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 F21 I0 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,504,714 |
G→A |
100% |
F711F (TTC→TTT) |
metL ← |
fused aspartokinase II and homoserine dehydrogenase II |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,504,714 | 0 | G | A | 97.2%
| 98.0
/ ‑3.8
| 36 | F711F (TTC→TTT) | metL | fused aspartokinase II and homoserine dehydrogenase II |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (14/21); total (14/22) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.25e-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 base substitution creates a homopolymer stretch. |
GCCCCATTTCGCGGGCCGCTTCCAGCCGTTGCACCATCTGCTCGTTCAGTTCATCGCCATTTTCAAAGAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGATTCCACACGTACCTGATCCGGT > W3110S.gb/3504647‑3504780
|
gCCCCATTTCGCGGGCCGCTTCGAGCCGTTGCACCATCTGCTCGTTCAGTTCATCGCCATTTTCAaaaaaa > 1:203946/1‑71 (MQ=255)
cgaTTTCGCGGGCGGCTTCGAGCCGTTGCTCCATCTGCTCGTTCAGTTCTTCGCCATTTTCAAAAAAATgg < 1:348437/69‑1 (MQ=255)
ccATTTCGCGGGCCGCTTCCAGCCGTTGCACCATCTGCTCGTTCAGTTCATCGCCATTTTCAAAAAAATgg > 1:2223440/1‑71 (MQ=255)
ccATTTCGCGGGCCGCTTCCAGCCGTTGCACCATCTGCTCGTTCAGTTCATCGCCATTTTCAAAAAAATgg < 1:363898/71‑1 (MQ=255)
aTTTCGCGGGCCGCTTCCAGCCGTTGCACCATCTGCTCGTTCAGTTCATCGCCATTTTCAAAAAAATGGTc < 1:1250857/71‑1 (MQ=255)
tttCGCGGGCCGCTTCCAGCCGTTGCACCATCTGCTCGTTCAGTTCATCGCCATTTTCAAAg < 1:189141/62‑1 (MQ=255)
cgGGCCGCTTCCAGCCGTTGCACCATCTGCTCGTTCAGTTCATCGCCATTTTCAAAGAAATGGTCGAtgct < 1:1292635/71‑1 (MQ=255)
ccGCTTCCAGCCGTTGCACCATCTGCTCGTTCAGTTCATCGCCATTTTCAaaaaaa > 1:1002767/1‑56 (MQ=255)
cGCTTCCAGCCGTTGCACCATCTGCTCGTTCAGTTCATCGCCATTTTCAAAAAAATGGTCGATGCTgccg < 1:2650082/70‑1 (MQ=255)
gCACCATCTGCTCGTTCAGTTCATCGCCATTTTCAAAAAAATGGTCGa > 1:2637328/1‑48 (MQ=255)
gCACCATCTGCTCGTTCAGTTCATCGCCATTTTCAAAAAAATGGTCGa > 1:318720/1‑48 (MQ=255)
aTCTGCTCGTTCAGTTCATCGCCATTTTCAAAAAAATGGTCGATGCTGCCGCCTTCGCa < 1:1276839/59‑1 (MQ=255)
tCTGCTCGTTCAGTTCATCGCCATTTTCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCAc > 1:601918/1‑70 (MQ=255)
tCTGCTCGTTCAGTTCATCGCCATTTTCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCAc > 1:1818237/1‑70 (MQ=255)
tGCTCGTTCAGTTCATCGCCATTTTCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAg > 1:2238793/1‑71 (MQ=255)
gCTCGTTCAGTTCATCGCCATTTTCAAAAAAATGGTc < 1:1672415/37‑1 (MQ=255)
cTCGTTCAGTTCATCGCCATTTTCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGc < 1:1472457/70‑1 (MQ=255)
gttcagttcaTCGCCATTTTCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGa < 1:2434704/69‑1 (MQ=255)
gttcagttcaTCGCCATTTTCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGa < 1:270647/69‑1 (MQ=255)
gttcagttcaTCGCCATTTTCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGAt < 1:1842027/70‑1 (MQ=255)
ttcaTCGCCATTTTCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGATTCcac < 1:2533912/69‑1 (MQ=255)
caTCGCCATTTTCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGATTCCACACg > 1:604699/1‑70 (MQ=255)
caTCGCCATTTTCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGATTCCACACg < 1:1418742/70‑1 (MQ=255)
caTCGCCATTTTCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGATTCCACACg < 1:1637133/70‑1 (MQ=255)
caTCGCCATTTTCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAACAGGCACCAGCGATTCCACACg < 1:1220681/70‑1 (MQ=255)
aTCGCCATTTTCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGATTCCACACGt < 1:2758764/70‑1 (MQ=255)
gCCATTTTCAAAAAAATGGTCGATGCTGCCGCCTTCGCaa > 1:2342568/1‑40 (MQ=255)
ccATTTTCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGATTCCACACGt < 1:2075931/66‑1 (MQ=255)
cATTTTCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGATTCCACACGTACCTGa < 1:301074/71‑1 (MQ=255)
ttttCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGATTCca < 1:1774591/58‑1 (MQ=255)
ttttCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGATTCCACACGTACCTGATc < 1:1618962/71‑1 (MQ=255)
ttCAAAAAAATGGTCGGTGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGATTCCACACGTa > 1:621488/1‑62 (MQ=255)
ttCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAg > 1:31598/1‑48 (MQ=255)
ttCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGATTCcaca > 1:582766/1‑58 (MQ=255)
ttCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGATTCCACACGTACCTGATcc < 1:1228190/70‑1 (MQ=255)
ttCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGATTCCACACGTACCTGATCCg > 1:2480319/1‑71 (MQ=255)
ttCAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGATTCCACACGTACCTGATCCg > 1:2412560/1‑71 (MQ=255)
cAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGATTCCACACGTACCTGATCCgg < 1:1469938/70‑1 (MQ=255)
cAAAAAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGATTCCACACGTACCTGATCCGGt > 1:849796/1‑71 (MQ=255)
|
GCCCCATTTCGCGGGCCGCTTCCAGCCGTTGCACCATCTGCTCGTTCAGTTCATCGCCATTTTCAAAGAAATGGTCGATGCTGCCGCCTTCGCAATGAGCAGGCACCAGCGATTCCACACGTACCTGATCCGGT > W3110S.gb/3504647‑3504780
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
