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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,099,110 |
T→C |
50.0% |
P295P (CCA→CCG) |
garP ← |
predicted (D)‑galactarate transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,099,110 | 0 | T | C | 50.0%
| ‑4.5
/ 63.6
| 70 | P295P (CCA→CCG) | garP | predicted (D)‑galactarate transporter |
| Reads supporting (aligned to +/- strand): ref base T (13/22); new base C (20/15); total (33/37) |
| Fisher's exact test for biased strand distribution p-value = 1.50e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGACATGCCTTTTTCCTGCACCAGATAAATCGGG > minE/2099044‑2099176
|
aCCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCt > 1:2729425/1‑67 (MQ=255)
aCCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTgg > 1:1244358/1‑69 (MQ=255)
aCCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTgg > 1:779619/1‑69 (MQ=255)
aCCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTgg > 1:1706415/1‑69 (MQ=255)
ttGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAg < 1:2874470/69‑1 (MQ=255)
ttGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAg < 1:1868613/69‑1 (MQ=255)
ttGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAg < 1:1561527/69‑1 (MQ=255)
ttGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAg < 1:58726/69‑1 (MQ=255)
ttGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAg < 1:475829/69‑1 (MQ=255)
tGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAg < 1:768935/68‑1 (MQ=255)
tGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAg < 1:1773131/68‑1 (MQ=255)
cAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCg > 1:2082090/1‑67 (MQ=255)
cAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGAc < 1:1243216/69‑1 (MQ=255)
cAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGAc < 1:2167340/69‑1 (MQ=255)
cAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGAc < 1:194552/69‑1 (MQ=255)
cAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGAc < 1:2990655/69‑1 (MQ=255)
cAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGAc < 1:772332/69‑1 (MQ=255)
cAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGAc < 1:1352525/69‑1 (MQ=255)
gATAATCCGAGAAGACACCTCCCAGCACTCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGAc < 1:1589243/67‑1 (MQ=255)
aTCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGAcc < 1:187159/69‑1 (MQ=255)
gaagaCACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACttt < 1:1215223/69‑1 (MQ=255)
gaagaCACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACttt < 1:2260991/69‑1 (MQ=255)
gaagaCACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACttt < 1:220707/69‑1 (MQ=255)
gaagaCACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACttt < 1:214328/69‑1 (MQ=255)
gaagaCACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACttt < 1:2037788/69‑1 (MQ=255)
gaagaCACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACttt < 1:1973742/69‑1 (MQ=255)
gaagaCACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACttt < 1:1289413/69‑1 (MQ=255)
gaCACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAg > 1:128757/1‑69 (MQ=255)
gaCACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAg > 1:2165214/1‑69 (MQ=255)
gaCACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAg > 1:1580357/1‑69 (MQ=255)
gaCACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAg > 1:2649787/1‑69 (MQ=255)
cacCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGAcc > 1:303915/1‑58 (MQ=255)
cacCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGag > 1:2906446/1‑68 (MQ=255)
cacCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGaa > 1:798740/1‑69 (MQ=255)
cacCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGaa > 1:2770317/1‑69 (MQ=255)
cacCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGaa > 1:246621/1‑69 (MQ=255)
tCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGa < 1:1488947/69‑1 (MQ=255)
tCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGa < 1:684888/69‑1 (MQ=255)
tCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGa < 1:2173098/69‑1 (MQ=255)
cccAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGa < 1:1386835/68‑1 (MQ=255)
ccAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGa < 1:227554/67‑1 (MQ=255)
ccgcccgcAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGACATGCCtttt < 1:971/69‑1 (MQ=255)
ccgcccgcAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGACATGCCtttt < 1:1282920/69‑1 (MQ=255)
ccgcccgcAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGACATGCCtttt < 1:390948/69‑1 (MQ=255)
ccgcccgcAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGACATGCCtttt < 1:3328746/69‑1 (MQ=255)
cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt > 1:1714281/1‑42 (MQ=38)
cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt > 1:672729/1‑42 (MQ=38)
cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt > 1:1701748/1‑42 (MQ=38)
cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt > 1:1706240/1‑42 (MQ=38)
cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt > 1:381416/1‑42 (MQ=38)
cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt > 1:312105/1‑42 (MQ=38)
cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt > 1:1783844/1‑42 (MQ=38)
cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt > 1:180052/1‑42 (MQ=38)
cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt > 1:2902879/1‑42 (MQ=38)
cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt > 1:1969256/1‑42 (MQ=38)
cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt > 1:2569876/1‑42 (MQ=38)
cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt > 1:286368/1‑42 (MQ=38)
cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt > 1:2851394/1‑42 (MQ=38)
cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt > 1:2641202/1‑42 (MQ=38)
cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt > 1:2836220/1‑42 (MQ=38)
cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt > 1:2649857/1‑42 (MQ=38)
cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt > 1:2181460/1‑42 (MQ=38)
cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt > 1:2749502/1‑42 (MQ=38)
cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACt > 1:2491174/1‑41 (MQ=38)
cAAAGCCACACAGTGCCGGAATCGAG‑‑GACCAGACCCACtt > 1:1411486/1‑40 (MQ=255)
acacaGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGACATGCCTTTTTCCTGCACCAGATa < 1:347100/69‑1 (MQ=255)
acacaGTGCCGGAATCGAGGCGACCAGACCCACttt < 1:2805526/36‑1 (MQ=255)
cacaGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGACATGCCTTTTTCCTGCACCAGATa < 1:503221/68‑1 (MQ=255)
gCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGACATGCCTTTTTCCTGCACCAGATAAATCggg < 1:275972/69‑1 (MQ=255)
gCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGACATGCCTTTTTCCTGCACCAGATAAATCggg < 1:469151/69‑1 (MQ=255)
cTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGACATGCCTTTTTCCTGCACCAGATAAATCggg < 1:932203/68‑1 (MQ=255)
|
ACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGACATGCCTTTTTCCTGCACCAGATAAATCGGG > minE/2099044‑2099176
|
| 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
