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 I209 R1
|
216 |
14.4 |
815930 |
96.1% |
784108 |
85.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,223,232 |
(A)8→7 |
coding (63/294 nt) |
BW25113_RS06140 → |
YcgL domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,223,225 | 0 | A | . | 100.0%
| 50.1
/ NA
| 13 | coding (56/294 nt) | BW25113_RS06140 | YcgL domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (6/7); total (6/7) |
ATGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCC > NZ_CP009273/1223137‑1223303
|
aTGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGaa > 1:53565/1‑90 (MQ=255)
aTGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGaa > 2:35013/1‑90 (MQ=255)
aaaCCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGaaaaaaag > 2:193638/1‑89 (MQ=255)
ttAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTcgc > 1:80030/1‑90 (MQ=255)
tAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTcgcg < 1:65239/90‑1 (MQ=255)
aaaGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCgt < 1:35013/90‑1 (MQ=255)
aaaGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCgt < 2:212695/90‑1 (MQ=255)
aaaGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGa < 1:193638/90‑1 (MQ=255)
gATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAAc < 1:177797/79‑1 (MQ=255)
gATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAAc > 2:177797/1‑79 (MQ=255)
gcaAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCa < 1:273873/90‑1 (MQ=255)
gCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATATTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTa > 2:309540/1‑90 (MQ=255)
gACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCgat > 1:332133/1‑86 (MQ=255)
gACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCgat < 2:332133/86‑1 (MQ=255)
gACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGAtt > 2:351539/1‑90 (MQ=255)
aTTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGcc > 2:861/1‑90 (MQ=255)
|
ATGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCC > NZ_CP009273/1223137‑1223303
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATT > NZ_CP009273/1223145‑1223298
|
ACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGC > SRR3722091.81273/1‑100 (MQ=60)
TAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAG < SRR3722091.66233/100‑1 (MQ=60)
AAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGG < SRR3722091.35511/100‑1 (MQ=60)
AAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATG < SRR3722091.196524/100‑1 (MQ=60)
GTGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGG < SRR3722091.180342/100‑1 (MQ=60)
GCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATG < SRR3722091.278386/100‑1 (MQ=60)
AGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATT > SRR3722091.337906/1‑100 (MQ=60)
|
ACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATT > NZ_CP009273/1223145‑1223298
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
