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 |
|
A7 F28 I1 R1
|
172 |
67.8 |
2301510 |
98.9% |
2276193 |
138.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,797,041 |
(T)8→9 |
coding (94/1260 nt) |
waaL → |
O‑antigen ligase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,797,033 | 1 | . | T | 97.1%
| 114.4
/ ‑3.4
| 34 | coding (86/1260 nt) | waaL | O‑antigen ligase |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base T (17/16); total (18/16) |
| 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 |
ACAGTCAAGCAGTTTTGGAAAAGTTATCATCATTATAAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATG‑‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTAATTTTACGTGGCAGACAAGAAAATTATAATATAAAAAACC > NC_000913/3796901‑3797161
|
aCAGTCAAGCAGTTTTGGAAAAGTTATCATCATTATAAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATG‑‑ttttttt > 1:519481/1‑140 (MQ=255)
tCAAGCAGTTTTGGAAAAGTTATCATCATTATAAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATG‑‑tttttttttca > 2:1147306/1‑137 (MQ=255)
ttttGGAAAAGTTATCATCATTATAAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGTTTTTTTTTTCAATGATaa > 2:1148568/1‑140 (MQ=255)
ttATCATCATTATAAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATtcgtcg < 2:519481/140‑1 (MQ=255)
ttATAAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACtt > 1:911689/1‑140 (MQ=255)
tataAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACttt > 2:761092/1‑140 (MQ=255)
tataAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACttt > 1:625793/1‑140 (MQ=255)
tataAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACttt > 1:347969/1‑140 (MQ=255)
aGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCa < 2:911689/140‑1 (MQ=255)
ggTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGTTTTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCa < 1:1148568/140‑1 (MQ=255)
gTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATG‑‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATaa > 1:1028582/1‑140 (MQ=255)
tAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATaa < 2:355000/140‑1 (MQ=255)
tAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATaa < 2:718750/140‑1 (MQ=255)
aaaCATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATaaaa > 1:532907/1‑140 (MQ=255)
aaaCATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATaaaa > 2:400203/1‑140 (MQ=255)
cATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAata < 2:347969/140‑1 (MQ=255)
cTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAAtatata > 1:194170/1‑140 (MQ=255)
aaCATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATataat < 1:621973/140‑1 (MQ=255)
cATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAatat < 2:91638/140‑1 (MQ=255)
cATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAatat < 1:1147306/140‑1 (MQ=255)
tCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCa < 2:194170/140‑1 (MQ=255)
tttAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAatat > 1:284186/1‑135 (MQ=255)
tttAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAatat < 2:284186/135‑1 (MQ=255)
tttAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTg > 1:102664/1‑140 (MQ=255)
tcattcatTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATataat < 1:749330/125‑1 (MQ=255)
tcattcatTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATataat > 2:749330/1‑125 (MQ=255)
cattcattGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGttt > 2:10720/1‑140 (MQ=255)
aaCCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTc > 2:636727/1‑140 (MQ=255)
tACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAAAGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTaa > 2:168116/1‑140 (MQ=255)
tcaATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTAATTTTACGTGGCAGAc > 1:1049801/1‑140 (MQ=255)
ttttAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTAATTTTACGTGGCAGACAAGaaaa < 1:10720/140‑1 (MQ=255)
taaCTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTAATTTTACGTGGCAGACAAGAAAATTATAATATaaa < 2:102664/140‑1 (MQ=255)
taaCTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTAATTTTACGTGGCAGACAAGAAAATTATAATATaaa < 1:1029391/140‑1 (MQ=255)
atatatTATGTTTTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTAATTTTACGTGGCAGACAAGAAAATTATAATATAAAAAAcc > 1:1030176/1‑140 (MQ=255)
atatatTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTAATTTTACGTGGCAGACAAGAAAATtata < 1:534306/127‑1 (MQ=255)
atatatTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTAATTTTACGTGGCAGACAAGAAAATtata > 2:534306/1‑127 (MQ=255)
|
ACAGTCAAGCAGTTTTGGAAAAGTTATCATCATTATAAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATG‑‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTAATTTTACGTGGCAGACAAGAAAATTATAATATAAAAAACC > NC_000913/3796901‑3797161
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
