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 F1 I0 R2
|
532 |
47.8 |
3863072 |
94.9% |
3666055 |
61.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,824,533:1 |
+G |
100% |
pseudogene (666/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,533 | 1 | . | G | 94.7%
| 178.0
/ 1.5
| 57 | pseudogene (666/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base . (0/3); new base G (23/31); total (23/34) |
| Fisher's exact test for biased strand distribution p-value = 2.65e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.83e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
AAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCG‑A‑G‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACT > W3110S.gb/3824463‑3824597
|
aaGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑a < 1:842064/71‑1 (MQ=255)
aaGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑a < 1:3172517/71‑1 (MQ=255)
aGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑A‑g < 1:1550367/71‑1 (MQ=255)
aGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑A‑g < 1:877079/71‑1 (MQ=255)
cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑A‑g‑g‑gg > 1:3408409/1‑70 (MQ=255)
cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑A‑g‑g‑gg > 1:2333825/1‑70 (MQ=255)
cAGGGGACGGCAGAAGGCGAACCGTTCACCCACGAAGAGTTACTCACCTTGTTGGCGCTGGCCCG‑A‑g > 1:2178739/1‑67 (MQ=255)
cAGGGGACGGCAGAAGGCGAACCGTTCACCCACGAAGAGTTACTCACCTTGTTGGCGCTGGCCCG‑A‑g > 1:1758876/1‑67 (MQ=255)
aGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑A‑g‑g‑ggga < 1:510270/71‑3 (MQ=255)
aCGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑Ggaatcga < 1:3463240/71‑1 (MQ=255)
aCGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑Ggaatcga < 1:2082046/71‑1 (MQ=255)
aCGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑Ggaatcga < 1:3158464/71‑1 (MQ=255)
gCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑Ggaatcgaatc < 1:2005220/71‑1 (MQ=255)
cAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATcc < 1:3321471/71‑1 (MQ=255)
aGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTg > 1:2754826/1‑71 (MQ=255)
gAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAg < 1:2643313/70‑1 (MQ=255)
aGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCg < 1:3456541/71‑1 (MQ=255)
aGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCg < 1:3634911/71‑1 (MQ=255)
gCCGTTCACCCATGAAGAGCTACTCACATTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGa < 1:1607274/71‑1 (MQ=255)
ccGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGAc < 1:388967/71‑1 (MQ=255)
ttCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑Ggaatcgaatc < 1:1171780/56‑1 (MQ=255)
ttCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑A‑g < 1:662987/43‑1 (MQ=38)
cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGa > 1:1817844/1‑65 (MQ=255)
cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAg < 1:1281680/70‑1 (MQ=255)
cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAg < 1:398828/70‑1 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAg < 1:1725043/69‑1 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGaa < 1:1908664/71‑1 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGaa < 1:2670935/71‑1 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGa < 1:1146178/70‑1 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑A‑G‑GCGGAATCGAATCCATTGTAGCGACGCAGa < 1:3100012/70‑1 (MQ=255)
ccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGaa > 1:66574/1‑69 (MQ=255)
cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑Ggaatcgaa > 1:3761213/1‑48 (MQ=255)
aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAgggc > 1:872260/1‑69 (MQ=255)
aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAggcg > 1:2043925/1‑71 (MQ=255)
tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑A‑g‑g‑ggga < 1:1406776/40‑3 (MQ=37)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGaa > 1:896045/1‑64 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGaa > 1:1317158/1‑64 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGaa > 1:3399611/1‑64 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGaa > 1:3490247/1‑64 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGaa > 1:3548122/1‑64 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGgcggcg > 1:2730550/1‑71 (MQ=255)
cTACTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTgg > 1:3361413/1‑70 (MQ=255)
cTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCa < 1:682923/40‑1 (MQ=25)
cTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTg < 1:68162/43‑1 (MQ=25)
cTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTg < 1:1821237/43‑1 (MQ=25)
cTCACCTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTg < 1:78031/43‑1 (MQ=25)
tCACCTTGTTGGCGCTGGCCCGAA‑G‑G‑GGAATCGAATCCATTGt < 1:1408013/43‑1 (MQ=25)
accTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGgcgc > 1:1826232/3‑61 (MQ=255)
accTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTgg > 1:989526/3‑64 (MQ=255)
accTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTgg > 1:2646424/3‑64 (MQ=255)
accTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt > 1:2518020/3‑70 (MQ=255)
accTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt > 1:1153426/3‑70 (MQ=255)
accTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt > 1:3221753/3‑70 (MQ=255)
cTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGc < 1:3347901/42‑1 (MQ=37)
cTTGTTGGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGc < 1:7739/42‑1 (MQ=37)
ttgttgGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt > 1:3632924/1‑71 (MQ=255)
ttgttgGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt > 1:717324/1‑71 (MQ=255)
ttgttgGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt > 1:1641703/1‑71 (MQ=255)
ttgGCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGc < 1:84170/38‑1 (MQ=37)
ggCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt > 1:1526648/1‑66 (MQ=255)
ggCGCTGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTa < 1:2938920/70‑1 (MQ=255)
ggCGCTGGCCCG‑A‑GTG‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTa < 1:3075069/70‑1 (MQ=255)
gcgctGGCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTa < 1:569/66‑1 (MQ=255)
gCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACt < 1:450894/71‑1 (MQ=255)
gCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACt < 1:2070924/71‑1 (MQ=255)
gCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACt < 1:1908807/71‑1 (MQ=255)
gCCCG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACt < 1:1677434/71‑1 (MQ=255)
cccG‑AGG‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACt < 1:34546/70‑1 (MQ=255)
|
AAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCG‑A‑G‑G‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACT > W3110S.gb/3824463‑3824597
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
