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 |
1,966,502 |
Δ1 bp |
coding (447/1662 nt) |
tar ← |
methyl‑accepting chemotaxis protein II |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,966,500 | 0 | A | . | 100.0%
| 181.6
/ NA
| 42 | coding (449/1662 nt) | tar | methyl‑accepting chemotaxis protein II |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (19/23); total (19/23) |
ATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAAT > NZ_CP009273/1966413‑1966582
|
atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat > 2:919694/1‑89 (MQ=255)
atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat > 1:267986/1‑89 (MQ=255)
atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat > 2:139691/1‑89 (MQ=255)
atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat > 1:749665/1‑89 (MQ=255)
tatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaata < 2:921707/90‑3 (MQ=255)
tatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaata < 2:865893/90‑3 (MQ=255)
tatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaata < 1:987959/90‑3 (MQ=255)
gATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTcc < 1:1200871/90‑1 (MQ=255)
aTACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCa > 1:1088049/1‑90 (MQ=255)
aGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTAt < 2:1217207/90‑1 (MQ=255)
aGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTAt < 2:540279/90‑1 (MQ=255)
gTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTAtt > 2:942503/1‑90 (MQ=255)
ttttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGc > 1:309048/1‑90 (MQ=255)
ttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa < 1:462413/90‑1 (MQ=255)
ttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa < 2:127693/90‑1 (MQ=255)
ttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa < 2:32215/90‑1 (MQ=255)
ttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa < 1:747064/90‑1 (MQ=255)
ttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa < 2:745679/90‑1 (MQ=255)
ttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATCCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa < 2:697207/90‑1 (MQ=255)
tCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCAt > 1:1110358/1‑90 (MQ=255)
gctgAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCt > 1:776045/1‑90 (MQ=255)
gctgAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCt > 2:829692/1‑90 (MQ=255)
gctgAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCt > 1:220587/1‑90 (MQ=255)
tgAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAg < 1:942503/90‑1 (MQ=255)
gCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaat < 2:1088049/90‑1 (MQ=255)
cGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTcc < 2:1006975/66‑1 (MQ=255)
cGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTcc > 1:1006975/1‑66 (MQ=255)
tACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaa > 1:777828/1‑90 (MQ=255)
cTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaatc < 2:292764/90‑1 (MQ=255)
gAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcag > 1:962164/1‑90 (MQ=255)
gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa < 1:1212824/68‑1 (MQ=255)
gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa > 2:1212824/1‑68 (MQ=255)
gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt < 2:267986/90‑1 (MQ=255)
gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt > 2:658935/1‑90 (MQ=255)
cGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATcagttcagtt < 2:777828/90‑1 (MQ=255)
ttCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAAc > 1:952257/1‑90 (MQ=255)
ttCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAAc > 2:736546/1‑90 (MQ=255)
cGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGc < 2:558158/90‑1 (MQ=255)
cGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGc < 1:270986/90‑1 (MQ=255)
cGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGc < 2:335300/90‑1 (MQ=255)
cGCCCATTGCATTTTCCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGc < 2:315672/90‑1 (MQ=255)
cattttgcattCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAACCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATa < 1:895804/90‑1 (MQ=255)
gcattCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGc > 1:162147/1‑75 (MQ=255)
gcattCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGc < 2:162147/75‑1 (MQ=255)
ccTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATAttt > 1:1066524/1‑90 (MQ=255)
ggCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCaa > 1:411984/1‑90 (MQ=255)
gCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaatc < 1:818951/46‑1 (MQ=39)
gCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaatc > 2:818951/1‑46 (MQ=39)
gCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAat > 1:1030024/1‑90 (MQ=255)
|
ATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAAT > NZ_CP009273/1966413‑1966582
|
| 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
GTCAGTGACGATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAATATTACGACTGGTAGCGAC > NZ_CP009273/1966403‑1966600
|
GTCAGTGACGATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAT > SRR3722089.759587/1‑100 (MQ=60)
GTCAGTGACGATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAT > SRR3722089.271416/1‑100 (MQ=60)
GACGATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTC < SRR3722089.39336/100‑1 (MQ=60)
CGATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCA > SRR3722089.1104448/1‑100 (MQ=60)
TATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTA < SRR3722089.1002615/100‑1 (MQ=60)
GCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGC > SRR3722089.312960/1‑100 (MQ=60)
GATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCA < SRR3722089.1219132/100‑1 (MQ=60)
ATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCAT > SRR3722089.1127163/1‑100 (MQ=60)
GTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCT > SRR3722089.786577/1‑100 (MQ=60)
GTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCT > SRR3722089.223383/1‑100 (MQ=60)
tataagagacAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGAT < SRR3722089.1231273/90‑1 (MQ=60)
TTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGAT < SRR3722089.756918/100‑1 (MQ=60)
TTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGAT < SRR3722089.467930/100‑1 (MQ=60)
CTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCActgtctcttataca > SRR3722089.1021962/1‑86 (MQ=60)
GCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAA > SRR3722089.788402/1‑100 (MQ=60)
TGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATC < SRR3722089.956316/100‑1 (MQ=60)
AGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAG > SRR3722089.976352/1‑100 (MQ=60)
gtcgtcggcagcgtcagatgtgtataagagacagCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTA < SRR3722089.830447/66‑1 (MQ=60)
GAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAAC > SRR3722089.966244/1‑100 (MQ=60)
CGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAG < SRR3722089.274449/100‑1 (MQ=60)
ATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGctgtc > SRR3722089.164166/1‑95 (MQ=60)
CATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAACCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATAT < SRR3722089.908762/100‑1 (MQ=60)
TTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTT > SRR3722089.1082539/1‑100 (MQ=60)
TCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAA > SRR3722089.416971/1‑100 (MQ=60)
CCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAAT > SRR3722089.1045414/1‑100 (MQ=60)
AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAATATTACGACTGGTAGCGAC < SRR3722089.846239/100‑1 (MQ=60)
|
GTCAGTGACGATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAATATTACGACTGGTAGCGAC > NZ_CP009273/1966403‑1966600
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
