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 F28 I2 R2
|
356 |
55.1 |
4139924 |
95.4% |
3949487 |
63.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,824,326 |
T→C |
pseudogene (459/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,326 | 0 | T | C | 98.6%
| 252.9
/ ‑5.1
| 70 | pseudogene (459/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (43/26); minor base A (1/0); total (44/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.51e-01 |
TGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCT > W3110S.gb/3824271‑3824391
|
tGGCGCTGTCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAAccc < 1:3261315/58‑1 (MQ=255)
gctcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa < 1:3046114/60‑1 (MQ=255)
gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGa > 1:3617346/1‑58 (MQ=255)
gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGa > 1:3167706/1‑58 (MQ=255)
gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGa > 1:1249454/1‑58 (MQ=255)
gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGa > 1:1096631/1‑58 (MQ=255)
gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa < 1:938408/63‑1 (MQ=255)
gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa < 1:2920025/63‑1 (MQ=255)
gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa < 1:3429957/63‑1 (MQ=255)
cTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGc < 1:2835262/71‑1 (MQ=255)
cTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGc < 1:1427225/71‑1 (MQ=255)
cTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGc < 1:1963341/71‑1 (MQ=255)
gcaGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAggg < 1:2688061/58‑1 (MQ=255)
gcaGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCg > 1:568024/3‑70 (MQ=255)
gcaGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCg > 1:4081166/3‑70 (MQ=255)
gcaGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCg > 1:3934917/3‑70 (MQ=255)
gcaGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCg > 1:364779/3‑70 (MQ=255)
gcaGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAA‑GGATGGTAGCCg > 1:1374254/3‑69 (MQ=255)
tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGATAGGGATGGTAGCCGCAGtt > 1:3271234/1‑70 (MQ=255)
tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGttt > 1:119641/1‑71 (MQ=255)
tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGttt > 1:2042008/1‑71 (MQ=255)
tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGttt > 1:4109726/1‑71 (MQ=255)
tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGtt > 1:482927/1‑70 (MQ=255)
cTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCACCCCGATGAAAGGGAAGGTAGCCGCAGTTTCTGt > 1:3173204/1‑71 (MQ=255)
cTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTg > 1:2279355/1‑70 (MQ=255)
cTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGt > 1:3428504/1‑71 (MQ=255)
cTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGt > 1:265506/1‑71 (MQ=255)
cTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGt > 1:3199845/1‑71 (MQ=255)
cTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGt > 1:433810/1‑71 (MQ=255)
cTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGt > 1:68842/1‑71 (MQ=255)
cTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAAACCGATGAAAGGGATGGTAGCCGCAGTTTCTGt > 1:1268436/1‑71 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCTCAGTTTCTg > 1:4115704/1‑67 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTg > 1:3223286/1‑67 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTg > 1:1001066/1‑67 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg < 1:3029107/71‑1 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg < 1:3241307/71‑1 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg < 1:796435/71‑1 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg < 1:2655133/71‑1 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg < 1:2484194/71‑1 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg < 1:2335770/71‑1 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg < 1:2010573/71‑1 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg < 1:1387823/71‑1 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg < 1:173020/71‑1 (MQ=255)
cTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt > 1:1010909/1‑68 (MQ=255)
cTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt > 1:1072125/1‑68 (MQ=255)
cTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt > 1:686191/1‑68 (MQ=255)
cTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt > 1:1188960/1‑68 (MQ=255)
cTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt > 1:1254352/1‑68 (MQ=255)
cTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt > 1:1379343/1‑68 (MQ=255)
cTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt > 1:2033662/1‑68 (MQ=255)
cTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt > 1:1407065/1‑68 (MQ=255)
aaCGGCAAGCTGAAAACCAACCCGATGAATGGGATGGTAGc < 1:1629328/41‑1 (MQ=38)
aCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt < 1:3769150/58‑1 (MQ=255)
aCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt < 1:110838/58‑1 (MQ=255)
aCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt < 1:1700588/58‑1 (MQ=255)
aCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCC‑CAGTTTCTGTCGGTAt < 1:1965917/57‑1 (MQ=255)
ggCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAg > 1:2052457/1‑37 (MQ=255)
ggCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTc > 1:694486/1‑47 (MQ=255)
ggCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtg > 1:3136947/1‑58 (MQ=255)
ggCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtg > 1:60841/1‑58 (MQ=255)
ggCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtg > 1:2842378/1‑58 (MQ=255)
ggCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtg > 1:546438/1‑58 (MQ=255)
aGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTTTCgg < 1:4087627/49‑1 (MQ=39)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc < 1:3145416/69‑1 (MQ=255)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg < 1:1529465/70‑1 (MQ=255)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg < 1:3906090/70‑1 (MQ=255)
aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCTGTATTGTAAACGGTGAAGCAATTTGCGATCt > 1:4001186/1‑71 (MQ=255)
aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTaaa > 1:2981635/1‑50 (MQ=255)
aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc > 1:569867/1‑70 (MQ=255)
aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCt > 1:3045409/1‑71 (MQ=255)
aCCAACCCGATGAAAGGGATGGTAGCCGAAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCt > 1:3262449/1‑71 (MQ=255)
|
TGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCT > W3110S.gb/3824271‑3824391
|
| 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
