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 F3 I122 R1
|
193 |
20.9 |
1228102 |
94.7% |
1163012 |
84.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,634,151 |
Δ1 bp |
coding (164/534 nt) |
rrrQ ← |
lysozyme |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,634,150 | 0 | G | . | 100.0%
| 36.8
/ NA
| 10 | coding (165/534 nt) | rrrQ | lysozyme |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base . (4/6); total (4/6) |
TTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCT > NZ_CP009273/1634064‑1634210
|
ttATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACtgtgcac > 1:449801/1‑87 (MQ=255)
cTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACa > 1:385342/1‑89 (MQ=255)
cTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACa < 2:385342/89‑1 (MQ=255)
gTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCat > 2:133386/1‑90 (MQ=255)
ttttCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATcgc < 1:325893/90‑1 (MQ=255)
ttttCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATcgc < 2:377240/90‑1 (MQ=255)
ccTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTa < 1:248725/90‑1 (MQ=255)
tCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGc < 1:133386/90‑1 (MQ=255)
cAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCAtt < 2:492225/90‑1 (MQ=255)
gTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATtgt > 2:203155/1‑90 (MQ=255)
gggAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACct > 2:264098/1‑90 (MQ=255)
|
TTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCT > NZ_CP009273/1634064‑1634210
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ 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
CATGCCAGCGCCTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCTGAGG > NZ_CP009273/1634052‑1634245
|
taagagacaGCCTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGC < SRR3721989.583346/91‑1 (MQ=60)
TGCCAGCGCCTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCAC > SRR3721989.459194/1‑100 (MQ=60)
CCAGCGCCTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCC < SRR3721989.560413/100‑1 (MQ=60)
CCTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGCCAG > SRR3721989.393084/1‑100 (MQ=60)
ctacactccttacgtcgtcggcagcgtcagatgtgtataagagacagGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGA < SRR3721989.210785/53‑1 (MQ=60)
gagatctacactccttacgtcgtcggcagcgtcagatgtgtataagagacagATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCG < SRR3721989.112683/48‑1 (MQ=60)
cctccttacgtcgtcggcagcgtcagatgtgtataagagacagATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCC < SRR3721989.320381/57‑1 (MQ=60)
TTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCAT < SRR3721989.332095/100‑1 (MQ=60)
CCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTG < SRR3721989.253148/100‑1 (MQ=60)
TCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGG < SRR3721989.135824/100‑1 (MQ=60)
ATCCACCGCTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCctgtctcttatacacatctgacgctg > SRR3721989.260629/1‑74 (MQ=60)
ATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTA > SRR3721989.298451/1‑100 (MQ=60)
ATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTA > SRR3721989.539512/1‑100 (MQ=60)
ATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTA > SRR3721989.114401/1‑100 (MQ=60)
gacagccactgtGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTA < SRR3721989.5230/88‑1 (MQ=60)
CACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCT > SRR3721989.217587/1‑100 (MQ=60)
ACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCTGAGG > SRR3721989.258998/1‑100 (MQ=60)
|
CATGCCAGCGCCTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCTGAGG > NZ_CP009273/1634052‑1634245
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
