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 |
|
A0 F0 I1 R1
|
16 |
48.9 |
1703346 |
91.6% |
1560264 |
146.2 |
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 | 77.1%
| 84.6
/ 21.3
| 35 | coding (40/1389 nt) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base . (3/5); new base A (12/15); total (15/20) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | NC_000913_3_pae_tpiA | 1,544,022 | 0 | C | A | 97.1%
| 100.1
/ NA
| 35 | L13F (TTG→TTT) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base C (1/0); new base A (13/20); total (15/20) |
| Fisher's exact test for biased strand distribution p-value = 4.12e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCG‑C‑G‑C‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAA > NC_000913_3_pae_tpiA/1543879‑1544170
|||
ttGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTCGACAACTGACTGATGTCCAGAGATTTCTTCGAGCTATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCG‑C‑G‑A‑a‑aa‑at < 2:643198/149‑2 (MQ=255)
gaTTAACGGTAACTGCGCTAAATAGAGTCCTAACACACAAGGGAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTATGGTTTCC‑ATTCG‑C‑G‑A‑a‑aa‑atgtta > 2:823000/1‑144 (MQ=255)
ggaccaaaGAGCAGCCAGACACAGAAGGTAAGTAGTAGACATTGGACCGTTAGACAAAGATTTTTTCTAGCAATATGTTTCCCTTTATTTTTCAATAAGGCTGGATTTTCTGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTtct < 2:58776/144‑1 (MQ=255)
gcgtTAAATGGCATCCAGACAAAGAAGGCAAGAAGTAGACAATTGACTGATATCTAGAGAGTTCTTCGAGCAATATGTTTTCCTTTATTTTCCTAGAAGGCCGGATTTTCTGGTTTCC‑AGTAG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTtct < 2:91220/149‑1 (MQ=255)
tAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCAtt < 1:129520/149‑1 (MQ=255)
tAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCAtt > 2:790792/1‑149 (MQ=255)
tAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCATTTATTTTCCCAGAAGGCCGGATTTTATGGTTTCC‑AGTCG‑A‑GAA‑A‑AA‑AGATAACGACTCTTTTTCTCAtttttc > 2:543937/1‑147 (MQ=255)
tCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCC‑C‑GAC‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGc > 2:469092/1‑149 (MQ=255)
acaGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGACGTGCCATATTg > 2:33487/1‑149 (MQ=255)
aGAAGGCAAGAAGTAGACAACTGAATGATATGCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGtt < 2:562077/149‑1 (MQ=255)
aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAAGTAC‑G‑A‑A‑A‑AA‑AGATAACGACTATTTTTATCAGTTTGCAGTGCAATATTGTTCCTcaca > 1:834460/1‑149 (MQ=255)
agaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACAt < 1:790792/149‑1 (MQ=255)
agagAACTGACTTATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGCAGCC‑A‑A‑A‑AA‑AGATCACGATTAGTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGcacac < 1:200728/149‑1 (MQ=255)
aaCTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGCCG‑C‑GAA‑A‑AA‑AAATACCGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTg < 2:353935/149‑1 (MQ=255)
gactgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTaa < 1:255650/149‑1 (MQ=255)
acttaTATCCATAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCC‑C‑C‑A‑ACAA‑AGATACCGACTCTTTTCCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGTTAAt < 2:202959/149‑1 (MQ=255)
gaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCG‑C‑G‑AAA‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGAGATATTGTTCCTGACATGCACAAATTGGTAATGaa > 1:277962/1‑149 (MQ=255)
taggcAGAGATTTGTTAGAGCAATATGTGTTCGTTTATTCTCCCAGAAGGCTGGTTTTTCTTGTTTCC‑AGTAG‑C‑G‑A‑A‑AAGAGCGAACGACTGTTTTTCTCATTTTACTGTCCGATATTGTTCCTCACATGCACAAATTGGTAATGaata < 2:112584/145‑3 (MQ=255)
tCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGGACACATTGGGAATGaaaaaa > 1:172408/1‑149 (MQ=255)
tcAGAGATTTTTTCGAGCAATTTGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaaa < 1:1294/148‑1 (MQ=255)
tttCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCCCAATTTCACACATTGGTAATGAAAAAAAGACaaaa < 1:204770/149‑1 (MQ=255)
cttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCAGTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAacac > 1:624789/1‑149 (MQ=255)
tcGAGGAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGa < 2:809418/149‑1 (MQ=255)
tcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGa < 2:68728/149‑1 (MQ=255)
aGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGt > 1:271370/1‑149 (MQ=255)
atGTGTTACTTTAATTTCCCAGAAGGTCGGATTTTCTGGGGTCC‑AGTCG‑CGG‑A‑A‑AA‑AGATAACGTCTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACTTGCAAACAATGGTAATGAAAAAAAGACAAAACACGAGGTAAGgcg < 2:631838/149‑1 (MQ=255)
tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa < 1:82429/149‑1 (MQ=255)
gAAGGCCGGATTTTCTGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAAtt > 2:245554/1‑149 (MQ=255)
gCCGGATTTTCTGGTTTCC‑AGTCG‑C‑GAG‑A‑AA‑AGATAACGACTATTTTTCTCCTTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGAGCAATAGCCAGTTATTAAAATTAAgg > 2:827191/1‑149 (MQ=255)
ccGGATTTTCTGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGa > 1:459280/1‑149 (MQ=255)
gATTTTCTGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGa < 1:235002/149‑1 (MQ=255)
tCTGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTgg > 1:346126/1‑149 (MQ=255)
tCTGGATTCC‑AGTAG‑C‑GAA‑A‑AA‑AAATAACGACTATTTTCATTAATTTGCAGTGCTATATTGTGCCTCACATGCACAAAAAAAAAAAAAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTgg < 2:479388/149‑1 (MQ=255)
tGGTTTCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGTAATggat < 2:8917/149‑3 (MQ=255)
ttCC‑AGTCG‑C‑GAA‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAg > 1:312143/1‑149 (MQ=255)
tcgcgaaa‑aa‑aGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGa > 1:777777/8‑149 (MQ=255)
cgcgaaa‑aa‑aGCTAACGACTATTTGTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACAAATTGGTAATGAAAAACAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGAt < 2:700422/143‑1 (MQ=255)
aa‑aa‑aGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGaaa < 1:245554/148‑1 (MQ=255)
aa‑aa‑aGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGaaa < 1:47757/148‑1 (MQ=255)
|||
TTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCG‑C‑G‑C‑A‑AA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAA > NC_000913_3_pae_tpiA/1543879‑1544170
|
| 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
