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 I208 R1
|
222 |
13.1 |
731276 |
96.6% |
706412 |
85.9 |
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%
| 85.7
/ NA
| 20 | coding (449/1662 nt) | tar | methyl‑accepting chemotaxis protein II |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (6/14); total (6/14) |
ATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCA > NZ_CP009273/1966413‑1966580
|
atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat > 2:167332/1‑89 (MQ=255)
atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat > 2:88577/1‑89 (MQ=255)
tatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaata < 2:27188/90‑3 (MQ=255)
aGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTAt < 1:167332/90‑1 (MQ=255)
cACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATa < 2:232981/90‑1 (MQ=255)
cACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATa < 2:224502/90‑1 (MQ=255)
tgctgAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATc < 1:43282/90‑1 (MQ=255)
tgAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAg < 1:122997/90‑1 (MQ=255)
cTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaatc < 1:333796/90‑1 (MQ=255)
cTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaatc < 2:294746/90‑1 (MQ=255)
tGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAatcaatca > 1:242620/1‑90 (MQ=255)
aGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagt > 2:41791/1‑90 (MQ=255)
gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaa < 2:183349/84‑1 (MQ=255)
gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaa > 1:183349/1‑84 (MQ=255)
ttCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGAt < 1:190002/70‑1 (MQ=255)
ttCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGAt > 2:190002/1‑70 (MQ=255)
ttCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAAc < 1:325946/90‑1 (MQ=255)
ttCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAAc < 1:163536/90‑1 (MQ=255)
tGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTtcatca < 1:153901/90‑1 (MQ=255)
ggCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt < 2:246034/51‑1 (MQ=255)
ggCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt > 1:74113/1‑51 (MQ=255)
ggCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt < 2:74113/51‑1 (MQ=255)
ggCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt > 1:246034/1‑51 (MQ=255)
|
ATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCA > NZ_CP009273/1966413‑1966580
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAATATTACGAC > NZ_CP009273/1966425‑1966590
|
AGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATC < SRR3722090.169061/100‑1 (MQ=60)
TGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCA < SRR3722090.43725/100‑1 (MQ=60)
TGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATC < SRR3722090.124306/100‑1 (MQ=60)
GAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCA > SRR3722090.245523/1‑100 (MQ=60)
taagagacagGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAG < SRR3722090.192071/90‑1 (MQ=60)
GGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTT > SRR3722090.185312/1‑100 (MQ=60)
CTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTA < SRR3722090.338142/100‑1 (MQ=60)
TTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAAT < SRR3722090.165194/100‑1 (MQ=60)
TTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAAT < SRR3722090.330176/100‑1 (MQ=60)
TCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCctgtctcttatacacatctccgagcccac > SRR3722090.248994/1‑71 (MQ=60)
TCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCctgtctcttatacacatctccgagcccac > SRR3722090.74934/1‑71 (MQ=60)
TGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAATATTACGAC < SRR3722090.155469/100‑1 (MQ=60)
|
AGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAATATTACGAC > NZ_CP009273/1966425‑1966590
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
