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 |
250,268 |
C→T |
24.2% |
pseudogene (197/756 nt) |
mbhA → |
ECK0231:JW5812:b0230; flagellar system protein, promoterless fragment |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 250,268 | 0 | C | T | 24.2%
| 92.4
/ 27.6
| 50 | pseudogene (197/756 nt) | mbhA | ECK0231:JW5812:b0230; flagellar system protein, promoterless fragment |
| Reads supporting (aligned to +/- strand): ref base C (23/14); new base T (6/6); total (29/21) |
| Fisher's exact test for biased strand distribution p-value = 5.12e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGATGCGCATATGGAAGCG > W3110S.gb/250200‑250332
|
gCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGTCa > 1:2806955/1‑71 (MQ=255)
gCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGTCa > 1:3490486/1‑71 (MQ=255)
ggAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCAcc > 1:4517727/1‑70 (MQ=255)
gAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGa < 1:2555522/71‑1 (MQ=255)
ggAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGTCACCGAGCTTGGTg < 1:399161/71‑1 (MQ=255)
gaAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGc < 1:1744230/71‑1 (MQ=255)
aaaaaaGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGTCACCGAg < 1:4336495/60‑1 (MQ=255)
aaaaaaGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCt > 1:1914896/1‑71 (MQ=255)
aaaaGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTgg > 1:818300/1‑71 (MQ=255)
aaaaGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTgg > 1:4305716/1‑71 (MQ=255)
aGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCaa > 1:3065383/1‑71 (MQ=255)
aTGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATc < 1:3405449/71‑1 (MQ=255)
tgAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCaa > 1:4129848/1‑70 (MQ=255)
aaTGAGAAAACGGCGCTGCTGAAGAAGAAATCCGTCACCGAGCTTGGTGAGCTGGCAACCAGTATCAacac > 1:1261823/1‑71 (MQ=255)
aaTGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGt > 1:1438888/1‑48 (MQ=255)
aaTGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAacac > 1:1605844/1‑71 (MQ=255)
aTGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAacac < 1:3835013/70‑1 (MQ=255)
aTGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAacac < 1:3648304/70‑1 (MQ=255)
tGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCaa < 1:1418808/66‑1 (MQ=255)
agaAAACGGCGCTGCTGAAGAAGAAATCCGTCACCGAGCTTGGTGAGCTGGCAACCAGTATCAacac > 1:1164072/1‑67 (MQ=255)
aaaaCGGCGCTGCTGAAGAAGAAATCCGTCACCGAGCTTGGt < 1:2959478/42‑1 (MQ=255)
aaaaCGGCGCTGCTGAAGAAGAAATCCGTCACCGAGCTTGGTGAGCTGGCAACCAGTATCAacac < 1:1156971/65‑1 (MQ=255)
aaaCGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCt < 1:1959218/46‑1 (MQ=255)
aaCGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGt > 1:559036/1‑55 (MQ=255)
aaCGGAGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGa > 1:1971943/1‑42 (MQ=255)
aCGGCGCTGCTGAAGAAGAAATCCGTCACCGAGCTTGGTGAGCTGGCAACCAGTATCaa < 1:3599501/59‑1 (MQ=255)
cGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGt < 1:543049/71‑1 (MQ=255)
cGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGt < 1:4107854/71‑1 (MQ=255)
ggCGCTGCTGAAGAAGAAATCCGTCACCGAGCTTGGTGAGCTGGCAACCAGTATCAaca > 1:382047/1‑59 (MQ=255)
ctgctgAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAg < 1:753834/47‑1 (MQ=255)
gctgAAGAAGAAATCCGTCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGa > 1:1766226/1‑66 (MQ=255)
ctgAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTTGCAACCAGTATCAACACCATTGCCCGTGATGCGCa < 1:3916888/71‑1 (MQ=255)
ctgAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCaa > 1:4146741/1‑50 (MQ=255)
ctgAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGATGCGCa > 1:4617071/1‑71 (MQ=255)
ctgAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGATGCGCa < 1:1863459/71‑1 (MQ=255)
tgAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGt < 1:3939337/62‑1 (MQ=255)
gaagaagaaATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAaca > 1:2118744/1‑50 (MQ=255)
gaagaagaaATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAaca > 1:3383765/1‑50 (MQ=255)
gaagaagaaATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAaca > 1:2911939/1‑50 (MQ=255)
aagaagaaATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCaa > 1:2358312/1‑47 (MQ=255)
aagaagaaATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGATGCGCata < 1:3702864/70‑1 (MQ=255)
agaagaaATCCGTCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGATGCGCat < 1:894561/68‑1 (MQ=255)
agaagaaATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGATg > 1:1905795/1‑63 (MQ=255)
agaagaaATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGATGCGCATATg > 1:209504/1‑71 (MQ=255)
agaagaaATCCG‑CACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGATGCGCATATgg < 1:1145476/71‑1 (MQ=255)
aTCCGCCACCGAGCTTGGTGAGCTTGCAACCAGTATCAACACCATTGCCCGTGATGCGCATATGGAAGCg > 1:2577498/1‑70 (MQ=255)
aTCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGATGCGCATATGGAAGCg > 1:2668433/1‑70 (MQ=255)
ccGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGa > 1:543192/1‑52 (MQ=255)
ccGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGa > 1:766223/1‑52 (MQ=255)
cGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGATGCGCatat > 1:70720/1‑60 (MQ=255)
|
GCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGATGCGCATATGGAAGCG > W3110S.gb/250200‑250332
|
| 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
