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 F4 I96 R1
|
227 |
23.3 |
882352 |
98.0% |
864704 |
126.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,016,420 |
T→C |
intergenic (‑45/‑174) |
sulA ← / → sxy |
cell division inhibitor SulA/CRP‑S regulon transcriptional coactivator Sxy |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,016,420 | 0 | T | C | 100.0%
| 24.4
/ NA
| 8 | intergenic (‑45/‑174) | sulA/sxy | cell division inhibitor SulA/CRP‑S regulon transcriptional coactivator Sxy |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (5/3); total (5/3) |
ACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTACATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGG > NZ_CP009273/1016342‑1016543
|
acgaAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTACACCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGt > 2:96491/1‑139 (MQ=255)
tgtgCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTACACCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGaaaa > 1:163615/1‑138 (MQ=255)
tgCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTACACCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACa < 2:174902/138‑1 (MQ=255)
gAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTACACCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCt > 1:106373/1‑139 (MQ=255)
tACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTACACCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGcccc > 1:253055/1‑139 (MQ=255)
aCTGTATGGATGTACAGTACACCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGt > 2:205129/1‑139 (MQ=255)
tATGGATGTACAGTACACCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTaa < 2:271968/138‑1 (MQ=255)
tGGATGTACAGTACACCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACgg < 1:96491/139‑1 (MQ=255)
|
ACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTACATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGG > NZ_CP009273/1016342‑1016543
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TCACTGATAAGCCCGGCTGTAGTGTTTTCCGTAGAGACACGCGCAATTTTACTTGCTGCGGATGAGAACGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTACATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGGATCCGTTAATGTGAATCATTCTTTT > NZ_CP009273/1016272‑1016568
|
TCACTGATAAGCCCGGCTGTAGTGTTTTCCGTAGAGACACGCGCAATTTTACTTGCTGCGGATGAGAACGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTACAC < SRR3722119.12084/149‑1 (MQ=60)
ACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTACACCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAAC > SRR3722119.165284/1‑150 (MQ=60)
GTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTACACCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTT > SRR3722119.107418/1‑151 (MQ=60)
AGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTACACCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCT > SRR3722119.255696/1‑151 (MQ=60)
ATGGATGTACAGTACACCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGGATCCGTTAATG < SRR3722119.97438/151‑1 (MQ=60)
ACAGTACACCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGGActgtctcttatacacatc > SRR3722119.259642/1‑133 (MQ=60)
ACAGTACACCCAGAGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGGATCCGTTAATGctgtctct > SRR3722119.339890/1‑143 (MQ=60)
CACCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGGATCCGTTAATGTGAATCATTCTTTT > SRR3722119.217149/1‑151 (MQ=60)
|
TCACTGATAAGCCCGGCTGTAGTGTTTTCCGTAGAGACACGCGCAATTTTACTTGCTGCGGATGAGAACGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTACATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGGATCCGTTAATGTGAATCATTCTTTT > NZ_CP009273/1016272‑1016568
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
