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 F3 I0 R1
|
560 |
56.4 |
4650532 |
94.9% |
4413354 |
59.3 |
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%
| 141.0
/ NA
| 42 | pseudogene (647/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (22/20); total (22/20) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
AGACGGGCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑GGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGC > W3110S.gb/3824446‑3824570
|
aGACGGGCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCt < 1:3233304/71‑1 (MQ=255)
aGACGGGCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCt > 1:3354445/1‑71 (MQ=255)
aGACGGGCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCt < 1:2787299/71‑1 (MQ=255)
aGACGGGCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCt < 1:3520068/71‑1 (MQ=255)
aGACGGGCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCt < 1:3725583/71‑1 (MQ=255)
cGGGCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCttgt > 1:2118548/1‑71 (MQ=255)
gcgcATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTgg < 1:2206413/71‑1 (MQ=255)
atcatTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCttgt < 1:1496498/64‑1 (MQ=255)
tcatTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTg > 1:389631/1‑71 (MQ=255)
atTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGc > 1:2463570/1‑71 (MQ=255)
ttGAAGTGCAGGGGACGGCAGACGGCGCGCCGTTCACCCATGAAGAGCTACTCTCCTTGTTGGCGCTGGcc > 1:1612025/1‑71 (MQ=255)
ttGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCttgt < 1:3517696/60‑1 (MQ=255)
ttGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGcc > 1:962690/1‑71 (MQ=255)
gAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGccc < 1:4561512/70‑1 (MQ=255)
gAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGccc > 1:962571/1‑70 (MQ=255)
aaGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCg < 1:1359733/70‑1 (MQ=255)
tGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGcg < 1:1251574/59‑2 (MQ=255)
tGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGa < 1:666498/68‑1 (MQ=255)
tGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑ggg > 1:169494/1‑71 (MQ=255)
aCGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcga < 1:609740/71‑1 (MQ=255)
ggCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaat > 1:1935389/1‑71 (MQ=255)
cAGAAGGCGAGCCGTTCACCAATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaatc > 1:1808500/1‑70 (MQ=255)
aaGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGATGGCCCGAGGGGGAATCGAATCCAt > 1:1088362/1‑70 (MQ=255)
gAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGc < 1:235365/71‑1 (MQ=255)
gAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGc < 1:3731694/71‑1 (MQ=255)
cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTg > 1:1138796/1‑59 (MQ=255)
cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg > 1:1660170/1‑70 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGaa < 1:777572/71‑1 (MQ=255)
cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggc > 1:2850328/1‑71 (MQ=255)
cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggc > 1:2841980/1‑71 (MQ=255)
cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggc < 1:2608057/71‑1 (MQ=255)
tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaatc < 1:86225/48‑1 (MQ=255)
gAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggcg > 1:539004/1‑69 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGc > 1:3362324/1‑55 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggcggc < 1:1986870/70‑1 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGCCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggcggc > 1:659279/1‑70 (MQ=255)
agagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg < 1:3714994/61‑1 (MQ=255)
tgCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg < 1:1028504/58‑1 (MQ=255)
agCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCa > 1:1297176/1‑58 (MQ=255)
agCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCa > 1:1291733/1‑58 (MQ=255)
agCTACTAACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGaa > 1:3995946/1‑61 (MQ=255)
cTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGa > 1:4638611/1‑58 (MQ=255)
|
AGACGGGCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑GGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGC > W3110S.gb/3824446‑3824570
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
