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 F97 I1 R1
|
15 |
61.0 |
2236302 |
90.0% |
2012671 |
142.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,173,363 |
Δ2 bp |
intergenic (‑1/+1) |
gatC ← / ← gatC |
pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,173,361 | 0 | C | . | 92.3%
| 197.0
/ 7.6
| 52 | pseudogene (2/442 nt) | gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| Reads supporting (aligned to +/- strand): ref base C (0/4); new base . (20/28); total (20/32) |
| Fisher's exact test for biased strand distribution p-value = 1.51e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | NC_000913 | 2,173,362 | 0 | C | . | 94.1%
| 195.4
/ 5.3
| 52 | pseudogene (1/442 nt) | gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| Reads supporting (aligned to +/- strand): ref base C (0/3); new base . (20/28); total (20/32) |
| Fisher's exact test for biased strand distribution p-value = 2.71e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTG > NC_000913/2173220‑2173497
||
gctgtCCACGGTGCACGGGCACCGCGATCGCCACGAAGACGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCTGCACACAAACAGCAATTAAAATGGTGAGTGTGATAATATTTAGGCTTGCGGATaccacc < 2:1006106/139‑1 (MQ=255)
ttCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCGCCTGATTACCCGGCACACAAACAGCAATTAAAATGGTAAGTAGGAAAAAAATAAGGCTTGCCGATaccaccgcc > 1:606203/1‑140 (MQ=255)
cACGATGCACGGCGACCCCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccaccgccgta < 1:319975/143‑7 (MQ=255)
ggCGACCGCCAGCGCCACGACGAAGCCTATGGTGGCAAGATCGCCCGTCGGCACCACCTCATTCCCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCcagca < 2:233318/143‑1 (MQ=255)
cGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGCTTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGACAAAAATCAGGCTTGCCGATACGA‑‑CCGCCGTATGGCCCAGCAGCAACg > 2:936262/1‑143 (MQ=255)
cGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACg > 1:589126/1‑143 (MQ=255)
cACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCCGATTACCCGGCACACAAACAGCAATTAAAATGGAGAGTGGGATAAAAATCAGGCTGGCCGATACCA‑‑CCGCCGGCGGTCCCAGCAACAACGCCGGACCac > 2:745673/1‑142 (MQ=255)
gcgacgaAGCCGCTGGTGGCAAGATCCCCAAACGGCAGCACCTTATTACCCGGCACACAAACAGCCATTAAGATGGTGAGTGGGATACAAATCAGGCTTGCCGCTACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAg < 2:79648/142‑1 (MQ=255)
aCGAAGAAGCCGATGGTGGCAAGATCGCCAAAGGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAg < 2:949470/143‑1 (MQ=255)
gaagCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAAAGGTGAGTGGGATAAAAACCAGGCTTGCCGATACCA‑‑CCGCCACATGTCCCCGCCGCAACAGCGGATCAAGGCCac > 2:361879/1‑142 (MQ=255)
agCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATT‑CCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCa < 1:471232/143‑1 (MQ=255)
cggATGGTGGCAAGATCGCCAATCGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAAGCAGGCTTGCGGATACCA‑‑CCGCCGTATGTCCGAGCAGCAACGCCGGATCAAGGCCAATCAg < 2:557619/141‑1 (MQ=255)
ccGATGGTGGCAAGATCGCCAAACGGCAGCACCGGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAg < 2:777392/143‑1 (MQ=255)
cGATGGTGGCAAGACCGCCAAACGGCAGCACCTGACTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCCGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAgg < 1:453292/143‑1 (MQ=255)
aTGGTGGCAAGAGCGCCAAGCGGGAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGaa < 2:979488/143‑1 (MQ=255)
gtggCAGGAGCGTCAATCGGCAGACACTGATAACCCGGCACATGAACAGCAATTATAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCTGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTc < 2:950379/143‑1 (MQ=255)
gtggCAAGACCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTc < 1:884286/143‑1 (MQ=255)
tggCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTcc > 2:313571/1‑143 (MQ=255)
cAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGa < 2:820244/143‑1 (MQ=255)
cAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGAGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGACGTATGTCCCAGCAGCCACGCCGGATCATGTCAAATCAGGAACTCCTGa > 1:692586/1‑143 (MQ=255)
gATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGCTAACAATCCGGCCTGCCGCTACCA‑‑CCGCCGTATGTCCCCGCAGCACCGCCCGATCAAGGCCCATCAGGAACTCCTGCccg > 2:210311/1‑143 (MQ=255)
gcgaagggCAGCACCTGGAGACCCGGAACACAAACAGCAATTAGAAGGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGaa < 1:92179/137‑1 (MQ=255)
aaaCGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACt > 1:343922/1‑143 (MQ=255)
aaaCGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACt < 1:743129/143‑1 (MQ=255)
tcGGCTGCTCCTGATTATCCGGCACTCAAACAGCAATGAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATAC‑‑CTCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTc < 2:700307/142‑1 (MQ=255)
aCGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTc > 2:678669/1‑143 (MQ=255)
cGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCg < 1:854003/143‑1 (MQ=255)
gcaggaGCTGGTGACCCGGCAGACGAGCAGCAAGTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTAGGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGcc < 2:96835/143‑1 (MQ=255)
gcagcaCCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGCTACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGcc < 1:154632/143‑1 (MQ=255)
aCCTGATTACGCGGCAGACATCGTGCAATTAACATGGTGAGTGGGATAAAACTCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTaa < 2:204799/143‑1 (MQ=255)
gggtatccGGCACACAAACAACAATTAAAACGGTGCGTGGGATAAAGATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGa < 2:361912/137‑1 (MQ=255)
tACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTa > 2:93744/1‑143 (MQ=255)
cGGCACCCACACGGCAATTCGAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAg < 2:668636/143‑1 (MQ=255)
aaaCAGCAATTAAAATGGTGAGTGGGATAAAAATCAAGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGGAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTa > 1:519808/1‑143 (MQ=255)
aGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACAGACGAACTTAACCTGTAAACGAATACGAGACTGCATAACGa > 1:977974/1‑143 (MQ=255)
aaTTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGACGTATGTCACAGCAGCAACGCCGCATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGACCCTCCTTAGCGAtcg > 2:505607/1‑141 (MQ=255)
ctcaaaaTCGGGAGCGGGATAAACATCAGGCTCGCCGAGACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAGCTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATggg < 2:1002029/140‑1 (MQ=255)
gggtgggtgGGATGAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTaaa < 2:1095617/142‑1 (MQ=255)
cgggcggTGGGATAAAGATACGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGACCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTaaa < 2:905639/137‑1 (MQ=255)
gactGGGATCAAACTCCGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACGCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAAccat < 2:452520/140‑1 (MQ=255)
aatGGGAAAAAAACCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAAccatc < 1:365393/141‑1 (MQ=255)
gATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCCGCAACGCCGGATCAAGGCCAATCAGAACCTCCTGACCGCCGAACTTCGCCTGGAACCGACTACGAGCCCGCTTAGCGATCAGCGATAACCCACCCagga > 2:340661/1‑143 (MQ=255)
aTAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTCAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACGATCCatgat > 2:289953/1‑143 (MQ=255)
aaaaaTCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCAGGATgg > 1:597953/1‑143 (MQ=255)
aactCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGt < 1:520119/140‑1 (MQ=255)
aaTCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGAATAATACACTTTTAGGTTCTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGtt < 1:509673/143‑1 (MQ=255)
tCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCGTCCATGATGGGtatc > 1:532425/1‑140 (MQ=255)
cAGGCTCGCCGACAC‑‑CCCCGCCGTCTGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCTAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTaa < 1:219461/143‑1 (MQ=255)
ggCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATc < 1:3527/143‑1 (MQ=255)
ggCGTGCCGATAC‑‑CCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATc < 2:1115858/143‑1 (MQ=255)
ttGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCGGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCAcc > 1:767133/1‑143 (MQ=255)
ttGCCGATACCA‑‑CCGCCGTATGTACCAGCAGCAACGCCGGATCACGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTCAACCATCCATAATGGCTTCAATCAcc > 1:767139/1‑143 (MQ=255)
gtGCCGATAC‑‑CCCCGCCGTATGTCCCAGCAGCCACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGTCTGTAAACGACTACGAGCCTGCTTAGCGATGGGTGTTAAACCATCCCTGATGGGTTTAATCAcc < 2:347850/142‑1 (MQ=255)
cGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGTCAATCAGGAACTTCTGACTGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTg < 1:77063/143‑1 (MQ=255)
cGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGACCTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTg > 1:35816/1‑143 (MQ=255)
||
GATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTG > NC_000913/2173220‑2173497
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
