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 |
|
A23 F79 I1 R1
|
20 |
28.5 |
998386 |
94.1% |
939481 |
141.6 |
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 | 96.8%
| 97.0
/ ‑5.4
| 31 | S162S (TCT→TCA) | wbbH | O‑antigen polymerase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); major base T (16/14); minor base C (1/0); total (17/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01 |
TATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGG > NC_000913_3_pae_tpiA/2106599‑2106870
|
tATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGAAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaa > 1:128713/1‑149 (MQ=255)
cTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAAtaactaaa > 2:23633/1‑149 (MQ=255)
tACGATGAATGAATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAg < 1:260164/149‑1 (MQ=255)
gATGAATGCATAAGAGATGATAACCATAAAGACAATTCGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATACATAAAGCaa > 2:336527/1‑149 (MQ=255)
tAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAACAAAAGTAGT‑TAg > 2:367819/1‑149 (MQ=255)
gagaTGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCACAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACTAAATAAATAAAGCAAAAGTAGT‑TAGAAt > 2:480101/1‑149 (MQ=255)
aaaGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGt > 2:146464/1‑149 (MQ=255)
gACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATTAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATg < 1:307572/149‑1 (MQ=255)
cAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt > 1:162552/1‑149 (MQ=255)
gTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TATAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGa < 1:146464/149‑1 (MQ=255)
ttCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCAAGTATACTGAGAAATTTCTTGAttt > 2:16079/1‑147 (MQ=255)
aGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTATTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTCCCTGTCTGCTCAGAAATTTCTTGAttcgtc > 2:158967/1‑144 (MQ=255)
ttGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAACTTTCTTGATGTGTCTTCAACa > 1:104624/1‑149 (MQ=255)
cAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATGAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCa < 1:468599/149‑1 (MQ=255)
aaaGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAg > 1:175974/1‑149 (MQ=255)
aaTGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCAt < 1:406889/148‑1 (MQ=255)
aTGAATAAAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAAAAtaactgtc < 2:62672/149‑8 (MQ=255)
gAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCAtctc > 1:344814/1‑149 (MQ=255)
aTACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTGGTATTAGTAAATTTTTTTGAGCAAATAAATAAAGC‑AAATTAGTGGAGAATGATTGGATGAATATATGCAGCAAAATTTCTTGCTGTTTCTTCACCATCAGCATCTCtt > 2:377811/1‑149 (MQ=255)
aCAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTAt < 2:344814/149‑1 (MQ=255)
cAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATc < 2:175974/149‑1 (MQ=255)
aaaTAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATc < 1:174852/148‑1 (MQ=255)
aaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCt > 2:55304/1‑149 (MQ=255)
aTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaagtaag < 1:16079/149‑1 (MQ=255)
gTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCt < 2:128713/149‑1 (MQ=255)
ttttACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTa > 2:324067/1‑149 (MQ=255)
acttacCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTcc < 1:55304/149‑1 (MQ=255)
tttGTATTAGTAAATTTTTTCGACCAATTAGATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGCAAGATATTCCCGAACTg > 1:485047/1‑149 (MQ=255)
ttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTgg < 2:290847/149‑1 (MQ=255)
tAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATctct < 2:178751/100‑1 (MQ=255)
tAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATctct > 1:178751/1‑100 (MQ=255)
|
TATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGG > NC_000913_3_pae_tpiA/2106599‑2106870
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
