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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,117,071 |
T→C |
F44S (TTC→TCC) |
rpmE → |
50S ribosomal protein L31 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,117,071 | 0 | T | C | 100.0%
| 77.1
/ NA
| 23 | F44S (TTC→TCC) | rpmE | 50S ribosomal protein L31 |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (10/13); total (10/13) |
CTGCTCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTTCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAA > NZ_CP009273/4116985‑4117150
|
ctgctCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCAc < 2:555166/90‑1 (MQ=255)
tGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCaaa > 1:1593/1‑90 (MQ=255)
tGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCaaa < 1:360976/90‑1 (MQ=255)
gCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAAc < 2:733723/90‑1 (MQ=255)
gCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTACCACCCGTTCTCCACTGGCAAAc < 1:161077/90‑1 (MQ=255)
aCGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTg < 1:608549/90‑1 (MQ=255)
cGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGa < 1:524664/90‑1 (MQ=255)
tAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATg < 2:411036/90‑1 (MQ=255)
aTGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGtt > 2:593677/1‑90 (MQ=255)
gAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGc < 2:208053/90‑1 (MQ=255)
ggTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGAc < 1:567896/90‑1 (MQ=255)
tGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCtt > 1:244636/1‑90 (MQ=255)
gAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTcaacaa > 1:75809/1‑90 (MQ=255)
gAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTcaacaa > 2:412564/1‑90 (MQ=255)
cTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGt < 1:412564/90‑1 (MQ=255)
tCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGtt > 2:498543/1‑90 (MQ=255)
aaGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGATGCTACCGGTGGCCGTGTTGACCGCTTCAACGAGCGGTTCAACATCCCGGgc > 1:269287/1‑90 (MQ=255)
gTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGgcag < 1:722927/90‑1 (MQ=255)
gTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGgcag < 2:12452/90‑1 (MQ=255)
tGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGgcagc > 2:375897/1‑90 (MQ=255)
cACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGgcagc > 1:721546/1‑87 (MQ=255)
cACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGgcagc < 2:721546/87‑1 (MQ=255)
cACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCaaa > 1:753232/1‑90 (MQ=255)
|
CTGCTCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTTCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAA > NZ_CP009273/4116985‑4117150
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ 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
AAATTACTGCTAGCTGCTCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTTCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAATAAGACCGGATT > NZ_CP009273/4116972‑4117162
|
cgagatctacacactgcatatcgtcggcagcgtcagatgtgtataagagacagGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTC < SRR3722073.105422/47‑1 (MQ=60)
TAGCTGCTCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAA > SRR3722073.1635/1‑100 (MQ=60)
AAGCTGCTCTTGCGGTAACGTAAGGAAAATACGCTCCACCGTTGGTCATGACCTGAACCTCGACGGGTGCAGCAAGTGCCCCCCGCTCGCCACTGGCAAA > SRR3722073.614425/1‑100 (MQ=60)
TGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATG < SRR3722073.368623/100‑1 (MQ=60)
GCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTACCACCCGTTCTCCACTGGCAAACAGCGTGATGT < SRR3722073.164321/100‑1 (MQ=60)
ACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTAC < SRR3722073.621232/100‑1 (MQ=60)
CGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACC < SRR3722073.535675/100‑1 (MQ=60)
CCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTT > SRR3722073.249766/1‑100 (MQ=60)
GGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACA < SRR3722073.579745/100‑1 (MQ=60)
GTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAA > SRR3722073.77562/1‑100 (MQ=60)
CTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCC < SRR3722073.421375/100‑1 (MQ=60)
CGTGAGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGATGCTACCGGTGGCCGTGTTGACCGCTTCAACGAGCGGTTCAACATCCCGGGC > SRR3722073.274986/1‑100 (MQ=60)
CAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAA > SRR3722073.736124/1‑100 (MQ=60)
CAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAA > SRR3722073.768474/1‑100 (MQ=60)
GTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAATAAGAC < SRR3722073.737531/100‑1 (MQ=60)
CCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAATAAGACCGGATT > SRR3722073.218393/1‑100 (MQ=60)
|
AAATTACTGCTAGCTGCTCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTTCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAATAAGACCGGATT > NZ_CP009273/4116972‑4117162
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
