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 I96 R1
|
172 |
34.7 |
2005794 |
96.2% |
1929573 |
85.4 |
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%
| 129.8
/ NA
| 31 | coding (165/534 nt) | rrrQ | lysozyme |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base . (11/20); total (11/20) |
CCTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAA > NZ_CP009273/1634062‑1634235
|
ccTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACtgtgc < 2:952038/90‑2 (MQ=255)
ccTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACtgtgc < 1:366518/90‑2 (MQ=255)
ttATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACtgtgcac > 1:156041/1‑87 (MQ=255)
ttATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACtgtgcac < 2:2335/90‑4 (MQ=255)
gCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACa > 2:698269/1‑90 (MQ=255)
tCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGa < 1:941171/90‑1 (MQ=255)
cAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGAt < 1:343323/90‑1 (MQ=255)
aTGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATgg < 1:547261/90‑1 (MQ=255)
aTGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATgg < 2:399435/90‑1 (MQ=255)
gTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCat < 2:673535/90‑1 (MQ=255)
gTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCat < 1:317564/90‑1 (MQ=255)
gTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCat < 2:205421/90‑1 (MQ=255)
gACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATg > 2:497951/1‑90 (MQ=255)
tgTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGa > 1:995055/2‑90 (MQ=255)
ggTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGa < 2:590144/90‑1 (MQ=255)
ggTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGa > 1:609504/1‑90 (MQ=255)
ggTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGa > 1:753755/1‑90 (MQ=255)
tCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAAc < 1:833856/90‑1 (MQ=255)
ttttCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATcgc < 1:118621/90‑1 (MQ=255)
ttttCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATcgc < 2:411689/90‑1 (MQ=255)
ttCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCgg < 1:828740/90‑1 (MQ=255)
aCAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCAt < 1:448748/90‑1 (MQ=255)
aCAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCAt < 1:547471/90‑1 (MQ=255)
aGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATtg < 1:109342/90‑1 (MQ=255)
atTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTa < 1:455590/90‑1 (MQ=255)
gggAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACct > 1:417920/1‑90 (MQ=255)
gggAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACct > 2:759916/1‑90 (MQ=255)
gggAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACct > 1:927112/1‑90 (MQ=255)
aaaCGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCttt > 1:671691/1‑90 (MQ=255)
aCGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCttttt < 2:675431/90‑1 (MQ=255)
atccaCCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAAc < 1:698269/90‑1 (MQ=255)
ccaccaCTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTg > 2:335281/1‑90 (MQ=255)
ccacTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTc > 2:514336/1‑90 (MQ=255)
acTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCaa < 1:524919/90‑1 (MQ=255)
acTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCaa < 2:885881/90‑1 (MQ=255)
|
CCTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAA > NZ_CP009273/1634062‑1634235
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ 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
CATGCCAGCGCCTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCTGAGG > NZ_CP009273/1634052‑1634245
|
CATGCCAGCGCCTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGC < SRR3722236.170969/100‑1 (MQ=60)
TGCCAGCGCCTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCAC < SRR3722236.47472/100‑1 (MQ=60)
TGCCAGCGCCTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCAC > SRR3722236.158317/1‑100 (MQ=60)
CGCCTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCAAC < SRR3722236.502725/100‑1 (MQ=60)
CCTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAG < SRR3722236.371696/100‑1 (MQ=60)
TCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATAT < SRR3722236.957781/100‑1 (MQ=60)
CAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATG < SRR3722236.348208/100‑1 (MQ=60)
ATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCC < SRR3722236.555696/100‑1 (MQ=60)
GCGTTGACCTTGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGA > SRR3722236.1012574/1‑100 (MQ=60)
GCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGA > SRR3722236.766683/1‑100 (MQ=60)
GCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGA > SRR3722236.619247/1‑100 (MQ=60)
GTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAAC < SRR3722236.322119/100‑1 (MQ=60)
TCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTA < SRR3722236.848419/100‑1 (MQ=60)
TTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCAT < SRR3722236.120278/100‑1 (MQ=60)
TTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTG < SRR3722236.843197/100‑1 (MQ=60)
ccttcgtcggcagcgtcagatgtgtataagagacagATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGT < SRR3722236.417575/64‑1 (MQ=60)
ACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTA < SRR3722236.455217/100‑1 (MQ=60)
ACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTA < SRR3722236.555910/100‑1 (MQ=60)
AGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACC < SRR3722236.110853/100‑1 (MQ=60)
GTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCT > SRR3722236.423764/1‑100 (MQ=60)
GTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCT > SRR3722236.943483/1‑100 (MQ=60)
ATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTT > SRR3722236.682876/1‑100 (MQ=60)
ATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTT < SRR3722236.462208/100‑1 (MQ=60)
ATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTA > SRR3722236.40339/1‑100 (MQ=60)
ATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTA < SRR3722236.52817/100‑1 (MQ=60)
ATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTA < SRR3722236.710041/100‑1 (MQ=60)
ATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTA > SRR3722236.350179/1‑100 (MQ=60)
ATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTA > SRR3722236.848062/1‑100 (MQ=60)
ATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTA > SRR3722236.890075/1‑100 (MQ=60)
ATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGACATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTA > SRR3722236.694132/1‑100 (MQ=60)
CCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACctgtctcttata > SRR3722236.207255/1‑88 (MQ=60)
CCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATC > SRR3722236.134208/1‑100 (MQ=60)
ACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCTGAGG < SRR3722236.532945/100‑1 (MQ=60)
|
CATGCCAGCGCCTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCTGAGG > NZ_CP009273/1634052‑1634245
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
