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 I206 R1
|
206 |
23.7 |
1314362 |
96.8% |
1272302 |
86.2 |
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 | . | 91.7%
| 35.2
/ ‑0.5
| 12 | coding (56/294 nt) | BW25113_RS06140 | YcgL domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base . (4/7); total (5/7) |
| Fisher's exact test for biased strand distribution p-value = 4.17e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.41e-01 |
TATGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCC > NZ_CP009273/1223136‑1223303
|
tATGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGa > 1:466495/1‑90 (MQ=255)
aaaGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCgt < 1:338593/90‑1 (MQ=255)
gagTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGtt < 2:123046/90‑1 (MQ=255)
gagTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGtt < 2:72778/90‑1 (MQ=255)
aTGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAAc < 2:423272/90‑1 (MQ=255)
ttGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACtgat > 2:51855/1‑90 (MQ=255)
tCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGt > 1:94351/1‑90 (MQ=255)
cGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTc < 1:53719/90‑1 (MQ=255)
gcaAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCa > 1:42933/1‑90 (MQ=255)
ccAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCgatg < 1:604765/90‑1 (MQ=255)
aTTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAAc > 1:134716/1‑47 (MQ=255)
aTTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAAc < 2:134716/47‑1 (MQ=255)
aTTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGcc > 2:504853/1‑90 (MQ=255)
|
TATGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCC > NZ_CP009273/1223136‑1223303
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ 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
CCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGATGGGCGGAAGAAACTGGTC > NZ_CP009273/1223146‑1223328
|
cagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCG < SRR3722088.622024/38‑1 (MQ=60)
AAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGG < SRR3722088.342140/100‑1 (MQ=60)
GTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGT > SRR3722088.95301/1‑100 (MQ=60)
TATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCA > SRR3722088.43373/1‑100 (MQ=60)
CGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTT < SRR3722088.54289/100‑1 (MQ=60)
GACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGctgtctcttatacacatctccgagcccacgaga > SRR3722088.136110/1‑67 (MQ=60)
CCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGC < SRR3722088.612212/100‑1 (MQ=60)
ATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGATGGG > SRR3722088.388679/1‑100 (MQ=60)
ATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGATGGG > SRR3722088.44116/1‑100 (MQ=60)
AAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCCCAGTTAGCGATGATTCTGCCGCTGGAT‑GGCGGAAGAAACTGGTC < SRR3722088.638992/100‑1 (MQ=60)
|
CCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGATGGGCGGAAGAAACTGGTC > NZ_CP009273/1223146‑1223328
|
| 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: ‑ |
