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 |
3,824,514 |
T→C |
100% |
pseudogene (647/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,514 | 0 | T | C | 100.0%
| 200.2
/ NA
| 61 | pseudogene (647/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (23/38); total (23/38) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCG‑A‑GG‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGG > W3110S.gb/3824453‑3824575
|
cgcATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGc < 1:1954548/71‑1 (MQ=255)
atTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGc > 1:2301723/1‑71 (MQ=255)
atTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGc > 1:1605555/1‑71 (MQ=255)
atTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGc > 1:618907/1‑71 (MQ=255)
atTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGc > 1:2721941/1‑71 (MQ=255)
gAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGccc > 1:361540/1‑70 (MQ=255)
aaGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCg < 1:1889923/70‑1 (MQ=255)
aaGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑a < 1:3172517/71‑1 (MQ=255)
aaGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑a < 1:842064/71‑1 (MQ=255)
aGTGCAGGGGACGTCAGAAGGCGAGGCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCg < 1:2000017/69‑1 (MQ=255)
aGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑A‑g < 1:877079/71‑1 (MQ=255)
aGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑A‑g < 1:1550367/71‑1 (MQ=255)
cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑A‑gg‑gg > 1:2333825/1‑70 (MQ=255)
cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑A‑gg‑gg > 1:3408409/1‑70 (MQ=255)
cAGGGGACGGCAGAAGGCGAACCGTTCACCCACGAAGAGTTACTCACCTTGTTGGCGCTGGCCCG‑A‑g > 1:1758876/1‑67 (MQ=255)
cAGGGGACGGCAGAAGGCGAACCGTTCACCCACGAAGAGTTACTCACCTTGTTGGCGCTGGCCCG‑A‑g > 1:2178739/1‑67 (MQ=255)
aGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑A‑gg‑ggga < 1:510270/71‑3 (MQ=255)
aCGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑Ggaatcga < 1:2082046/71‑1 (MQ=255)
aCGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑Ggaatcga < 1:3158464/71‑1 (MQ=255)
aCGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑Ggaatcga < 1:3463240/71‑1 (MQ=255)
ggCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGc < 1:1705803/48‑1 (MQ=255)
ggCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGc < 1:2883033/48‑1 (MQ=255)
gCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑Ggaatcgaatc < 1:2005220/71‑1 (MQ=255)
cAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATcc < 1:3321471/71‑1 (MQ=255)
aGGCGAGCCGTTCACCCATGAAGAGCTACTCACCttgttg > 1:2557118/1‑40 (MQ=255)
aGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTg > 1:2754826/1‑71 (MQ=255)
gCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGc < 1:1931384/40‑1 (MQ=255)
gAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAg < 1:2643313/70‑1 (MQ=255)
aGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCg < 1:3456541/71‑1 (MQ=255)
aGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCg < 1:3634911/71‑1 (MQ=255)
gCCGTTCACCCATGAAGAGCTACTCACATTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCGa < 1:1607274/71‑1 (MQ=255)
ccGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCGAc < 1:388967/71‑1 (MQ=255)
ttCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGc < 1:1838773/38‑1 (MQ=38)
ttCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGc < 1:3059116/38‑1 (MQ=38)
ttCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑Ggaatcgaatc < 1:1171780/56‑1 (MQ=255)
ttCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑A‑g < 1:662987/43‑1 (MQ=38)
cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCGa > 1:1817844/1‑65 (MQ=255)
cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCGACGCAg < 1:1281680/70‑1 (MQ=255)
cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCGACGCAg < 1:398828/70‑1 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCGACGCAg < 1:1725043/69‑1 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCGACGCAGaa < 1:2670935/71‑1 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCGACGCAGaa < 1:1908664/71‑1 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCGACGCAGa < 1:1146178/70‑1 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑A‑GGCGGAATCGAATCCATTGTAGCGACGCAGa < 1:3100012/70‑1 (MQ=255)
ccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCGACGCAGaa > 1:66574/1‑69 (MQ=255)
cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑Ggaatcgaa > 1:3761213/1‑48 (MQ=255)
aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCGACGCAGAAgggc > 1:872260/1‑69 (MQ=255)
aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCGACGCAGAAggcg > 1:2043925/1‑71 (MQ=255)
tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCG‑A‑gg‑ggga < 1:1406776/40‑3 (MQ=37)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCGACGCAGaa > 1:896045/1‑64 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCGACGCAGaa > 1:3548122/1‑64 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCGACGCAGaa > 1:3490247/1‑64 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCGACGCAGaa > 1:3399611/1‑64 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCGACGCAGaa > 1:1317158/1‑64 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCGACGCAGAAGgcggcg > 1:2730550/1‑71 (MQ=255)
cTACTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTgg > 1:3361413/1‑70 (MQ=255)
cTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCa < 1:682923/40‑1 (MQ=25)
cTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTg < 1:68162/43‑1 (MQ=25)
cTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTg < 1:78031/43‑1 (MQ=25)
cTCACCTTGTTGGCGCTGGCCCG‑AGGG‑GGAATCGAATCCATTg < 1:1821237/43‑1 (MQ=25)
tCACCTTGTTGGCGCTGGCCCGAA‑GG‑GGAATCGAATCCATTGt < 1:1408013/43‑1 (MQ=25)
|
CGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCG‑A‑GG‑GGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGG > W3110S.gb/3824453‑3824575
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
