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 I231 R1
|
218 |
12.8 |
703680 |
97.2% |
683976 |
86.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,961,177 |
C→A |
A40S (GCC→TCC) |
cheZ ← |
protein phosphatase CheZ |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,961,177 | 0 | C | A | 90.9%
| 30.3
/ ‑2.5
| 11 | A40S (GCC→TCC) | cheZ | protein phosphatase CheZ |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base A (5/5); total (5/6) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.20e-01 |
CGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCA > NZ_CP009273/1961092‑1961241
|
cGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGa > 1:42207/1‑90 (MQ=255)
tCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATcc < 1:288889/90‑1 (MQ=255)
tGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATCCAGCCCCAGt > 2:6147/1‑90 (MQ=255)
gCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGt < 2:24080/90‑1 (MQ=255)
acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc < 1:30860/90‑1 (MQ=255)
gTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTcgc > 1:192584/1‑83 (MQ=255)
gTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTcgc < 2:192584/83‑1 (MQ=255)
cGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTCGCCCAGCATACGCGTCAGGCTGCCGATgc < 1:328701/90‑1 (MQ=255)
aTGGCTTCCGCCGCTTCGGCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCa > 1:49005/1‑90 (MQ=255)
cTTCGGCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGc < 1:185384/63‑1 (MQ=255)
cTTCGGCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGc > 2:185384/1‑63 (MQ=255)
|
CGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCA > NZ_CP009273/1961092‑1961241
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ 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
GTTCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGCTCGTCAG > NZ_CP009273/1961082‑1961269
|
GTTCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGA > SRR3722116.42707/1‑100 (MQ=60)
TCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATC < SRR3722116.338868/100‑1 (MQ=60)
CAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATCC < SRR3722116.145269/100‑1 (MQ=60)
GCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATCCAGCC < SRR3722116.74879/100‑1 (MQ=60)
TCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATCCAGCCCCAGTT < SRR3722116.293105/100‑1 (MQ=60)
GGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATCCtgtctcttatacacatctga > SRR3722116.154928/1‑80 (MQ=60)
GCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCAT > SRR3722116.194985/1‑100 (MQ=60)
ACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCG < SRR3722116.31231/100‑1 (MQ=60)
atgtgtataagagacaGGCTTCCGCCGCTTCGGCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCG < SRR3722116.187688/84‑1 (MQ=60)
CGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCA > SRR3722116.49604/1‑100 (MQ=60)
CGGGGATGGCTTCCGCCGCTTCGGCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTCGCCCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGAT < SRR3722116.333603/100‑1 (MQ=60)
GCAATGGACTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCtgtctcttatacacatc > SRR3722116.322655/1‑83 (MQ=60)
|
GTTCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGCTCGTCAG > NZ_CP009273/1961082‑1961269
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
