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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
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%
| 59.5
/ NA
| 15 | 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 . (8/7); total (8/7) |
TCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAATTTTTTCCGCA > NZ_CP009273/949944‑950117
|
tCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGtt > 1:134603/1‑90 (MQ=255)
cgacgaGATACTAACAAAGCATTATAGATGAGAAACTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGttttat < 2:715172/90‑3 (MQ=255)
aCTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACg < 2:342432/90‑1 (MQ=255)
cTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACgg < 2:392613/90‑1 (MQ=255)
cAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTa < 1:443084/90‑1 (MQ=255)
cAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTa < 2:605033/90‑1 (MQ=255)
cATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAatat < 1:632045/90‑1 (MQ=255)
tGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATc > 1:410177/1‑90 (MQ=255)
tatCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTaa > 1:427589/1‑90 (MQ=255)
tctcGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTaaaa > 2:669455/1‑90 (MQ=255)
cGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTa > 1:638315/1‑51 (MQ=255)
cGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTa < 2:638315/51‑1 (MQ=255)
ccGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAatat > 2:716774/1‑40 (MQ=38)
ccGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAatat < 1:716774/40‑1 (MQ=38)
ccGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAAt > 1:478042/1‑90 (MQ=255)
gTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAAttt > 2:163870/1‑90 (MQ=255)
cATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAATTTTTTCCGCa > 2:67946/1‑90 (MQ=255)
|
TCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAATTTTTTCCGCA > NZ_CP009273/949944‑950117
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ 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
TAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAATTTTTTCCGCATCCTCCGCTAAAACAGTT > NZ_CP009273/949940‑950135
|
TAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGC < SRR3722112.140117/100‑1 (MQ=60)
CAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGAT < SRR3722112.449228/100‑1 (MQ=60)
GCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATC > SRR3722112.415605/1‑100 (MQ=60)
ttgacattcgtcggcagcgtcagatgtgtataagagacaGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCC < SRR3722112.727964/61‑1 (MQ=60)
CATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCC < SRR3722112.641826/100‑1 (MQ=60)
ATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAA > SRR3722112.433334/1‑100 (MQ=60)
GATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATctgtctcttatacacatctgacgctgccg > SRR3722112.648229/1‑71 (MQ=60)
GCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAAT > SRR3722112.484891/1‑100 (MQ=60)
TATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAATTTTTTCCGCATCCTCCGCTAAAACAGTT < SRR3722112.184308/100‑1 (MQ=60)
|
TAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAATTTTTTCCGCATCCTCCGCTAAAACAGTT > NZ_CP009273/949940‑950135
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
