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 I231 R1
|
218 |
12.8 |
703680 |
97.2% |
683976 |
86.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,310,789 |
C→T |
A92A (GCG→GCA) |
phnH ← |
phosphonate C‑P lyase system protein PhnH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,310,789 | 0 | C | T | 93.8%
| 48.6
/ ‑3.8
| 16 | A92A (GCG→GCA) | phnH | phosphonate C‑P lyase system protein PhnH |
| Reads supporting (aligned to +/- strand): ref base C (1/0); new base T (5/10); total (6/10) |
| Fisher's exact test for biased strand distribution p-value = 3.75e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01 |
GCACCCGCTTCCGGCGCAACGGCGGTGCCGGTGGAAAGGGCGTTGAGCTGTTCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTCGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAACGCAGGCTCTGGTTGACGATATCGTTATTTAATGGGGTAGA > NZ_CP009273/4310703‑4310872
|
gCACCCGCTTCCGGCGCAACGGCGGTGCCGGTGGAAAGGGCGTTGAGCTGTTCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTTGcc < 1:318602/90‑1 (MQ=255)
gcggTGCCGGTGGAAAGGGCGTTGAGCTGTTCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTTGCCTGTTCCGGCTGGCTGACCAgc < 1:109996/90‑1 (MQ=255)
tGGAAAGGGCGTTGAGCTGTTCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTTGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTgg > 2:108793/1‑90 (MQ=255)
cGTTGAGCTGTTCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTTGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAAc > 1:178979/1‑90 (MQ=255)
ttGAGCTGTTCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTTGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAACGc < 2:178979/90‑1 (MQ=255)
tGAGCTGTTCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTTGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAACGCa < 2:135571/90‑1 (MQ=255)
tGTTCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTTGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAACGCAGGctc < 2:208146/90‑1 (MQ=255)
gTTCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTTGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGCTATGAAAACCCAGGctct > 1:62473/1‑90 (MQ=255)
tCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTTGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAACGCAGGCTCTgg < 1:98694/90‑1 (MQ=255)
tCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTTGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAACGCAGGCTCTgg > 2:53013/1‑90 (MQ=255)
cTGGAAATCGCCTCATCCGTCACCGCGAAGGTCGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAACGCAGGCTCTGGTTg > 1:131161/1‑90 (MQ=255)
ccTCATCCGTCACCGCGAAGGTTGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAACGCAGGCTCTGGTTGACGATATCGt < 2:59828/90‑1 (MQ=255)
tCATCCGTCACCGCGAAGGTTGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAACGCAGGCTCTGGTTGACGATATCGTTa < 1:438/90‑1 (MQ=255)
gcgAAGGTTGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAACGCAGGCTCTGGTTGACGATATCGTTATTTAATGGGGTa > 2:192688/1‑90 (MQ=255)
cgAAGGTTGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAACGCAGGCTCTGGTTGACGATATCGTTATTTAATGGGGTAg < 2:151047/90‑1 (MQ=255)
gAAGGTTGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAACGCAGGCTCTGGTTGACGATATCGTTATTTAATGGGGTAGa < 1:150593/90‑1 (MQ=255)
|
GCACCCGCTTCCGGCGCAACGGCGGTGCCGGTGGAAAGGGCGTTGAGCTGTTCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTCGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAACGCAGGCTCTGGTTGACGATATCGTTATTTAATGGGGTAGA > NZ_CP009273/4310703‑4310872
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ 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
AATCAGCGTCGCACCCGCTTCCGGCGCAACGGCGGTGCCGGTGGAAAGGGCGTTGAGCTGTTCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTCGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAACGCAGGCTCTGGTTGACGATATCGTTATTTAATGGGGTAGAAAGCCACACC > NZ_CP009273/4310693‑4310882
|
AATCAGCGTCGCCCCCGCTTCCGGCGCAACGGCGGTGCCGGTGGAAAGGGGGTTGAGCTGTTCGCTGGAAATCGCCTCATCCGTCACCGAGAAGGTTGCC < SRR3722116.277075/100‑1 (MQ=60)
GCACCCGCTTCCGGCGCAACGGCGGTGCCGGTGGAAAGGGCGTTGAGCTGTTCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTTGCCTGTTCCGGCT < SRR3722116.323337/100‑1 (MQ=60)
GCGGTGCCGGTGGAAAGGGCGTTGAGCTGTTCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTTGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGG < SRR3722116.111338/100‑1 (MQ=60)
GTGGAAAGGGCGTTGAGCTGTTCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTTGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAAC > SRR3722116.181169/1‑100 (MQ=60)
GCGTTGAGCTGTTCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTTGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGCTATGAAAACCCAGGCTCT > SRR3722116.63245/1‑100 (MQ=60)
GAGCTGTTCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTCGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAACGCAGGCTCTGGTTG > SRR3722116.132701/1‑100 (MQ=60)
TCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTTGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAACGCAGGCTCTGGTTGACGATAT < SRR3722116.99903/100‑1 (MQ=60)
TCATCCGTCACCGCGAAGGTTGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAACGCAGGCTCTGGTTGACGATATCGTTATTTAATGGGG < SRR3722116.445/100‑1 (MQ=60)
GAAGGTTGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAACGCAGGCTCTGGTTGACGATATCGTTATTTAATGGGGTAGAAAGCCACACC < SRR3722116.152315/100‑1 (MQ=60)
|
AATCAGCGTCGCACCCGCTTCCGGCGCAACGGCGGTGCCGGTGGAAAGGGCGTTGAGCTGTTCGCTGGAAATCGCCTCATCCGTCACCGCGAAGGTCGCCTGTTCCGGCTGGCTGACCAGCGGCGCGTTGGTATGAAAACGCAGGCTCTGGTTGACGATATCGTTATTTAATGGGGTAGAAAGCCACACC > NZ_CP009273/4310693‑4310882
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
