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 |
|
A5 F17 I0 R1
|
87 |
56.5 |
4283937 |
98.6% |
4223961 |
62.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,255,918 |
C→T |
10.9% |
G538S (GGC→AGC) |
ycgV ← |
predicted adhesin |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,255,918 | 0 | C | T | 10.9%
| 161.4
/ 9.1
| 55 | G538S (GGC→AGC) | ycgV | predicted adhesin |
| Reads supporting (aligned to +/- strand): ref base C (25/23); new base T (4/2); total (30/25) |
| Fisher's exact test for biased strand distribution p-value = 6.75e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01 |
CGTGATTACCAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCAAATGTG > W3110S.gb/1255849‑1255988
|
cGTGATTACCAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGcc < 1:454280/70‑1 (MQ=255)
cGTGATTACCAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGcc < 1:157478/70‑1 (MQ=255)
cGTGATTACCAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCca < 1:131684/71‑1 (MQ=255)
aTTACCAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCcaacaa > 1:341560/1‑71 (MQ=255)
aTTACCAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCcaacaa > 1:2007434/1‑71 (MQ=255)
aTTACCAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCAATACCCTCGCcaacaa > 1:3966811/1‑71 (MQ=255)
cAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACAt > 1:2240488/1‑69 (MQ=255)
gCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACTCTCGCCAACAACATCAg > 1:1450067/1‑70 (MQ=255)
gCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACACCATTACCCTCGCcaacaa > 1:1593593/1‑64 (MQ=255)
tCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCca < 1:1969061/53‑1 (MQ=255)
ccGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCataa > 1:3757822/1‑70 (MQ=255)
ccGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCata < 1:4032366/69‑1 (MQ=255)
cTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATaaa < 1:3175030/71‑1 (MQ=255)
tGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAg > 1:4207511/1‑71 (MQ=255)
cAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAACAACATCAGCACGCataata > 1:1982495/1‑61 (MQ=255)
cAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGt > 1:351944/1‑71 (MQ=255)
aaTAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGt < 1:2504297/70‑1 (MQ=255)
aTAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGtt < 1:592986/70‑1 (MQ=255)
tAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCa > 1:404588/1‑49 (MQ=255)
tAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCa > 1:3566378/1‑49 (MQ=255)
aaaTCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATc > 1:2300124/1‑44 (MQ=255)
aaaTCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTAcc > 1:332719/1‑71 (MQ=255)
aaTCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACAt > 1:1537989/1‑42 (MQ=255)
cTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACt < 1:891580/58‑1 (MQ=255)
cTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACt < 1:3250462/58‑1 (MQ=255)
ttattattaACGCCATTACCCTCGCCAACAACATc > 1:1785195/1‑35 (MQ=255)
tattattaACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGc < 1:1837368/63‑1 (MQ=255)
attattaACGCCATTACCCTCGCAAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTtct > 1:1192311/1‑71 (MQ=255)
ttattaACGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAgg < 1:2314015/49‑1 (MQ=255)
ttattaACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTc > 1:3797040/1‑63 (MQ=255)
ttattaACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAgg < 1:349540/66‑1 (MQ=255)
ttattaACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTtct < 1:480388/70‑1 (MQ=255)
ttattaACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTtc < 1:2588803/69‑1 (MQ=255)
ttattaACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTtc < 1:2738405/69‑1 (MQ=255)
tattaACGCCATTACCCTCGCCAACAACATCAGCACGCat < 1:1597186/40‑1 (MQ=255)
tattaACGCCATTACCCTCGCCAACAACATCAGCACGCat < 1:2668054/40‑1 (MQ=255)
tattaACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCt < 1:352864/61‑1 (MQ=255)
tattaACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCa > 1:1978991/1‑63 (MQ=255)
tattaACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCa > 1:3325517/1‑63 (MQ=255)
attaACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAgg < 1:2029868/64‑1 (MQ=255)
attaACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTa > 1:1899519/1‑71 (MQ=255)
ttaACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAgg < 1:3731753/63‑1 (MQ=255)
aaCGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGt > 1:375324/1‑71 (MQ=255)
aaCGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGt > 1:3172899/1‑71 (MQ=255)
aCGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGATCAGTTtc > 1:2813233/1‑63 (MQ=255)
cGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAgg > 1:671209/1‑42 (MQ=255)
cGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAgg > 1:2185978/1‑42 (MQ=255)
cGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGttt < 1:1193770/71‑1 (MQ=255)
cGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGtt > 1:2496484/1‑70 (MQ=255)
ccATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTa < 1:2270488/70‑1 (MQ=255)
aTTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTAc > 1:3659687/1‑63 (MQ=255)
ttACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGt < 1:2746814/43‑1 (MQ=255)
tACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAAtgtg > 1:2216023/1‑71 (MQ=255)
aCCCTCGCTAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAAtgtg < 1:2757398/70‑1 (MQ=255)
aCCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTaa > 1:1252422/1‑66 (MQ=255)
aCCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAAtgtg < 1:3273466/70‑1 (MQ=255)
aCCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTgg > 1:1569308/1‑71 (MQ=255)
cTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCa > 1:654944/1‑70 (MQ=255)
tCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGt > 1:4217131/1‑58 (MQ=255)
gCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAgg < 1:854630/46‑1 (MQ=255)
gCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCaaa < 1:2750493/69‑1 (MQ=255)
gCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCAAAtg > 1:1777774/1‑71 (MQ=255)
gCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCAAAt < 1:3219529/70‑1 (MQ=255)
ccAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTa > 1:984081/1‑52 (MQ=255)
ccAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGttt < 1:2070534/57‑1 (MQ=255)
ccAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCAAAtgt < 1:520426/71‑1 (MQ=255)
caacaaCATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGtt > 1:2200556/1‑46 (MQ=255)
caacaaCATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCAAAtgtg > 1:1484234/1‑71 (MQ=255)
caacaaCATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCAAAtgt < 1:3222089/70‑1 (MQ=255)
|
CGTGATTACCAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCAAATGTG > W3110S.gb/1255849‑1255988
|
| 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
