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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
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%
| 89.9
/ NA
| 22 | coding (449/1662 nt) | tar | methyl‑accepting chemotaxis protein II |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (6/16); total (6/16) |
ATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTT > NZ_CP009273/1966413‑1966575
|
atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat > 2:44455/1‑89 (MQ=255)
atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat > 2:32017/1‑89 (MQ=255)
atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat > 2:523313/1‑89 (MQ=255)
atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat < 1:32017/90‑2 (MQ=255)
atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat < 2:76425/90‑2 (MQ=255)
atCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaataa < 1:569181/90‑4 (MQ=255)
aTACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCa > 1:249330/1‑90 (MQ=255)
aGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTAt < 2:234340/90‑1 (MQ=255)
ttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa < 1:206562/90‑1 (MQ=255)
ttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa < 1:51407/90‑1 (MQ=255)
ttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa < 1:447640/90‑1 (MQ=255)
gctgAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCt > 1:477591/1‑90 (MQ=255)
tgAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAg < 1:328097/90‑1 (MQ=255)
cTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaatc < 1:488026/90‑1 (MQ=255)
cTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaatc < 1:520691/90‑1 (MQ=255)
aGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTAGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaatc < 1:254299/87‑1 (MQ=255)
aGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTAGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaatc > 2:254299/1‑87 (MQ=255)
gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt < 2:111921/90‑1 (MQ=255)
gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt < 2:237893/90‑1 (MQ=255)
gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt < 1:210961/90‑1 (MQ=255)
gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt < 2:477591/90‑1 (MQ=255)
gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt < 2:417522/90‑1 (MQ=255)
ttCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAAc < 1:214996/90‑1 (MQ=255)
cattttgcattCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATa < 2:95383/90‑1 (MQ=255)
ttgcattCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGttt > 1:67170/1‑90 (MQ=255)
tGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATAttttt > 2:324364/1‑90 (MQ=255)
gCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCtg < 2:101353/62‑1 (MQ=255)
gCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCtg > 1:101353/1‑62 (MQ=255)
|
ATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTT > NZ_CP009273/1966413‑1966575
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ 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
TGACGATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAAT > NZ_CP009273/1966408‑1966582
|
gatgtgtataagagacagGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCT < SRR3722111.206548/82‑1 (MQ=60)
CGATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCA > SRR3722111.252258/1‑100 (MQ=60)
ATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGT < SRR3722111.32403/100‑1 (MQ=60)
ATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTAT < SRR3722111.578133/100‑1 (MQ=60)
GTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCT > SRR3722111.484908/1‑100 (MQ=60)
nnnnnnnnnnnnnnnnnnnnGAGCAAACGCTTCGCCCATTGCTTTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGAT < SRR3722111.265642/80‑1 (MQ=60)
TTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGAT < SRR3722111.209103/100‑1 (MQ=60)
TTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGAT < SRR3722111.454410/100‑1 (MQ=60)
TTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGAT < SRR3722111.52027/100‑1 (MQ=60)
TGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATC < SRR3722111.332490/100‑1 (MQ=60)
CTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTA < SRR3722111.495523/100‑1 (MQ=60)
CTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTA < SRR3722111.528828/100‑1 (MQ=60)
CTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTAGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTA < SRR3722111.257292/100‑1 (MQ=60)
GCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGC < SRR3722111.213541/100‑1 (MQ=60)
TTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAAT < SRR3722111.217618/100‑1 (MQ=60)
CCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTT > SRR3722111.67965/1‑100 (MQ=60)
CCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTctgtctcttatacacatc > SRR3722111.102616/1‑82 (MQ=60)
|
TGACGATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAAT > NZ_CP009273/1966408‑1966582
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
