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 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,726,562 |
(T)5→4 |
coding (971/2574 nt) |
clpB ← |
ATP‑dependent chaperone ClpB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,726,558 | 0 | T | . | 100.0%
| 50.8
/ NA
| 13 | coding (975/2574 nt) | clpB | ATP‑dependent chaperone ClpB |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (6/7); total (6/7) |
TCTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGC > NZ_CP009273/2726469‑2726621
|
tCTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCt > 2:37651/1‑90 (MQ=255)
cTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCtt < 1:106940/90‑1 (MQ=255)
ttCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATg > 1:457379/1‑66 (MQ=255)
ttCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATg < 2:457379/66‑1 (MQ=255)
ttCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAATcgtc > 2:372987/1‑90 (MQ=255)
aaCAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTg < 2:148763/90‑1 (MQ=255)
aaCAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTg < 2:252668/90‑1 (MQ=255)
cAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGc < 1:418407/90‑1 (MQ=255)
gAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTg < 1:348045/86‑1 (MQ=255)
gAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTg > 2:348045/1‑86 (MQ=255)
aaGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCAcc < 1:167000/90‑1 (MQ=255)
aGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCt > 1:257224/1‑90 (MQ=255)
caacaaACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTg > 2:450025/1‑90 (MQ=255)
aacaaacaCTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGc < 1:37651/90‑1 (MQ=255)
cTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCAcgc > 1:452584/1‑90 (MQ=255)
|
TCTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGC > NZ_CP009273/2726469‑2726621
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ 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
CTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGCGCCGGTTTCAGCATGTTTCCGGCGTCCAT > NZ_CP009273/2726470‑2726656
|
CTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTAC < SRR3722114.108069/100‑1 (MQ=60)
CAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATctgtctcttataca > SRR3722114.463090/1‑86 (MQ=60)
CTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCT > SRR3722114.259797/1‑100 (MQ=60)
AACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGC < SRR3722114.352033/100‑1 (MQ=60)
CAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAG < SRR3722114.423537/100‑1 (MQ=60)
AAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGC < SRR3722114.168651/100‑1 (MQ=60)
AACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCAC < SRR3722114.38009/100‑1 (MQ=60)
CAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGC > SRR3722114.458228/1‑100 (MQ=60)
GCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGCGCCGGTTTCAGCATGTTTCCG > SRR3722114.445262/1‑100 (MQ=60)
tcTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGCGCCGGTTTCAGCATGTTTCCGGCGTCCAT > SRR3722114.526018/3‑100 (MQ=60)
|
CTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGCGCCGGTTTCAGCATGTTTCCGGCGTCCAT > NZ_CP009273/2726470‑2726656
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
