1 (MQ=60)
TAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTCTAGGCCAGTACCTCGCATGG‑TTTTATGC < SRR3722089.368038/100‑1 (MQ=60)
TAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGC < SRR3722089.305349/100‑1 (MQ=60)
TAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGC < SRR3722089.373275/100‑1 (MQ=60)
CGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGG < SRR3722089.949615/100‑1 (MQ=60)
tgtgtataagagacagGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAG < SRR3722089.263403/84‑1 (MQ=60)
ACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATAT < SRR3722089.852046/100‑1 (MQ=60)
TTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAA > SRR3722089.793459/1‑100 (MQ=60)
GATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATT > SRR3722089.999505/1‑100 (MQ=60)
GCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAATTTTTTCCGCATCCTCCGCT < SRR3722089.856885/100‑1 (MQ=60)
GTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAATTTTTTCCGCATCCTCCGCTAAAAC > SRR3722089.408310/1‑100 (MQ=60)
|
TAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAATTTTTTCCGCATCCTCCGCTAAAAC > NZ_CP009273/949940‑950131
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
