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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,276,251 |
Δ1 bp |
coding (932/3744 nt) |
narG → |
nitrate reductase subunit alpha |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,276,249 | 0 | G | . | 100.0%
| 46.3
/ NA
| 12 | coding (930/3744 nt) | narG | nitrate reductase subunit alpha |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base . (5/7); total (5/7) |
CACACCAGACTACGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGATGGGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTACACCGACATGC > NZ_CP009273/1276162‑1276331
|
cacaCCAGACTACGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGATgcc < 2:366225/90‑3 (MQ=255)
aCGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAAtgct < 2:82727/90‑1 (MQ=255)
gAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACg < 1:380735/78‑1 (MQ=255)
gAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACg > 2:380735/1‑78 (MQ=255)
aaaCTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCAcc < 2:244915/90‑1 (MQ=255)
gtgCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGAc > 1:440027/1‑90 (MQ=255)
gtgCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGAc > 2:286182/1‑90 (MQ=255)
aTCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAAccc < 1:286182/90‑1 (MQ=255)
aTCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAAccc < 2:186855/90‑1 (MQ=255)
ggcACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTAt > 2:214208/1‑90 (MQ=255)
gggCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTAt > 1:390711/1‑90 (MQ=255)
gCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTaca < 2:390711/90‑1 (MQ=255)
cTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTACACCGACATGc < 2:440027/90‑1 (MQ=255)
|
CACACCAGACTACGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGATGGGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTACACCGACATGC > NZ_CP009273/1276162‑1276331
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ 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
CCAGACTACGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGATGGGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTACACCGACATGCCGATGCTGGTGATGCTGG > NZ_CP009273/1276166‑1276349
|
agAGACTACGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCG < SRR3722092.387957/98‑1 (MQ=60)
TCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGAC > SRR3722092.448654/1‑100 (MQ=60)
ATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTAT < SRR3722092.291123/100‑1 (MQ=60)
CACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTAT > SRR3722092.398167/1‑100 (MQ=60)
GGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTACACCGACATGCCGATGCTGGTGA > SRR3722092.26514/1‑100 (MQ=60)
ggatGGCCAAGTAATGATGAGTGAATTCCCCCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTACACCGACATGCCGATGCTGGTGATG < SRR3722092.84597/96‑1 (MQ=60)
GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTACACCGACATGCCGATGCTGGTGATGCTGG > SRR3722092.360898/1‑100 (MQ=60)
|
CCAGACTACGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGATGGGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTACACCGACATGCCGATGCTGGTGATGCTGG > NZ_CP009273/1276166‑1276349
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
