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 |
|
A24 F31 I2 R1
|
18 |
53.0 |
1873152 |
93.2% |
1745777 |
143.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913_3_pae_tpiA |
2,106,741 |
A→T |
S162S (TCT→TCA) |
wbbH ← |
O‑antigen polymerase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913_3_pae_tpiA | 2,106,741 | 0 | A | T | 98.2%
| 178.3
/ ‑3.3
| 55 | coding (486/1167 nt) | wbbH | O‑antigen polymerase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); major base T (23/31); minor base . (1/0); total (24/31) |
| Fisher's exact test for biased strand distribution p-value = 4.36e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.35e-01 |
ACTCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAC > NC_000913_3_pae_tpiA/2106595‑2106882
|
aCTCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGa < 2:372533/149‑1 (MQ=255)
aCTCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGa < 2:683814/149‑1 (MQ=255)
aTTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaa < 2:762084/149‑1 (MQ=255)
aaCACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaataa > 1:158781/1‑149 (MQ=255)
tACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTT‑GACCAAATAAATAAAGc > 1:745638/1‑149 (MQ=255)
aTGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGGATTCAGTATAATTGCAAAGATAAATACAATAAAAAAAATTAAAGTAAATGTTTTATTTACCATTGTATTAGTAAATTTTTTTGACCAaataaatacggaaaa > 2:703635/1‑142 (MQ=255)
tGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCaaaa < 1:216343/149‑1 (MQ=255)
tGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATAAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCaaaa < 1:395557/149‑1 (MQ=255)
tgatAACAATAAAGACAATTTGATTAACAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGAtt < 2:659709/149‑1 (MQ=255)
aaCCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAATCAAAAGTAGTTAGAATGATTGGCt > 2:260619/1‑149 (MQ=255)
ccATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGACGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGc > 1:741625/1‑149 (MQ=255)
cATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCa > 2:589846/1‑149 (MQ=255)
aTAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCAt < 1:630565/149‑1 (MQ=255)
aCAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGc < 2:359418/149‑1 (MQ=255)
cAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCt < 1:407616/149‑1 (MQ=255)
cAATATGCTTACCAGTATTCAGTATAATTTCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCt < 1:547068/149‑1 (MQ=255)
aaTTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTg > 1:479488/1‑149 (MQ=255)
aaTTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTg > 1:328519/1‑149 (MQ=255)
ttACCAGTGTTCAGTATAAATGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATGAGTAAATTTTTTTGAGCGAATAAATAGAGCAAAAGTAGTTAGAACGAATAGCTGCATGTATGCTGAGAAAtt > 2:791608/1‑149 (MQ=255)
ccAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATAAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATTTATGCTGCGAAATTTCt > 2:407996/1‑149 (MQ=255)
cAGTATTTATTATAATTGCAAAGAAGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt < 1:309099/149‑1 (MQ=255)
gTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGATGCATGTATGCTGACAAATTTCTTGa > 2:850229/1‑149 (MQ=255)
tATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAt < 1:252115/149‑1 (MQ=255)
ttaaGTTTAATTGCAAAGATGAAGACAATAAAAACGAGTAAAGTAAATGTTTTACTTACTTTTGTTCTAGTAAAATTTTTTATCACATTATATAAAAAAAAATTAATTAGAATGATTAAGTCTATGTATACTTAGATATTTCTTggttt > 2:761943/4‑145 (MQ=255)
tataATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAagtagt < 1:378587/102‑1 (MQ=255)
tataATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAagtagt > 2:378587/1‑102 (MQ=255)
aaTTGTAAATATTAATACAATAAAAACAAGGAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCaa < 1:169696/149‑1 (MQ=255)
aaTTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCaa > 1:88258/1‑149 (MQ=255)
aaTGGCAAAGATTAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCaa < 1:169686/149‑1 (MQ=255)
gCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAACCAATCAGAGGGAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATc > 1:688790/1‑149 (MQ=255)
gaagaaTGAATGCAATCACATCAAGAACAGTAAATGTTGTAGTGAGGTTTGTATTAGTATATCTTTGTGAGCAAAAATAAAAAGCAAAACTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCa < 2:891301/144‑1 (MQ=255)
aaaGATTAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAg < 1:188575/149‑1 (MQ=255)
aCAATAAACATAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTAt < 1:35674/149‑1 (MQ=255)
aaaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAAtt < 1:575000/149‑1 (MQ=255)
aaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTc < 2:841589/149‑1 (MQ=255)
aCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCat > 2:60637/1‑149 (MQ=255)
aagtaaagtaAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCatat < 1:633839/149‑1 (MQ=255)
gtaaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAt < 2:294383/110‑1 (MQ=255)
gtaaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAt > 1:294383/1‑110 (MQ=255)
taaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCCGCATCTCTTATCAAATTCATATAGc > 1:86183/1‑149 (MQ=255)
aaagtaaaTGTGTTACTTATCCTTGTATTAGTAAAATTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGAATGGCTGCATGTATCCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCt < 2:843018/149‑1 (MQ=255)
agtaaaTTTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTATAATGATTGGCTGCATGTAGGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaa < 2:816994/149‑1 (MQ=255)
gtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGCTGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtagg > 1:354463/1‑147 (MQ=255)
tGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGc < 2:158781/149‑1 (MQ=255)
tGTTCTACTTACCTTTGTATTAGAAAATTTTTTTGACCAAATAAACAAAGCAAAAGTAGTTATAATGATTGGCTGCATTTATGCTGACAAACTTATTGTTGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGc < 1:791608/149‑1 (MQ=255)
ttttACTTACCTTTGTATTAGTAAATTTTTTTGACCACTCTAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTa > 1:925161/1‑149 (MQ=255)
ttttACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAACATCTCTTATCAAATTCATATAGCTAAGTAAGCTa > 2:613364/1‑149 (MQ=255)
cTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACt > 1:338021/1‑149 (MQ=255)
cTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGGTAGAATGATTGACTGCATAAAAGCTAAGAAATTTCTTGATGTTTCTTCAACATCAGCATCTCTTTTCAAATTCATATAGACATGTAATCTAGTCACGAACt > 2:738911/1‑149 (MQ=255)
tGTATTAGTAAATTTTTTTGACCAAATCAATAAATCAAACGTAGATATAATGATTGCCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGt < 2:666472/149‑1 (MQ=255)
ttAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAATTACAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGtt < 1:260619/149‑1 (MQ=255)
tAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTa < 1:589846/149‑1 (MQ=255)
tAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTa > 1:720491/1‑149 (MQ=255)
aaTTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTaa < 2:720491/149‑1 (MQ=255)
aTTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAc < 2:88258/149‑1 (MQ=255)
|
ACTCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAC > NC_000913_3_pae_tpiA/2106595‑2106882
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
