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 |
|
A8 F23 I0 R1
|
29 |
39.7 |
1391800 |
89.8% |
1249836 |
148.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913_3_hsa_tpiA |
2,106,741 |
A→T |
100% |
S162S (TCT→TCA) |
wbbH ← |
O‑antigen polymerase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913_3_hsa_tpiA | 2,106,741 | 0 | A | T | 100.0%
| 103.6
/ NA
| 34 | S162S (TCT→TCA) | wbbH | O‑antigen polymerase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (17/17); total (17/17) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATA‑AAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTG‑CATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAC > NC_000913_3_hsa_tpiA/2106597‑2106882
|
tctATTAACACCTACGATGAATGCATAAGAGATGATAACCATA‑AAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTAACTTTGTATTAGTAAATTTTTTTGAca > 2:439724/1‑148 (MQ=255)
tATTAACACCTACGATGAATGCATAAGAGATGATAACCATA‑AAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaa > 1:427478/1‑149 (MQ=255)
acCTACGATGAATGCATAAGAGATGATAACCATA‑AAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAaataaata > 1:218433/1‑149 (MQ=255)
acCTACGATGAATGCATAAGAGATGATAACCATA‑AAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAaataaata > 1:265441/1‑149 (MQ=255)
cTACGATGAATGCATAAGAGATGATAACCATA‑AAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAAtaaataaa < 1:305070/149‑1 (MQ=255)
cTACGATGAATGCATAAGAGATGATAACCATA‑AAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAAAAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACAAAAtaaataaa > 1:647708/1‑149 (MQ=255)
gAATGCATAAGAGATGAT‑GCAATATAATAGAGGTTGCTTACCAGTATTCAGTATAATTTCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAag < 1:646946/149‑1 (MQ=255)
ttcATAAGACATTAAAACCATA‑AAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTAGTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAagtag < 2:272665/147‑1 (MQ=255)
aaTAAGAGAAGAAAACCATA‑AAGACAATTGTCGTACCAGAATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGAAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGtt < 2:305257/148‑1 (MQ=255)
tgatAACCATA‑AAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGAtt < 2:391771/149‑1 (MQ=255)
tgatAACCATA‑AAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGAtt > 2:434605/1‑149 (MQ=255)
tgatAACCATA‑AAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATAAtt > 2:388407/1‑149 (MQ=255)
aCCATA‑AAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATAGTTTTCTTCGCTTTGTATTAGTAAACTTTTTTGACCACATAAATAAACAAAAAGTAGTTAGAATGAtttcctc > 2:423685/1‑144 (MQ=255)
tA‑AAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTACTTAGCATGTTTGGCTG‑CATg > 2:151973/1‑149 (MQ=255)
aGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTG‑CATGTAt < 1:573363/149‑1 (MQ=255)
aTTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTG‑CATGTATGCTga < 2:427478/149‑1 (MQ=255)
tttGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACACAAAAAACAAGTAAAGTAACTGTTTTACTTACCTTTGTATTAATAAATTTCTTTGACAAAATAAATAAAGCAAAACTAGTTAGATTTATTGGCTG‑CCTGTAtattgaa > 2:387394/1‑143 (MQ=255)
tttGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGACTG‑CATTTATGCTtag > 2:535918/1‑149 (MQ=255)
aCCAGGATTCAGTATAAGTGCAAAGATGAATACAATCAAAACAAGTAAAGGAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGACTGGCTG‑CATGTATGCTGAGAAATTTc < 2:225632/149‑1 (MQ=255)
cAGTATTGAGTATAATTGCAAAGATGAATTCAATAAAAACAAGTAAAGTAAATGTTTTACTTAACTTTGTATTAGTAAATTTTTTTGACCAAAAAAATAAAGCAAAAGTAGTTAGAATGATTGGCTG‑CATGTCTGCTGAGAAATTTcgt < 2:340845/149‑3 (MQ=255)
tATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTG‑CATGTATGCTGAGAAATTTCTTGAt < 1:34550/149‑1 (MQ=255)
aaaGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTG‑CATGTATGCTGAGAAATTTCTTGa > 2:244289/1‑132 (MQ=255)
aaaGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTG‑CATGTATGCTGAGAAATTTCTTGa < 1:244289/132‑1 (MQ=255)
aGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTG‑CATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCa > 1:587669/1‑149 (MQ=255)
aGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTAACCAAATAAATAAAGCAAAAGTAGTTACCATGACT‑GCTGTGGTGTATACTAAGAAATTTGATGATGTTTATTCAACATCAGCa > 1:332228/1‑149 (MQ=255)
tACAATAAAATCAAGTAAAGTAAATGTTTTACTGACCTTTGCACTAGTAAATATTTTTGACCACCTCTGTGCTGGAAAAGTAGTTATGTTGATTGTCTG‑CATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTa < 1:685163/149‑1 (MQ=255)
aCAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTG‑CATGTATGCTGAGAAATTTCTTGANGTGNCTTNAAANTCAGCATCTCTTAt > 1:592387/1‑149 (MQ=255)
aTAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTG‑CATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCaa > 1:140439/1‑149 (MQ=255)
agtaaaTGTTTTACTTAGCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTG‑CATGTATGCTGAGAAATTTCTTGATGTGTCTACAACATTAGCATCGCTTATCAAAGTCAGATAGCtaa < 2:340327/149‑1 (MQ=255)
tGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTG‑CATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGc < 1:290318/149‑1 (MQ=255)
ttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTG‑CATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTgg < 1:205871/149‑1 (MQ=255)
aTTTTTTTCACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTG‑CATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAc < 1:616246/149‑1 (MQ=255)
ttttttTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTG‑CATGTATGCTga < 2:195079/60‑1 (MQ=255)
ttttttTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTG‑CATGTATGCTga > 1:195079/1‑60 (MQ=255)
|
TCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATA‑AAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTG‑CATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAC > NC_000913_3_hsa_tpiA/2106597‑2106882
|
| 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
