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 |
|
A3 F2 I1 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
Exported |
222,997 |
T→A |
47.8% |
intergenic (+52/‑128) |
lpcA → / → prfH |
D‑sedoheptulose 7‑phosphate isomerase/predicted peptide chain release factor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | Exported | 222,997 | 0 | T | A | 47.8%
| 50.7
/ 91.3
| 71 | intergenic (+52/‑128) | lpcA/prfH | D‑sedoheptulose 7‑phosphate isomerase/predicted peptide chain release factor |
| Reads supporting (aligned to +/- strand): ref base T (18/11); new base A (15/16); total (39/32) |
| Fisher's exact test for biased strand distribution p-value = 3.12e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AAAAGAGATGGTTAAGTAAGTCTGGCGTAGGCCGGATAAGACGTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGAATAAT > Exported/222927‑223067
|
aaaaGAGATGGTTAAGTAAGTCTGGCGTAGGCCGGATAAGACGTTTACGCCGCATCCGGCATTTGTGCGct < 1:3333644/71‑1 (MQ=255)
aaaaGAGATGGTTAAGTAAGTCTGGCGTAGGCCGGATAAGACGTTTACGCCGCATCCGGCATTTGTGCGct < 1:1090087/71‑1 (MQ=255)
aaaaGAGATGGTTAAGTAAGTCTGGCGTAGGCCGGATAAGACGTTTACGCCGCATCCGGCATTTGTGCGct > 1:155804/1‑71 (MQ=255)
aaaGAGATGGTTAAGTAAGTCTGGCGTAGGCCGGATAAGACGTTTACGCCGCATCCGGCATTTGTGCGctg < 1:764669/71‑1 (MQ=255)
agagATGGTTAAGTAAGTCTGGCGTAGGCCGGATAAGACGTTTACGCCGCATCCGGCATTTGTGCGctgat > 1:1296964/1‑71 (MQ=255)
agagATGGTTAAGTAAGTCTGGCGTAGGCCGGATAAGACGTTTACGCCGCATCCGGCATTTGTGCGctgat > 1:3852053/1‑71 (MQ=255)
tGGTTAAGTAAGTCTGGCGTAGGCCGGATAAGACGTTTACGCCGCATCCGGCATTTGTGCGctgatgcctg < 1:1196182/71‑1 (MQ=255)
agtaagtCTGGCGTAGGCCGGATAAGACGTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCg < 1:3505789/70‑1 (MQ=255)
agtCTGGCGTAGGCCGGATAAGACGTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCt < 1:1655151/71‑1 (MQ=255)
cTGGCGTAGGCCGGATAAGACGTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGAc > 1:434380/1‑71 (MQ=255)
tgTAGGCCGGACAAGACGTTTA‑‑TCGCATCCGGCAGTCGTGTGcagatgcct < 1:2467046/50‑1 (MQ=9)
tgTAGGCCGGACAAGACGTTTA‑‑TCGCATCCGGCAGTCGTGTGCAGATGCCTGATGCGACGCTAACGCGTCt < 1:3991590/70‑1 (MQ=9)
tgTAGGCCGGACAAGACGTTTA‑‑TCGCATCCGGCAGTCGTGTGCAGATGCCTGATGCGACGCTAACGCGTCt < 1:4325091/70‑1 (MQ=9)
ggCCGGATAAGACGTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTa < 1:3968490/71‑1 (MQ=255)
ggCCGGATAAGACGTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTa > 1:4039942/1‑71 (MQ=255)
ggCCGGACAAGACGTTTA‑‑TCGCATCCGGCAGTCGTGTGCAGATGCCTGATGCGACGCTAACGCGTCTTAt > 1:2766014/1‑70 (MQ=9)
ggCCGGACAAGACGTTTA‑‑TCGCATCCGGCAGTCGTGTGCAGATGCCTGATGCGACGCTAACGCGTCTTAt < 1:3118110/70‑1 (MQ=9)
ggCCGGACAAGACGTTTA‑‑TCGCATCCGGCAGTCGTGTGCAGATGCCTGATGCGACGCTAACGCGTCTTAt < 1:4582333/70‑1 (MQ=9)
ggCCGGACAAGACGTTTA‑‑TCGCATCCGGCAGTCGTGTGCAGATGCCTGATGCGACGCTAACGCGTCTTAt < 1:4683535/70‑1 (MQ=9)
ggCCGGACAAGACGTTTA‑‑TCGAATCCGGCAGTCGTGTGCAGATGCCTGATGCGACGCTAACGCGTCTTAt < 1:834604/70‑1 (MQ=2)
gCCGGATAAGGCGTTTATGCCGCATCCGGCAGTTATGCGCAGATGCCTGATGCGACGCTGGCGCGTCTTa > 1:4619478/1‑70 (MQ=11)
cGGATAAGGCGTTTACGCCGCATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGt < 1:2226868/64‑1 (MQ=14)
ggATAAGGCGTTTATGCCGCATCCGGCAGTTATGCGcagatgcctgatgc < 1:1756742/50‑1 (MQ=11)
ggATAAGGCGTTTATGCCGCATCCGGCAGTTATGCGcagatgcctgatgc < 1:422928/50‑1 (MQ=11)
ggATAAGGCGTTTACGCCGCATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTAt > 1:1063915/1‑68 (MQ=14)
ggACAAGACGTTTA‑‑TCGCATCCGGCAGTCGTGTGCAGATGCCTGATGCGACGCTAACGCGTCTTATc < 1:3573976/67‑1 (MQ=9)
gATAAGGCGTTTACGCCGCATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCagg > 1:4350560/1‑69 (MQ=11)
gATAAGGCGTTTACGCCGCATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCagg > 1:824945/1‑69 (MQ=11)
gATAAGGCGTTTACGCCGCATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCagg > 1:5554197/1‑69 (MQ=11)
gATAAGACGTTTACGCCGCATCCGGCATTTGTGCGctgatgcct < 1:1701772/44‑1 (MQ=255)
aTAAGACGTTTACGCCGCATCCGGCATTTGTGCGctgatgcctga > 1:2609340/1‑45 (MQ=255)
aTAAGACGTTTACGCCGCATCCGGCATTTGTGCGctgatgcctga > 1:3616525/1‑45 (MQ=255)
aTAAGACGTTTACGCCGCATCCGGCATTTGTGCGctgatgcctga > 1:1805980/1‑45 (MQ=255)
tAAGGCGTTTACGCCGCATCCGGCAGTTGTACGCAGGTGCCTGATGCGACGCTGGCGCGTCTTATCATGcc < 1:3814930/71‑1 (MQ=11)
tAAGACGTTTACGCCGCATCCGGCATTTGTGCGctga > 1:4290447/1‑37 (MQ=255)
aggcGTTTATGCCGCATCCGGCAGTTATGCGCAGATGCCTGATGCGACGCTGGCGCGTCTTATCATGCCTa < 1:1875605/68‑1 (MQ=11)
aggcGTTTACGCCGCATCCGGCAGTTGTACGCAGGTGCCTGATGCGACGCTGGCGCGTCTTATCATGCCt < 1:75157/67‑1 (MQ=11)
aGACGTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTa > 1:3666333/1‑71 (MQ=255)
aGACGTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTa > 1:989136/1‑71 (MQ=255)
ggcGTTTACGCCGCATCCGGCAGTTGTACGCAGGTGCCTGATGCGACGCTGGCGCGTCTTATCATGCCTAc < 1:5436686/69‑1 (MQ=11)
gTTTATGCCGCATCCGGCAGTTATGCGCAGATGCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACaaa > 1:1943052/1‑71 (MQ=14)
gTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATg > 1:1076548/1‑63 (MQ=255)
gTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGc > 1:2237443/1‑64 (MQ=255)
gTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACaaa > 1:2742367/1‑71 (MQ=255)
tttATGCCGCATCCGGCAGTTATGCGCAGATGCCTGATGCGACGCTGGCGCGTCTTATc < 1:3095830/59‑1 (MQ=11)
ttcaCGCCGCATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCAGACCTACAAAt < 1:316021/68‑1 (MQ=11)
ttATGCCGCATCCGGCAGTTATGCGCAGATGCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACaaact > 1:187324/1‑69 (MQ=11)
ttACGCCGCATCCGGCATTTGTGCGATGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATc > 1:2157744/1‑71 (MQ=255)
tACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCt > 1:3034541/1‑71 (MQ=255)
tACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCt > 1:5551855/1‑71 (MQ=255)
tACGCCGCATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGc > 1:5012285/1‑43 (MQ=14)
caCGCCGCATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCAGGCCTACAAAtt > 1:3545990/2‑69 (MQ=11)
caCGCCGCATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCAGACCTACAAAttc > 1:4035262/2‑69 (MQ=11)
caCGCCGCATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCAGACCTACAAAttc > 1:2380082/2‑69 (MQ=11)
cgccgcATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCAGGCCTACAAAttct < 1:3513868/70‑4 (MQ=11)
ccgcATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTAc > 1:4984833/1‑71 (MQ=255)
ccgcATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTAc < 1:5228399/71‑1 (MQ=255)
cgcATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTAcg < 1:4007667/71‑1 (MQ=255)
cgcATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGt > 1:557805/1‑46 (MQ=14)
gcATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTAcgc > 1:3970778/1‑71 (MQ=255)
gcATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCAGGCCTACa < 1:1360600/60‑1 (MQ=11)
cATCCGGCA‑CTGTGTGCCGATGCCTGATGCGACGCTGACGCGTTTTATCATGCCTAcg < 1:1850183/58‑2 (MQ=14)
tCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCAGGCCTACAAAttc > 1:1944324/1‑60 (MQ=11)
cATTTGTGCGCTGATGCCTGATGCGACGCTGCCGCGTCTTATCATGCCTACAAATCTGTACGCGAACCg > 1:1816658/1‑69 (MQ=255)
cATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCg > 1:2460913/1‑69 (MQ=255)
cATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCg > 1:374981/1‑69 (MQ=255)
cATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTa < 1:1381827/71‑1 (MQ=255)
tttGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACaa < 1:1505484/51‑1 (MQ=255)
ctgtgtgCCGATGCCTGATGCGACGCTGACGCGTTTTATCAt < 1:3307470/41‑1 (MQ=14)
ctgtgtgCCGATGCCTGATGCGACGCTGACGCGTTTTATCAt < 1:1633189/41‑1 (MQ=14)
tgtgtgCCGATGCCTGATGCGACGCTGACGCGTTTTAt < 1:599282/38‑1 (MQ=14)
tgtgtgCCGATGCCTGATGCGACGCTGACGCGTTTTAt < 1:4718543/38‑1 (MQ=14)
tgtgCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAg > 1:3118635/1‑68 (MQ=255)
tgtgCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAg > 1:2547384/1‑68 (MQ=255)
tgtgCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGcc > 1:2958194/1‑71 (MQ=255)
gtgtGCCGATGCCTGATGCGACGCTGACGCGTTTTATCATGc > 1:1661702/1‑42 (MQ=14)
gtgtGCCGATGCCTGATGCGACGCTGACGCGTTTTATCATGc > 1:1834998/1‑42 (MQ=14)
gtgtGCCGATGCCTGATGCGACGCTGACGCGTTTTATCATGc > 1:4043461/1‑42 (MQ=14)
gtgtGCCGATGCCTGATGCGACGCTGACGCGTTTTATCATGc > 1:2721273/1‑42 (MQ=14)
gtgtGCCGATGCCTGATGCGACGCTGACGCGTTTTATCATGCCTa > 1:3473134/1‑45 (MQ=11)
gtgtGCCGATGCCTGATGCGACGCTGACGCGTTTTATCATGCCTa > 1:3616852/1‑45 (MQ=11)
gtgCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCAGGCCTACAAAtt > 1:4971846/1‑50 (MQ=14)
tgCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGa < 1:2791128/71‑1 (MQ=255)
cgcTGATGCCTGATGTGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGaa < 1:2414668/70‑1 (MQ=255)
cgcTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGcc < 1:1277350/67‑1 (MQ=255)
gcTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGaata < 1:14595/71‑1 (MQ=255)
ctgatgcctgatgcGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGaata < 1:4647595/70‑1 (MQ=255)
tgatgcctgatgcGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGaataat > 1:3498067/1‑71 (MQ=255)
|
AAAAGAGATGGTTAAGTAAGTCTGGCGTAGGCCGGATAAGACGTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGAATAAT > Exported/222927‑223067
|
| 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
