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 |
|
A17 F70 I0 R1
|
565 |
64.8 |
2371218 |
98.3% |
2330907 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
2,172,350 |
A→T |
10.0% |
L175Q (CTG→CAG) |
gatD ← |
galactitol‑1‑phosphate dehydrogenase, Zn‑dependent and NAD(P)‑binding |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,172,350 | 0 | A | T | 10.0%
| 157.6
/ 9.2
| 50 | L175Q (CTG→CAG) | gatD | galactitol‑1‑phosphate dehydrogenase, Zn‑dependent and NAD(P)‑binding |
| Reads supporting (aligned to +/- strand): ref base A (21/24); new base T (2/3); total (23/27) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.84e-01 |
TGCATTTGCGGCGCGCTCATTTCGCTACTGTTAAATGTTTGCATCGCACCGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGCTCAATAAAAGCCCCATCCTCAATAGGCATATCCGTGGGTAGAGCAAAGA > NC_000913/2172212‑2172491
|
tGCATTTGCGGCGCGCTCATTTCGCTACTGTTAAATGTTTGCATCGCACCGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAAt > 3:264212/1‑149 (MQ=255)
gCATTTGCGGCGCGCTCATTTCGCTACTGTTAAATGTTTGCATCGCACCGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATg < 4:264212/149‑1 (MQ=255)
cATTTGCGGCGCGCTCATTTCGCTACTGTTAAATGTTTGCATCGCACCGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACGCTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCTGCTGGCCattca < 2:595801/149‑5 (MQ=255)
tttGCGGCGCGCTCATTTCGCTACTGTTAAATGTTTGCATCGCACCGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCTGCTGGCCattcagt < 2:140252/149‑7 (MQ=255)
tGCGGCGCGCTCATTTCGCTACTGTTAAATGTTTGCATCGCACCGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTcc < 1:202759/149‑1 (MQ=255)
gcgcTCATTTCGCTACTGTTAAATGTTTGGATCGCACCGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCAcc > 3:349541/1‑149 (MQ=255)
gcTCATTTCGCTACTGTTAAATGTTTGCATCGCACCGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCaa < 4:128192/149‑1 (MQ=255)
tCATTTCGCTACTGTTAAATGTTTGCATCGCACCGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCTGCTGGCCattcagt > 1:289305/1‑131 (MQ=255)
tCATTTCGCTACTGTTAAATGTTTGCATCGCACCGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCTGCTGGCCattcagt < 2:289305/137‑7 (MQ=255)
aTTTCGCTACTGTTAAATGTTTGCATCGCACCGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCaataat < 2:305669/149‑1 (MQ=255)
cTACTGTTAAATGTTTGCATCGCACCGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAAc < 4:113417/149‑1 (MQ=255)
ttAAATGTTTGCATCGCACCGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCaataat > 4:569571/1‑137 (MQ=255)
ttAAATGTTTGCATCGCACCGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCaataat < 3:569571/137‑1 (MQ=255)
tAAATGTTTGCATCGCACCGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTa > 4:58369/1‑149 (MQ=255)
gTTTGCATCGCACCGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATtctc > 4:210943/1‑149 (MQ=255)
aTCGCACCGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAAcc < 1:219340/149‑1 (MQ=255)
aCCGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTgcg > 1:10936/1‑149 (MQ=255)
cGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCt > 4:513917/1‑149 (MQ=255)
ttttGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGaa > 1:524620/1‑149 (MQ=255)
ttttGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGaa < 4:322859/149‑1 (MQ=255)
tttGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGaaa < 3:472828/149‑1 (MQ=255)
ttGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGaaaa < 4:246509/149‑1 (MQ=255)
tgccagtgccagTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAg < 1:361223/149‑1 (MQ=255)
gccagtgccagtTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGc < 3:367137/149‑1 (MQ=255)
ccagtgccagtTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCa < 2:442838/149‑1 (MQ=255)
ccagtTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGa > 4:242505/1‑149 (MQ=255)
cagtTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGAc > 3:170751/1‑149 (MQ=255)
tAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGc > 4:242462/1‑149 (MQ=255)
aTGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGCTc > 1:502169/1‑149 (MQ=255)
tGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCGGACCAACGGTAATCGGCTCa > 3:85568/1‑149 (MQ=255)
gATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGCTCAATaa > 3:24629/1‑149 (MQ=255)
tCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGCTCAATaaaa < 4:170751/149‑1 (MQ=255)
tCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGCTCAATAAAAGCCCCa > 2:266735/1‑149 (MQ=255)
acacTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGCTCAATAAAAGCCCCATc < 2:10936/149‑1 (MQ=255)
acTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGCTCAATAAAAGCCCCATCCt > 1:268203/1‑149 (MQ=255)
ctctTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGCTCAATAAAAGCCCCATCCTc > 1:327625/1‑149 (MQ=255)
ttGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAAAAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGCTCAATAAAAGCCCCATCCTCAATa < 1:479118/149‑1 (MQ=255)
tGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGCTCAATAAAAGCCCCATCCTCAATAg < 3:210943/149‑1 (MQ=255)
tCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGttt > 1:123783/1‑67 (MQ=255)
tCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGttt < 2:123783/67‑1 (MQ=255)
ccAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTAt > 1:43749/1‑69 (MQ=255)
ccAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTAt < 2:43749/69‑1 (MQ=255)
ccAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGCTCAATAAAAGCCCCATCCTCAATAGGCata > 1:325767/1‑149 (MQ=255)
aGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGCTCAATAAAAGCCCCATCCTCAATAGGCATATc < 4:24629/149‑1 (MQ=255)
cgcgACAGCGCACTGATTGGCCAGCAGGCCAATGGTTCCGGCACCAGTAATAATATCGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGCTCAATAAAAGCCCCATCCTCAATAGGCATATCCg < 4:349541/149‑1 (MQ=255)
gACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGCTCAATAAAAGCCCCATCCTCAATAGGCATATCCGTgg < 3:242462/149‑1 (MQ=255)
gACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGCTCAATAAAAGCCCCATCCTCAATAGGCATATCCGTgg < 2:502169/149‑1 (MQ=255)
aCTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGCTCAATAAAAGCCCCATCCTCAATAGGCATATCCGTGGGTAGAGCa > 4:295953/1‑149 (MQ=255)
cTGAATGGCAAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGATCAATAAAAGCCCCATCCTCAATAGGCATATCCGTGGGTAGAGCaa < 2:521516/149‑1 (MQ=255)
attGGCCTGCTGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGCTCAATAAAAGCCCCATCCTCAATAGGCATATCCGTGGGTAGAGCAAAGa > 1:160969/3‑149 (MQ=255)
|
TGCATTTGCGGCGCGCTCATTTCGCTACTGTTAAATGTTTGCATCGCACCGAAAGATTTTGCCAGTGCCAGTTTTTCTGAACTAATGTCGATCGCCGTCACACTCTTTGCTCCCAGCGCGACAGCGCACTGAATGGCCAGCAGGCCAATGGTTCCGGCACCAATAATAATAACGTTTTTATTCTCACAACCTTGCGCTAAATGAAAAGCATGCAGACCAACGGTAATCGGCTCAATAAAAGCCCCATCCTCAATAGGCATATCCGTGGGTAGAGCAAAGA > NC_000913/2172212‑2172491
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
