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 F5 I102 R1
|
278 |
39.1 |
2251254 |
95.8% |
2156701 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
509,698 |
A→C |
T84P (ACG→CCG) |
cueR → |
Cu(I)‑responsive transcriptional regulator |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 509,698 | 0 | A | C | 100.0%
| 98.4
/ NA
| 28 | T84P (ACG→CCG) | cueR | Cu(I)‑responsive transcriptional regulator |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (16/12); total (16/12) |
GCAGGTGGGCTTTAACCTGGAAGAGAGCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCACGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATGCGCGACCAGCTGCTGGCACTGGCGAATGCCTGC > NZ_CP009273/509610‑509784
|
gCAGGTGGGCTTTAACCTGGAAGAGAGCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCg < 2:539563/91‑1 (MQ=255)
cAGGTGGGCTTTAACCTGGAAGAGAGCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGc < 1:404071/91‑1 (MQ=255)
ggTGGGCTTTAACCTGGAAGAGAGCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTg > 1:346743/1‑91 (MQ=255)
ggTGGGCTTTAACCTGGAAGAGAGCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTg > 2:967456/1‑91 (MQ=255)
gCTTTAACCTGGAAGAGAGCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGaa > 2:406541/1‑91 (MQ=255)
tttAACCTGGAAGAGAGCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAgg < 1:710468/91‑1 (MQ=255)
agagCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGa > 2:775054/1‑91 (MQ=255)
agagCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGa < 1:985037/91‑1 (MQ=255)
agagCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGa > 2:111353/1‑91 (MQ=255)
gagCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACCGCGCCCGCTGGAGAAGGTGGCGGAGATCGaa > 2:662077/1‑91 (MQ=255)
agCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAAc > 2:858725/1‑91 (MQ=255)
gTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTgagg < 1:816381/91‑1 (MQ=255)
gTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTgagg < 2:229015/91‑1 (MQ=255)
tGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTgagga < 1:111353/91‑1 (MQ=255)
cTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGAAACATTGAGGAGCTGc > 2:151849/1‑91 (MQ=255)
cGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATg > 2:124214/1‑91 (MQ=255)
cGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATg > 1:669829/1‑91 (MQ=255)
ccGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATGcgcg > 1:353383/1‑91 (MQ=255)
gCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATGCGCGACCAg < 1:918490/91‑1 (MQ=255)
gCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGAt < 1:984397/48‑1 (MQ=255)
gCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGAt > 2:984397/1‑48 (MQ=255)
acaGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATGCGCGACCAgctgct < 2:940444/91‑1 (MQ=255)
gcgcCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATGCGCGACCAGCTGCTGGc > 1:574270/1‑91 (MQ=255)
gACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATGCGCGACCAGCTGCTGGCACTgg > 2:599291/1‑91 (MQ=255)
gACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATGCGCGACCAGCTGCTGGCACTgg > 2:723635/1‑91 (MQ=255)
gACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATGCGCGACCAGCTGCTGGCACTgc > 2:735807/1‑90 (MQ=255)
aCGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATGCGCGACCAGCTGCTGGCACTGGCGAAtgcc < 2:200354/91‑1 (MQ=255)
cGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATGCGCGACCAGCTGCTGGCACTGGCGAAtgcct < 2:353383/91‑1 (MQ=255)
gcgcCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATGCGCGACCAGCTGCTGGCACTGGCGAAtgcctgc > 1:943442/1‑91 (MQ=255)
|
GCAGGTGGGCTTTAACCTGGAAGAGAGCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCACGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATGCGCGACCAGCTGCTGGCACTGGCGAATGCCTGC > NZ_CP009273/509610‑509784
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AGGCACGGCAGGTGGGCTTTAACCTGGAAGAGAGCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCACGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATGCGCGACCAGCTGCTGGCACTGGCGAATGCCTGCCCTGGCGATGAC > NZ_CP009273/509603‑509796
|
AGGCACGGCAGGTGGGCTTTAACCTGGAAGAGAGCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTG > SRR3722125.353941/1‑101 (MQ=60)
GGCACGGCAGGTGGGCTTTAACCTGGAAGAGAGCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGG < SRR3722125.336029/101‑1 (MQ=60)
CAGGTGGGCTTTAACCTGGAAGAGAGCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGT < SRR3722125.412566/101‑1 (MQ=60)
gaagacggcatacgagatcatgcctagtctcgtgggctcggagatgtgtataagagacagGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAG < SRR3722125.24794/41‑1 (MQ=60)
TTTAACCTGGAAGAGAGCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGAT < SRR3722125.725785/101‑1 (MQ=60)
tctcgtgggctcggagatgtgtataagagacaGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACAC < SRR3722125.1006379/69‑1 (MQ=60)
AGAGCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATT < SRR3722125.1007031/101‑1 (MQ=60)
AGCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGA < SRR3722125.804929/101‑1 (MQ=60)
GTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATC < SRR3722125.834266/101‑1 (MQ=60)
TGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCC < SRR3722125.113438/101‑1 (MQ=60)
ATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATG > SRR3722125.684249/1‑101 (MQ=60)
GTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATGCGCG > SRR3722125.360774/1‑101 (MQ=60)
CAGCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATGCGCGACCAGCTGCTGGC > SRR3722125.586560/1‑101 (MQ=60)
GCGGCACAGCGCCGACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATGCGCGACCAGCTGCTGGCAC < SRR3722125.938871/101‑1 (MQ=60)
ACGTCAAACGGCGCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATGCGCGACCAGCTGCTGGCACTGGCGAATGCCTGC > SRR3722125.964426/1‑101 (MQ=60)
GCCCGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATGCGCGACCAGCTGCTGGCACTGGCGAATGCCTGCCCTGGCGATGAC < SRR3722125.877649/101‑1 (MQ=60)
|
AGGCACGGCAGGTGGGCTTTAACCTGGAAGAGAGCGGCGAGCTGGTGAATCTGTTTAACGACCCGCAGCGGCACAGCGCCGACGTCAAACGGCGCACGCTGGAGAAGGTGGCGGAGATCGAACGACACATTGAGGAGCTGCAATCCATGCGCGACCAGCTGCTGGCACTGGCGAATGCCTGCCCTGGCGATGAC > NZ_CP009273/509603‑509796
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
