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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,759,232 |
(G)6→7 |
intergenic (‑97/‑45) |
yfjM ← / → rnlA |
DUF1524 domain‑containing protein/type II toxin‑antitoxin system toxin mRNA endoribonuclease RnlA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,759,226 | 1 | . | G | 100.0%
| 31.0
/ NA
| 10 | intergenic (‑91/‑51) | yfjM/rnlA | DUF1524 domain‑containing protein/type II toxin‑antitoxin system toxin mRNA endoribonuclease RnlA |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (5/5); total (5/5) |
GTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑GGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTT > NZ_CP009273/2759139‑2759302
|
gtgGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑gg > 1:23615/1‑90 (MQ=255)
ggACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑gggg < 1:652273/90‑1 (MQ=255)
cTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑ggggggg > 2:294047/1‑89 (MQ=255)
tGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑gggggggt < 2:743603/90‑3 (MQ=255)
tGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑gggggggt < 2:656570/90‑3 (MQ=255)
gCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑gggggggta > 1:726274/1‑87 (MQ=255)
cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑gggggggtat < 1:168114/90‑5 (MQ=255)
cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑gggggggtat < 2:453256/90‑5 (MQ=255)
cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑gggggggtat < 1:529082/90‑5 (MQ=255)
tGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGGTATTATTGTAGAGTTTCCCCat < 2:23615/90‑1 (MQ=255)
cccTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGGTATTATTGTAGAGTTTCCCCatat < 1:540367/90‑1 (MQ=255)
cccTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGGTATTATTGTAGAGTTTCCCCatat < 2:569825/90‑1 (MQ=255)
tGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATg > 2:595454/1‑90 (MQ=255)
tGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATg > 1:206545/1‑90 (MQ=255)
gCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATcc > 2:167403/1‑90 (MQ=255)
gCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATcc > 1:503474/1‑90 (MQ=255)
gCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑gggggg > 1:564774/1‑50 (MQ=255)
gCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑gggggg < 2:564774/50‑1 (MQ=255)
ggTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACaa > 2:66192/1‑90 (MQ=255)
ggCTAAATTTAGCAAATCAATACACTTCAGGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCa < 2:726274/90‑1 (MQ=255)
tCAATACACTTCAGGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACtt < 1:167403/90‑1 (MQ=255)
|
GTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑GGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTT > NZ_CP009273/2759139‑2759302
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ 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
TTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑GGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGGGCAAATATCGAGACTG > NZ_CP009273/2759135‑2759331
|
TTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑GGGGGGgt < SRR3722073.485583/100‑3 (MQ=60)
TTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑GGGGGGgta > SRR3722073.740927/1‑97 (MQ=60)
GGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGGTATTATT < SRR3722073.665676/100‑1 (MQ=60)
CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGGTATTATTGTAGAG < SRR3722073.171429/100‑1 (MQ=60)
CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGGTATTATTGTAGAG < SRR3722073.540157/100‑1 (MQ=60)
GCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATG > SRR3722073.210761/1‑100 (MQ=60)
CCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGG < SRR3722073.551664/100‑1 (MQ=60)
TAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGGTATTATTGTctgtctcttatacacatctgacgctgccga > SRR3722073.576554/1‑70 (MQ=60)
TAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCC > SRR3722073.514107/1‑100 (MQ=60)
ccgccatcgtcggcagcgtcagatgtgtaataagagacagATACACTTCAGGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGA < SRR3722073.746248/60‑1 (MQ=60)
TCAATACACTTCAGGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTC < SRR3722073.170716/100‑1 (MQ=60)
CAATACACTTCAGGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCA > SRR3722073.461086/1‑100 (MQ=60)
ATACACTTCAGGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGG > SRR3722073.216424/1‑100 (MQ=60)
CTTCAGGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCctgtctcttatacacatctgacgctgccgacgaatgcagtgtgtagatctcggtggtcg > SRR3722073.516300/1‑41 (MQ=60)
CTTCAGGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCctgtctcttatac > SRR3722073.486980/1‑87 (MQ=60)
CTTCAGGGGGGGTATTATTGTAGAGGTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGGGCAAA > SRR3722073.46168/1‑100 (MQ=60)
GGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGGGCctgtctcttata > SRR3722073.439242/1‑88 (MQ=60)
GTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGGGCAAATATCGAGACTG < SRR3722073.56016/100‑1 (MQ=60)
|
TTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑GGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGGGCAAATATCGAGACTG > NZ_CP009273/2759135‑2759331
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
