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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,961,176 |
G→C |
A40G (GCC→GGC) |
cheZ ← |
protein phosphatase CheZ |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,961,176 | 0 | G | C | 91.7%
| 32.0
/ ‑2.8
| 12 | A40G (GCC→GGC) | cheZ | protein phosphatase CheZ |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base C (7/4); total (7/5) |
| Fisher's exact test for biased strand distribution p-value = 4.17e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.60e-01 |
GCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCT > NZ_CP009273/1961087‑1961228
|
gcgcCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATgg > 1:474758/1‑90 (MQ=255)
tGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGt < 1:38865/90‑1 (MQ=255)
cATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCaa < 2:474758/90‑1 (MQ=255)
cATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCaa < 1:443313/90‑1 (MQ=255)
caacaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTcgc > 1:432747/1‑90 (MQ=255)
acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc < 1:28995/90‑1 (MQ=255)
acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc < 2:65711/90‑1 (MQ=255)
gTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCAt > 1:38081/1‑90 (MQ=255)
gTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCAt > 2:281563/1‑90 (MQ=255)
aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg > 2:174516/1‑90 (MQ=255)
aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg > 2:313536/1‑90 (MQ=255)
tCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAgg > 1:524601/1‑90 (MQ=255)
gcgcgcATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCt > 2:287511/1‑90 (MQ=255)
|
GCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCT > NZ_CP009273/1961087‑1961228
|
| 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
ACACTGTTCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGCTCGTCAG > NZ_CP009273/1961077‑1961269
|
ACACTGTTCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGG > SRR3722092.484183/1‑100 (MQ=60)
ACACTGTTCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGC > SRR3722092.170556/1‑100 (MQ=60)
TCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATC < SRR3722092.134467/100‑1 (MQ=60)
TGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAAC < SRR3722092.39542/100‑1 (MQ=60)
GTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGC > SRR3722092.441183/1‑100 (MQ=60)
CATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGC < SRR3722092.452021/100‑1 (MQ=60)
GCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCAT > SRR3722092.38745/1‑100 (MQ=60)
ACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCG < SRR3722092.29500/100‑1 (MQ=60)
GTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGG > SRR3722092.535121/1‑100 (MQ=60)
GCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCctgtctcttatacacatctgacgctgccg > SRR3722092.409130/1‑71 (MQ=60)
|
ACACTGTTCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGCTCGTCAG > NZ_CP009273/1961077‑1961269
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
