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 |
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%
| 88.6
/ NA
| 22 | coding (449/1662 nt) | tar | methyl‑accepting chemotaxis protein II |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (9/13); total (9/13) |
GATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAAT > NZ_CP009273/1966420‑1966582
|
gATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTcc > 2:199238/1‑90 (MQ=255)
gATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTcc < 1:89438/90‑1 (MQ=255)
aGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTAt < 1:511611/90‑1 (MQ=255)
tttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGcc > 2:195114/1‑90 (MQ=255)
tCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTAtt > 2:75730/1‑85 (MQ=255)
tCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTAtt < 1:75730/85‑1 (MQ=255)
aGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGAt < 1:378974/90‑1 (MQ=255)
aGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAg > 1:149072/1‑77 (MQ=255)
aGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAg < 2:149072/77‑1 (MQ=255)
aGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagt > 1:6517/1‑90 (MQ=255)
gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt < 1:195114/90‑1 (MQ=255)
gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt < 2:200930/90‑1 (MQ=255)
gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt < 1:63096/90‑1 (MQ=255)
aaCGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagttcag > 2:60268/1‑90 (MQ=255)
cGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGc < 1:480/90‑1 (MQ=255)
cGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGc < 1:280221/90‑1 (MQ=255)
cGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGc < 2:89014/90‑1 (MQ=255)
aTTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTgtgt > 1:478317/1‑90 (MQ=255)
ttCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa > 2:195876/1‑40 (MQ=38)
ttCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa < 1:195876/40‑1 (MQ=38)
tGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTtcatca < 2:38129/90‑1 (MQ=255)
gCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAat > 2:227434/1‑90 (MQ=255)
|
GATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAAT > NZ_CP009273/1966420‑1966582
|
| 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
GATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAATATTACGACTGGTAG > NZ_CP009273/1966420‑1966596
|
GATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCA < SRR3722109.90554/100‑1 (MQ=60)
AGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATC < SRR3722109.519366/100‑1 (MQ=60)
GTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCT < SRR3722109.76646/100‑1 (MQ=60)
ttgacattcgtcggcagcgtcagatgtgtataagagacagGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGAT < SRR3722109.198267/60‑1 (MQ=60)
AGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAG < SRR3722109.384342/100‑1 (MQ=60)
GGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCctg > SRR3722109.150911/1‑97 (MQ=60)
GGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGT > SRR3722109.6615/1‑100 (MQ=60)
GCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGC < SRR3722109.197497/100‑1 (MQ=60)
GCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGC < SRR3722109.63840/100‑1 (MQ=60)
CGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGT > SRR3722109.485525/1‑100 (MQ=60)
CGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAG < SRR3722109.283760/100‑1 (MQ=60)
CGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAG < SRR3722109.486/100‑1 (MQ=60)
GGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAATATTAC > SRR3722109.498383/1‑100 (MQ=60)
AGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAATATTACGACTGGTAG < SRR3722109.315968/100‑1 (MQ=60)
|
GATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAATATTACGACTGGTAG > NZ_CP009273/1966420‑1966596
|
| 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: ‑ |
