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 |
|
A13 F6 I1 R1
|
15 |
27.8 |
1046532 |
91.3% |
955483 |
145.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913_3_pae_tpiA |
1,544,022 |
1 bp→AA |
coding (39/1389 nt) |
narU ← |
nitrate/nitrite transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913_3_pae_tpiA | 1,544,021 | 1 | . | A | 79.0%
| 40.2
/ 8.0
| 19 | coding (40/1389 nt) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base . (2/2); new base A (9/6); total (11/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.94e-01 |
| * | NC_000913_3_pae_tpiA | 1,544,022 | 0 | C | A | 94.7%
| 46.6
/ NA
| 19 | L13F (TTG→TTT) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base A (11/7); total (11/8) |
| Fisher's exact test for biased strand distribution p-value = 4.21e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01 |
TGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑A‑AA‑A‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGA‑AAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATG > NC_000913_3_pae_tpiA/1543896‑1544146
|||
tGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AA‑A‑GATACCGACTATTTTtc > 2:76591/1‑149 (MQ=255)
tAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AA‑A‑GATAACGACTATTTTTCTCAtttttc > 2:236207/1‑147 (MQ=255)
tCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AA‑A‑GATAACGACTATTTTTCTCATTTTGCAGTGc > 1:503531/1‑149 (MQ=255)
cAGAAACAGAAGGTAAGAAGTAAACAACTGGCTGATATCCAGAGATTTCTTCGAGTAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAATAACG‑C‑ATAA‑A‑GATAACGACTCTGTTTCTCATTTTGCAGTGCCa < 2:88812/149‑1 (MQ=255)
agaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCGGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AA‑A‑GATAACGACTATTTTTCTCATTTTGCCGTGCCATATTGTTCCTCACAt > 2:403124/1‑149 (MQ=255)
agcaGACAACCGACTGATATCCAGCGATTTCTTCGACTAATATGTGTTCCTTTATTTTCTCAGCAGGCCGGATTTTCCGGTTTCCAGTCGCG‑A‑A‑AAGA‑GATAACCACTATTTTGCTCATTTTGCAGTGCCATATTGTTCCTCCCGTGct < 2:482100/146‑2 (MQ=255)
aaCTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTACTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AA‑A‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTg < 1:434276/149‑1 (MQ=255)
tgactgaTATCAAGATGGTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAA‑AA‑A‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCCCCCATTGGTa > 2:324598/1‑149 (MQ=255)
gaTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AA‑A‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGA‑AAAAAAGACaa < 1:245115/149‑1 (MQ=255)
gttgAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AA‑A‑GATAACGACTATTTTTCTCATTTTTCAGTGCCATGTTGTTCCTCACAGGCACACATCGGTAATGC‑AAAAAACACAAAACACg > 2:138321/4‑149 (MQ=255)
ctacagaaaTAGGTTTTCCTTTATTTTCCCAGAAGGCCGAATTTTCTGGTTTGCAGTCGCG‑A‑A‑AA‑AGGATAACGACTATTTTTCTCATTTTGCAGTGCCATCTTGTTCCTCACATTCACACATT‑GTTATGAGAAAAAAGACTAAACACg > 2:114638/8‑149 (MQ=255)
cTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AA‑A‑GATAACGACTATTTTTCTCATTTTGCAGTGCAATATTGTTCCTCACATGCACACATTGGTAGTGA‑AAAAACAACAAAAAACGAGGTAAGGCGCAATGGcc > 2:360296/1‑149 (MQ=255)
tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AA‑A‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGA‑AAAAAAGACaaaa < 2:442770/126‑1 (MQ=255)
tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AA‑A‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGA‑AAAAAAGACaaaa > 1:442770/1‑126 (MQ=255)
tttATTTTCCCAAGAGCCTGGATTTTCGGGTTTCCAGTCGCGAA‑A‑AA‑A‑GATAACGACTATGTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGA‑AAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa < 1:68960/149‑1 (MQ=255)
tCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AA‑A‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGA‑AAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGttatta < 1:180524/149‑1 (MQ=255)
aGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AA‑A‑GATAACGGCTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACAGGCACACATTGGTAATGA‑AAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTaa < 1:82073/149‑1 (MQ=255)
gCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AA‑A‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGA‑AAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAgg > 1:330921/1‑149 (MQ=255)
ggATTTTCTGGTTTCCAGTCGCGAA‑A‑AA‑A‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGA‑AAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATg > 2:442548/1‑149 (MQ=255)
|||
TGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑A‑AA‑A‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGA‑AAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATG > NC_000913_3_pae_tpiA/1543896‑1544146
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
