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 |
|
A1 F113 I1 R1
|
17 |
62.1 |
2245352 |
90.5% |
2032043 |
142.8 |
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 | . | 98.1%
| 230.3
/ ‑3.3
| 53 | 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 (1/0); new base . (32/20); total (33/20) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
| * | NC_000913 | 2,173,362 | 0 | C | . | 98.1%
| 230.3
/ ‑3.3
| 53 | 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 (1/0); new base . (32/20); total (33/20) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
CACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGT > NC_000913/2173226‑2173496
||
cACGCTGCACGGCGACCGCCTTCGCCACGAAGAAGCGGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccaccgccgta < 1:147921/143‑7 (MQ=255)
cACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccaccgccgtg > 1:244588/1‑137 (MQ=255)
aCGGCGACCGCCATCGCCACGAAGAAGCCGATGTTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACCAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCcag < 1:101386/143‑1 (MQ=255)
aCGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCGGTATGTCCgag > 1:45862/1‑143 (MQ=255)
ggCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCcagca > 1:725988/1‑143 (MQ=255)
ggCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCcacaa < 1:422967/143‑4 (MQ=255)
ggCGACCGCCAGCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCcagca < 1:647472/143‑1 (MQ=255)
cGCCATCGCCACGAAGAAGCAGATTGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACg > 2:981814/1‑143 (MQ=255)
cATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCg < 2:696663/143‑1 (MQ=255)
gCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACATGAATACGCGGCACACAAACAGCAATCAAAATGGTGAGTGGCATAAACAGCAGGCTTGCCGATACCA‑‑CCGCCATATAGCACAGCAACAACGGCGGaac > 2:442143/1‑141 (MQ=255)
aCGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCCGCACCTGATTACGCGGCACACAAACAGCAATGCAAATAGTGCGCGGGATAAACATCAGCCTTGCCGACACCACCCCAC‑‑AATGTCCCAGCACCAACGCCgactcacg > 2:822270/1‑136 (MQ=255)
aCGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAGATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCCGCAACGCCGGATCAAg > 1:345464/1‑143 (MQ=255)
aCGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAg < 1:673115/143‑1 (MQ=255)
gCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGGCCCAGCAGCAACGCCGGATCAAGGCCAAGCa > 2:326425/1‑143 (MQ=255)
cGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAgg > 1:1037713/1‑143 (MQ=255)
cGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAgg > 2:402969/1‑143 (MQ=255)
gATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGa > 1:180595/1‑143 (MQ=255)
ggCAAGAGCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATCAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCTGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCt < 1:721156/143‑1 (MQ=255)
gCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTg < 2:710171/143‑1 (MQ=255)
aaGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTACAATGGTGAGTGGGCTAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGCATCAAGGCCAATCAGGAACTCCTGAc > 1:770988/1‑143 (MQ=255)
aTCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGCCCCAGCAGCAACGCCGGAGCAAGGCCACTCAGGAACTCCTTAccgc > 1:50597/1‑143 (MQ=255)
aTCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGACTTGAAGAAACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCCGGccgc > 2:670775/1‑143 (MQ=255)
tCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGAccgcc > 1:971190/1‑143 (MQ=255)
ccAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGTTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGaa > 1:1064990/1‑143 (MQ=255)
ccAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAACTCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCCGGAACTCCTGACCGCCGaa > 2:654950/1‑143 (MQ=255)
cagcaCCGGAGTACCCGGCACACAAACGGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGGATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCt < 2:140767/143‑1 (MQ=255)
gcaCCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAATGCCAATCAGGAACTCCTGACCGCCGAGCTCAGCCTga > 2:1062143/1‑142 (MQ=255)
aCCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTaa > 1:983539/1‑143 (MQ=255)
gttcttccccGGCACGCAAACAGCAATTAAAATGGTGAGTGGGATAAACATCAGGCTTGCCGATACCA‑‑CCGCCGCATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAAc < 1:483565/136‑1 (MQ=255)
cTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGCCTCAGCAGCGACGACGGCTCAAGGCCAATCAGGAACTCCTGACCGCCGCACTTCGCCTCTaaaa > 2:275128/1‑142 (MQ=255)
gATTACCCGGCACCCACACCGCAACGAAAATGGCGAGGGGGATAAAAATCAGGCTGGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGa < 1:1047791/143‑1 (MQ=255)
gATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGCTACCA‑‑CCACCGTATGTCGCGGGTGCAACGCCGGATCCAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGa > 1:514959/1‑143 (MQ=255)
cccGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTAGGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGGACAACGCCCTTTAACGACTACg > 2:663064/1‑143 (MQ=255)
ccGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCGCAGCAGCAACGCCGGATCAAGGCCACTCAGGAACTCCTGACCGCGGAACTTCGCCCGCAAACGACTACgg > 2:633732/1‑142 (MQ=255)
ccGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGa > 1:335682/1‑143 (MQ=255)
cGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAACCGAccaagaa > 1:316762/1‑137 (MQ=255)
acaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTCAACGACTACGAGCCTGCt > 1:741280/1‑143 (MQ=255)
acaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACAGCCGCACTTCGCCTGTAAACGACTACGAGCCTGCt > 1:462137/1‑143 (MQ=255)
caAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCtt < 1:28540/143‑1 (MQ=255)
aaaCGGCGATTAAAATGGTGACTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTa < 2:102364/143‑1 (MQ=255)
aaaCAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGCACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACCAGCCTGCtca > 2:142682/1‑141 (MQ=255)
aaaCAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTa < 1:774143/143‑1 (MQ=255)
aaaCAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTa < 2:971190/143‑1 (MQ=255)
aaaCAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCAGTATGTCCCAGCAGAAACGCCGGATCAAGGCCAACCAGGAACTCCTGACCGCCGAACTTCGCCTGCAAACGACTACGAGCCCGCtca > 2:690738/1‑141 (MQ=255)
aGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTAAGCCCCAACAGCAACGCCGAATCAAGGCCAATCAGGAACTCCTGACCACCCAACCTCGCCTGTAAACGACAAACAGCCTGCTTAGCgc > 2:1005711/1‑142 (MQ=255)
taaTTAAAATGGTCCGTGGGATAACAATCAGGCTTGCCGACACCA‑‑CCGCCGTATGTACCAGCAGCAACGCCGGATCAAGGCCAATCAGCAACTCCTGACCGCCGAAATTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATg < 2:430569/142‑1 (MQ=255)
aGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTCGCGATGGGCGTTACAccacc > 2:438646/1‑141 (MQ=255)
tGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAAccatcca < 2:725988/143‑1 (MQ=255)
gggATAAAAATCAGGCTTGCCGACACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAAccatccat < 1:35089/143‑1 (MQ=255)
ggATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGACCTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCatg > 1:793964/1‑143 (MQ=255)
aTAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAGGAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACGACGAGCCTGCTTAGCGATGGGCGTTAAGCCATCCacgat > 2:17972/1‑143 (MQ=255)
tAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAATGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAATCGACTACGAGCCTGCTTAGCGATGGGCGGTAGAGCCTGCatgatg > 2:893983/1‑143 (MQ=255)
aaaaaTCAGGCTTGCCGATCCCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATgg < 1:64221/143‑1 (MQ=255)
ttGCCGATCCCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCAcc < 1:957876/143‑1 (MQ=255)
ccGATACCA‑‑CCGCCGTACGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGt < 1:402969/143‑1 (MQ=255)
||
CACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGT > NC_000913/2173226‑2173496
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
