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 F50 I1 R3
|
779 |
308.9 |
10220750 |
96.7% |
9883465 |
138.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP025268 |
2,997,537 |
(A)8→7 |
intergenic (‑140/+83) |
CXP41_RS15625 ← / ← CXP41_RS24400 |
response regulator transcription factor/hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP025268 | 2,997,530 | 0 | A | . | 100.0%
| 99.5
/ NA
| 22 | intergenic (‑133/+90) | CXP41_RS15625/CXP41_RS24400 | response regulator transcription factor/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (14/8); total (14/8) |
TCCCATATATTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATT > NZ_CP025268/2997392‑2997655
|
tCCCATATATTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTaa < 2:3130773/140‑1 (MQ=255)
ccATATATTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTaaaa < 1:2110295/140‑1 (MQ=255)
agccTGAGTGTAAATGCTTTAACGCATTCCTTTATAATCATCCCTTCCATTATTATTATAAGCAAATTCCAAATAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACcaca > 2:291216/3‑140 (MQ=255)
ccTGAGTGTAAATGCTTTAACGCATTCATTTTTAATCATCCCTTCCAGTATTATTATACGCAAAATCCAAAGTATCCATTGATGAAATAATAATAAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAGAATACCACTgg > 2:2419379/1‑140 (MQ=255)
aGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCAtt > 2:3677825/1‑140 (MQ=255)
aGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCAtt > 1:3396314/1‑140 (MQ=255)
gtAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTaaa < 1:23835/140‑1 (MQ=255)
cTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCAt > 1:3464048/1‑140 (MQ=255)
cTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCAt > 1:4011087/1‑140 (MQ=255)
ttAACGCATTCATTTATAATCATCCCTTCCATGATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATga > 2:2645055/1‑140 (MQ=255)
ttcattTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTa > 1:4513141/1‑140 (MQ=255)
cattTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTaaa < 1:2425616/140‑1 (MQ=255)
atcCCTTCCATTATTATTATAATCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACATGCATTAAAAAATCATGAGATTATTAAAATATTACAAtt < 2:3203344/140‑1 (MQ=255)
atcCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACTACAGGCATTAAAAAATGATGAGATGATTAAAATATTACAAtt > 2:2859288/1‑140 (MQ=255)
atcCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAAtt > 2:75691/1‑140 (MQ=255)
ccTTACATTATTATTATAATCAAAATACAAAGAATACATTGATAAAAAAATAATGAAATATAATTAAAAAAAAAATTTTTGCAT‑AAAAAAATAACACAGGCATTAAAAAATCATGAAATAAATAACATATTAAAATAAGa < 2:507256/140‑1 (MQ=255)
aGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTaa > 2:1648019/1‑140 (MQ=255)
aaTCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTg > 2:4726005/1‑140 (MQ=255)
aaGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTGGAGCCAg < 1:2873775/140‑1 (MQ=255)
aTACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAg < 1:3207738/140‑1 (MQ=255)
tgaAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAACAATCCCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTTAGCCAGGGAGCTATAAGTc > 2:2375671/1‑140 (MQ=255)
tgaAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTc > 2:1269297/1‑140 (MQ=255)
ataACTAAAAACAAAATTGTTGCGT‑AAAACAATACCACAGGCATTAAAAAGTCCTGAGATAATTAAAATATTACAATTAGATTCTATTCAAATCATTAAACTTCAGCAAGGGAGCTATTAGTCCCCAGGGCTTGCCaaat < 2:2081040/140‑2 (MQ=255)
ataaaatTTTTGCGT‑AAAAAAATACCACAGGCCTTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAattatt < 1:1573936/140‑1 (MQ=255)
|
TCCCATATATTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATT > NZ_CP025268/2997392‑2997655
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CCATATATTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAAC > NZ_CP025268/2997394‑2997680
|
CCATATATTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAG < SRR14920166.2114652/151‑1 (MQ=60)
TATTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATT > SRR14920166.3403539/1‑151 (MQ=60)
GAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCAT > SRR14920166.3471364/1‑151 (MQ=60)
GAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCAT > SRR14920166.4019869/1‑151 (MQ=60)
GTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGA < SRR14920166.23914/151‑1 (MQ=60)
GCTTTAACTCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTA > SRR14920166.4523129/1‑151 (MQ=60)
gagcgcgactgccacaatataagcctcctagagtccgtcgtttttttcaagcagaagacggcatacgagatctgcgcatgtctcgtgggctcggagatgtgtataagagacagATACCACAGGCATTAAAAAATCATGAGATGATTAAAAT < SRR14920166.1156716/38‑1 (MQ=60)
CATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATT < SRR14920166.2430551/151‑1 (MQ=60)
AAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTGGAGCCAGGGAGCTATAAG < SRR14920166.2879866/151‑1 (MQ=60)
ATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCT < SRR14920166.3214662/151‑1 (MQ=60)
ATAAAATTTTTGCGT‑AAAAAAATACCACAGGCCTTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAG < SRR14920166.1577146/151‑1 (MQ=60)
TAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACCATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAAC < SRR14920166.2650406/151‑1 (MQ=60)
|
CCATATATTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAAC > NZ_CP025268/2997394‑2997680
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
