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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
502,414 |
T→C |
D42G (GAT→GGT) |
ybaK ← |
Cys‑tRNA(Pro)/Cys‑tRNA(Cys) deacylase YbaK |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 502,414 | 0 | T | C | 100.0%
| 50.1
/ NA
| 16 | D42G (GAT→GGT) | ybaK | Cys‑tRNA(Pro)/Cys‑tRNA(Cys) deacylase YbaK |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (12/4); total (12/4) |
GACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGATCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACG > NZ_CP009273/502334‑502498
|
gACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCa > 1:653201/1‑90 (MQ=255)
gACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTaa > 2:402961/1‑90 (MQ=255)
cACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTc > 1:411208/1‑90 (MQ=255)
cACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTc > 2:340431/1‑90 (MQ=255)
aaGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGcc < 1:177106/90‑1 (MQ=255)
tttCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAAtt > 1:375995/1‑90 (MQ=255)
tCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCa > 1:315307/1‑90 (MQ=255)
gTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCgg > 1:289984/1‑90 (MQ=255)
gTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCgg > 1:483863/1‑90 (MQ=255)
gTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCgg > 1:539166/1‑90 (MQ=255)
cTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGt > 1:123409/1‑90 (MQ=255)
gCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGc < 2:411208/90‑1 (MQ=255)
accaGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCg > 1:216629/1‑90 (MQ=255)
accaGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCg > 1:412936/1‑90 (MQ=255)
aCCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAAc < 1:325114/90‑1 (MQ=255)
ccTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACg < 2:253775/90‑1 (MQ=255)
|
GACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGATCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACG > NZ_CP009273/502334‑502498
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ 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
TTAAGATCCAGTTGACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGATCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACGAAATCTTGTTTTTTT > NZ_CP009273/502321‑502513
|
ccaccgagatctacacattgacattcgtcggcagcgtcagatgtgtataagagacagCCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGATCCGGAT < SRR3722112.213721/43‑1 (MQ=60)
AGATCCAGTTGACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCA > SRR3722112.663391/1‑100 (MQ=60)
GCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTC > SRR3722112.416647/1‑100 (MQ=60)
CGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATT > SRR3722112.380867/1‑100 (MQ=60)
AAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTT < SRR3722112.179277/100‑1 (MQ=60)
GTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTnnnnnnnnnnnnnnnnnnnn > SRR3722112.538758/1‑80 (MQ=60)
GTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCA > SRR3722112.318942/1‑100 (MQ=60)
TCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGG > SRR3722112.293340/1‑100 (MQ=60)
TCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGG > SRR3722112.490820/1‑100 (MQ=60)
TCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGG > SRR3722112.547222/1‑100 (MQ=60)
TCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGT > SRR3722112.124937/1‑100 (MQ=60)
GTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCG > SRR3722112.219238/1‑100 (MQ=60)
GTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCG > SRR3722112.418392/1‑100 (MQ=60)
TTGTAGACCTGACCCGAATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACGAAA > SRR3722112.597108/1‑100 (MQ=60)
ACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACGAAATCTTGT < SRR3722112.328969/100‑1 (MQ=60)
CCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACGAAATCTTGTTTTTTT > SRR3722112.580140/1‑100 (MQ=60)
|
TTAAGATCCAGTTGACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGATCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACGAAATCTTGTTTTTTT > NZ_CP009273/502321‑502513
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
