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 I122 R1
|
193 |
20.9 |
1228102 |
94.7% |
1163012 |
84.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,416,405 |
A→G |
intergenic (+31/+40) |
rplI → / ← yjfZ |
50S ribosomal protein L9/DUF2686 family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,416,405 | 0 | A | G | 100.0%
| 98.3
/ NA
| 28 | intergenic (+31/+40) | rplI/yjfZ | 50S ribosomal protein L9/DUF2686 family protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (14/14); total (14/14) |
TTCCAGGTTCACAGCGAAGTATTCGCGAAAGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGACCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCACCATTCTCTTGTGTCCATAAG > NZ_CP009273/4416318‑4416490
|
ttCCAGGTTCACAGCGAAGTATTCGCGAAAGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGcc > 2:462195/1‑90 (MQ=255)
cgcgAAAGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTa > 1:56855/1‑90 (MQ=255)
cgcgAAAGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTa > 1:57221/1‑90 (MQ=255)
aaGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGTTTTCTAttttt > 1:299623/1‑90 (MQ=255)
aaGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCtt > 1:306734/1‑81 (MQ=255)
aaGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCtt < 2:306734/81‑1 (MQ=255)
aaGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTAttttt > 2:449604/1‑90 (MQ=255)
gATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTc < 2:153180/90‑1 (MQ=255)
aTCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCa < 1:449604/90‑1 (MQ=255)
tAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCt > 2:197127/1‑71 (MQ=255)
tAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCt < 1:197127/71‑1 (MQ=255)
gtagCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTc > 1:517883/1‑90 (MQ=255)
tagCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCg < 2:158477/90‑1 (MQ=255)
gAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGt < 2:208961/90‑1 (MQ=255)
gAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGt > 2:292268/1‑90 (MQ=255)
gAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGt < 2:517883/90‑1 (MQ=255)
ataatTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAg > 2:410242/1‑90 (MQ=255)
ataatTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAg < 1:394113/90‑1 (MQ=255)
ttATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTc > 1:87697/1‑90 (MQ=255)
ttATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTc > 2:338501/1‑90 (MQ=255)
ttATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTc < 2:452969/90‑1 (MQ=255)
ttATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTc < 2:558552/90‑1 (MQ=255)
ttATTCAACGAAACGTAAAACCGCCGGCCATTGGTCGGCGTTTTTTTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTc < 1:509572/90‑1 (MQ=255)
aTTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCAc < 1:338501/90‑1 (MQ=255)
agaCGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCACCATTctct > 1:477330/1‑90 (MQ=255)
accGCCGGCCATTGGTCCGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCACCATTCTCTTGTGTCCAt < 2:299623/88‑1 (MQ=255)
aaCGCCGGCCATTGGTCGGCGTTCTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCACCATTCTCTTGTGTCCAt < 1:485412/90‑1 (MQ=255)
gCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCACCATTCTCTTGTGTCCATAAg > 2:344062/1‑90 (MQ=255)
|
TTCCAGGTTCACAGCGAAGTATTCGCGAAAGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGACCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCACCATTCTCTTGTGTCCATAAG > NZ_CP009273/4416318‑4416490
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 31 ≤ 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
CACGAAGTGAGCTTCCAGGTTCACAGCGAAGTATTCGCGAAAGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGACCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCACCATTCTCTTGTGTCCATAAGTCAGGAT > NZ_CP009273/4416306‑4416497
|
CACGAAGTGAGCTTCCAGGTTCACAGCGAAGTATTCGCGAAAGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGG > SRR3721989.25621/1‑100 (MQ=60)
gttctacactccttacgtcgtcggcagcgtcagatgtgtataagagacagCGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCA < SRR3721989.449640/50‑1 (MQ=60)
GAAGTGAGCTTCCAGGTTCACAGCGAAGTATTCGCGAAAGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCA < SRR3721989.191510/100‑1 (MQ=60)
GCGAAGTATTCGCGAAAGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTA > SRR3721989.58216/1‑100 (MQ=60)
GCGAAGTATTCGCGAAAGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTA > SRR3721989.57847/1‑100 (MQ=60)
aagagacaGAAAGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTT < SRR3721989.200729/92‑1 (MQ=60)
GTATTCGCGAAAGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGTTTTCTATTTTT > SRR3721989.305247/1‑100 (MQ=60)
GTATTCGCGAAAGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTT > SRR3721989.312534/1‑100 (MQ=60)
ATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTT < SRR3721989.458993/100‑1 (MQ=60)
CGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTC > SRR3721989.528955/1‑100 (MQ=60)
GAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTC > SRR3721989.89277/1‑100 (MQ=60)
ATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCAC < SRR3721989.402099/100‑1 (MQ=60)
TTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCACCATTCTCT > SRR3721989.487380/1‑100 (MQ=60)
TTATTCAACGAAACGTAAAACCGCCGGCCATTGGTCGGCGTTTTTTTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCACCATTCTCT < SRR3721989.520442/100‑1 (MQ=60)
ATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCACCATTCTCTTG < SRR3721989.344972/100‑1 (MQ=60)
GTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCACCATTCTCTTGTGTCCATAAGTC > SRR3721989.204130/1‑100 (MQ=60)
AACGCCGGCCATTGGTCGGCGTTCTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCACCATTCTCTTGTGTCCATAAGTCAGGAT < SRR3721989.495663/100‑1 (MQ=60)
|
CACGAAGTGAGCTTCCAGGTTCACAGCGAAGTATTCGCGAAAGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGACCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCACCATTCTCTTGTGTCCATAAGTCAGGAT > NZ_CP009273/4416306‑4416497
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
