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 I205 R1
|
220 |
17.5 |
961422 |
97.1% |
933540 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,961,177 |
C→G |
A40P (GCC→CCC) |
cheZ ← |
protein phosphatase CheZ |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,961,177 | 0 | C | G | 100.0%
| 61.6
/ NA
| 19 | A40P (GCC→CCC) | cheZ | protein phosphatase CheZ |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base G (11/8); total (11/8) |
CGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGC > NZ_CP009273/1961092‑1961262
|
cGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGa > 1:475203/1‑90 (MQ=255)
cTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATc < 1:80418/90‑1 (MQ=255)
tCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCa > 2:30986/1‑90 (MQ=255)
aTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCgcag < 2:165710/90‑1 (MQ=255)
aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg > 1:211225/1‑90 (MQ=255)
aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg > 2:210249/1‑90 (MQ=255)
aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg > 1:349100/1‑90 (MQ=255)
cGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTc < 2:168621/90‑1 (MQ=255)
gATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCa > 1:24928/1‑90 (MQ=255)
aTCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAg < 1:268455/90‑1 (MQ=255)
tCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAgg > 2:285481/1‑90 (MQ=255)
tCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAgg > 2:319014/1‑90 (MQ=255)
gATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATgcgcgc < 2:475203/90‑1 (MQ=255)
ggCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAAt > 1:145547/1‑90 (MQ=255)
cTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATa > 1:282606/1‑62 (MQ=255)
cTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATa < 2:282606/62‑1 (MQ=255)
cgcTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGcc < 1:387553/90‑1 (MQ=255)
cGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTg < 2:439241/90‑1 (MQ=255)
aTGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGc > 2:467184/1‑90 (MQ=255)
|
CGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGC > NZ_CP009273/1961092‑1961262
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ 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
GTTCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGCTCGTCAGCAGGT > NZ_CP009273/1961082‑1961274
|
GTTCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGA > SRR3722087.480729/1‑100 (MQ=60)
TCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATC < SRR3722087.149967/100‑1 (MQ=60)
TCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATC < SRR3722087.175738/100‑1 (MQ=60)
GCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCC < SRR3722087.388166/100‑1 (MQ=60)
CTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGT < SRR3722087.81168/100‑1 (MQ=60)
ACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCG > SRR3722087.213067/1‑100 (MQ=60)
ACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCG > SRR3722087.353009/1‑100 (MQ=60)
TAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCA > SRR3722087.25119/1‑100 (MQ=60)
ATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATG < SRR3722087.271097/100‑1 (MQ=60)
CATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAAT > SRR3722087.146887/1‑100 (MQ=60)
TCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCctgtctcttatacacatc > SRR3722087.285429/1‑82 (MQ=60)
CGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGC < SRR3722087.392028/100‑1 (MQ=60)
CTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGCTC > SRR3722087.93679/1‑100 (MQ=60)
GGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGCTCGTCAGCAGGT > SRR3722087.342246/1‑100 (MQ=60)
|
GTTCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGCTCGTCAGCAGGT > NZ_CP009273/1961082‑1961274
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
