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 I2 R1
|
16 |
27.9 |
994488 |
92.8% |
922884 |
143.7 |
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 | 95.5%
| 59.3
/ NA
| 22 | S162S (TCT→TCA) | wbbH | O‑antigen polymerase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); major base T (12/9); minor base G (0/1); total (12/10) |
| Fisher's exact test for biased strand distribution p-value = 4.55e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCA‑TATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCTCA > NC_000913_3_pae_tpiA/2106609‑2106886
|
tACGATGAATGCATAAGAGATGCTAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATAAATACAATAAAAACAAATAAAGTACATGTTTTACTTACCTTTGTATAAGTAAATTACTTTCAACAAATAAATCAAg > 2:227568/1‑149 (MQ=255)
gATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTATTTACCTTTGTATTTGTAAATTTTTTTGATCAAATAATTATAGCac > 2:76051/1‑148 (MQ=255)
tGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAagtag > 1:286554/1‑149 (MQ=255)
tAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAg > 2:479161/1‑149 (MQ=255)
aaaaCAATTCGCTTACCAGTATTCAGGAGAATTGGAAAGATGAATACAAGAAAAACAAGAAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTGGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTa < 2:41406/146‑1 (MQ=255)
tttGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTgag > 2:466614/1‑149 (MQ=255)
cAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt > 1:333346/1‑149 (MQ=255)
aGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTg < 1:479161/149‑1 (MQ=255)
tATTAAGTATAATTGCAAAGATGAATACAAGAAAAACAAGTATAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAt < 2:452107/149‑1 (MQ=255)
ttgaGTATAATAGCAAAGATGCATTGAATGAAAACAAGTAACGAAAATGTTTTATTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgt < 2:330023/146‑1 (MQ=255)
ttCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTTCTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgt > 1:328852/1‑149 (MQ=255)
ttCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGGTGAGAAATTTCTTGAtga > 1:452107/1‑148 (MQ=255)
ttCAGTATAATTGAAAAGATGAATACAAAAAAAACAAATAACGTAAATGGTTTACTTACCTTTGTATTAGTAAAGTTTTTTCACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgt < 2:206615/149‑1 (MQ=255)
aGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTc > 1:238345/1‑149 (MQ=255)
tACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCGTCTCTTa > 1:252831/1‑149 (MQ=255)
aaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCa > 2:276359/1‑149 (MQ=255)
taaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCA‑TATAGCtaatt > 2:62743/1‑147 (MQ=255)
cttatCTTTGTCTTCTTATATCCTTTTGAGCAAATAAATAAAGCAAAAGTAGTTAGAATTATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACCTCAGCATCTCTTATCAAATTCA‑TATAGCTAAGTAAGCTAGTccc < 1:240219/149‑1 (MQ=255)
tgaatAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGATGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCA‑TATAGCTAAGTAAGCTAGTCCCGAACTGGTa < 2:247912/145‑1 (MQ=255)
gTATTAGTAAATTGTTTTGACCAAATAAATAAAGCAAAAGTAGGTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCA‑TATAGCTAAGTAAGCTAGTCCCGAACTGGTa < 2:248278/149‑1 (MQ=255)
tAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCACTACTG‑GAGTTAAGCTAGTCCCGAACTGGTAGTTACtt < 1:246033/149‑1 (MQ=255)
aTTTTTTTGACCAAAGAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCA‑TATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAc < 2:328852/149‑1 (MQ=255)
ttttGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCCTGTCTATCTACGAGTTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCA‑TATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCTCa < 1:466614/149‑1 (MQ=255)
|
TACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCA‑TATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCTCA > NC_000913_3_pae_tpiA/2106609‑2106886
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
