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 |
|
A5 F8 I0 R1
|
43 |
62.4 |
4721813 |
98.4% |
4646263 |
62.0 |
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 | 97.9%
| 165.2
/ ‑3.4
| 47 | pseudogene (666/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base G (16/30); total (17/30) |
| Fisher's exact test for biased strand distribution p-value = 3.62e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| 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. |
CAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑GGGG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCG > W3110S.gb/3824468‑3824594
|
cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggg < 1:2243050/70‑1 (MQ=255)
aGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑ggggga < 1:325776/71‑3 (MQ=255)
gACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGg‑aatcg < 1:2437694/71‑1 (MQ=255)
gCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGACCCGAGGGGg‑aatcgaatc < 1:4499115/71‑1 (MQ=255)
cAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGg‑aatcgaatc > 1:2640708/1‑70 (MQ=255)
aGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCa > 1:1454572/1‑71 (MQ=255)
aGAAGGCGAGCAGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCa > 1:3339346/1‑71 (MQ=255)
aGAAGGCGAGCAGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCa > 1:3344862/1‑71 (MQ=255)
aaGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCTAATCCAtt > 1:1623665/1‑71 (MQ=255)
aGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTg < 1:2896200/71‑1 (MQ=255)
aGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCg < 1:833556/71‑1 (MQ=255)
gCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGa > 1:2021230/1‑71 (MQ=255)
ttCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGt < 1:3903044/62‑1 (MQ=255)
ttCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGc < 1:3579384/65‑1 (MQ=255)
ttCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑ggggga < 1:2668799/48‑3 (MQ=255)
tCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACg > 1:1014895/1‑68 (MQ=255)
cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAg < 1:3662907/70‑1 (MQ=255)
cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAg > 1:2363465/1‑70 (MQ=255)
cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAg < 1:1253262/70‑1 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGaa < 1:1395267/71‑1 (MQ=255)
cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGAAggc > 1:3968211/1‑71 (MQ=255)
tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCa > 1:4114454/1‑50 (MQ=255)
tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCa > 1:712740/1‑50 (MQ=255)
tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTg < 1:3738464/53‑1 (MQ=255)
tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGc < 1:382667/57‑1 (MQ=255)
tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGAAggc < 1:1861839/69‑1 (MQ=255)
gAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGg‑aatcgaat < 1:2683285/46‑1 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCATAAGgcggcg > 1:3084796/1‑71 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGAAggcggc < 1:1469392/70‑1 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGAAggcggc < 1:3730553/70‑1 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGAAggcg < 1:4199753/68‑1 (MQ=255)
agagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGgcgc < 1:1183897/71‑1 (MQ=255)
agagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGgcgc < 1:2303595/71‑1 (MQ=255)
gagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCt < 1:1566880/71‑1 (MQ=255)
aCTCACCTTGTTGGCGCTGGCCCGA‑GGGGTAATCGAATCCATTGTAGCGACg > 1:3708060/1‑52 (MQ=255)
cTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCa < 1:1455440/69‑1 (MQ=255)
cTCACCTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCa < 1:642195/69‑1 (MQ=255)
cTTGTTGGCGCTGGCCCGAGGGGG‑AATCGAATCCATTg < 1:2291068/38‑1 (MQ=25)
tgttgGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAttt > 1:2357567/1‑71 (MQ=255)
tgttgGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt > 1:1521075/1‑70 (MQ=255)
tgttgGCGCTGGCCCGAGGGGG‑AATCGAATCCATT‑TAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt > 1:2991052/1‑69 (MQ=255)
gttgGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGa > 1:2467183/1‑47 (MQ=255)
ttgGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAACCTGAttttt < 1:1262096/71‑1 (MQ=255)
ttgGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAttttt < 1:3770800/71‑1 (MQ=255)
ttgGCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAttttt < 1:3787248/71‑1 (MQ=255)
ggCGCTGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTa < 1:118110/70‑1 (MQ=255)
gctGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGc < 1:356837/70‑1 (MQ=255)
ctGGCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCg < 1:1073137/71‑1 (MQ=255)
ggCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAg < 1:2113545/37‑1 (MQ=38)
ggCCCGAGGGGG‑AATCGAATCCATTGTAGCGACGCAg < 1:3725278/37‑1 (MQ=38)
|
CAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑GGGG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCG > W3110S.gb/3824468‑3824594
|
| 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
