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 R2
|
162 |
60.6 |
4616657 |
98.5% |
4547407 |
62.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,255,918 |
C→T |
12.5% |
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 | 12.5%
| 132.9
/ 9.4
| 48 | G538S (GGC→AGC) | ycgV | predicted adhesin |
| Reads supporting (aligned to +/- strand): ref base C (15/27); new base T (4/2); total (19/29) |
| Fisher's exact test for biased strand distribution p-value = 1.97e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.07e-01 |
CGTGATTACCAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCAAATGTG > W3110S.gb/1255849‑1255988
|
cGTGATTACCAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGcc > 1:3770595/1‑70 (MQ=255)
gTGATTACCAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCcaa > 1:2841092/1‑71 (MQ=255)
tGATTACCAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCcaac < 1:3450291/71‑1 (MQ=255)
aTTACCAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCcaacaa > 1:3742515/1‑71 (MQ=255)
ttACCAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCaacaac < 1:331413/71‑1 (MQ=255)
actactCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAACAACATCAGCAc < 1:404644/71‑1 (MQ=255)
ctactCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACg < 1:2816867/71‑1 (MQ=255)
ctactCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACg > 1:341181/1‑71 (MQ=255)
tCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCcaac < 1:319710/55‑1 (MQ=255)
tCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCa < 1:4428800/62‑1 (MQ=255)
cccGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAACAACATCAGCACGCataa > 1:1407069/1‑71 (MQ=255)
ccGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACAt > 1:3141649/1‑58 (MQ=255)
gCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAACAACATCAGCACGCataata > 1:4396520/1‑70 (MQ=255)
cTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCa > 1:2883094/1‑60 (MQ=255)
tGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGcc < 1:3954119/46‑1 (MQ=255)
atTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTAc > 1:3356977/1‑71 (MQ=255)
ttCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCat < 1:2632900/59‑1 (MQ=255)
ttCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACt < 1:4586630/71‑1 (MQ=255)
cAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAAAAACATCAGCACGCATAATAAAGGTACTGt > 1:3279517/1‑71 (MQ=255)
aaTAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAGGTACTGt < 1:2884720/70‑1 (MQ=255)
aaTAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGtt < 1:1947685/71‑1 (MQ=255)
aaTAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGt < 1:846658/70‑1 (MQ=255)
aTAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCa < 1:1987730/47‑1 (MQ=255)
aTAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCACAATAAAGGTACTGTTa > 1:3362156/1‑71 (MQ=255)
tAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAGGTACTGCTAc > 1:3723020/1‑71 (MQ=255)
aaTCCCCTTTATTATTAACGCCATTACCCTCGCcaacaa > 1:1167761/1‑39 (MQ=255)
aaTCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATc > 1:662518/1‑43 (MQ=255)
aTCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGc > 1:3096975/1‑71 (MQ=255)
tCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCt < 1:2101683/71‑1 (MQ=255)
cccTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGtt < 1:412276/63‑1 (MQ=255)
cccTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTc < 1:687652/70‑1 (MQ=255)
cTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCat < 1:2537053/46‑1 (MQ=255)
tttATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGt > 1:2998973/1‑71 (MQ=255)
tattattaACGCCATTACCCTCGCCAACAACATCAGCACGCa > 1:1540714/1‑42 (MQ=255)
attattaACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCt < 1:1962807/63‑1 (MQ=255)
ttattaACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACt < 1:1967827/53‑1 (MQ=255)
tattaACGCCATTACCCTCGCCAACAACATCAGCACGCAtaataa < 1:3315045/45‑1 (MQ=255)
ttaACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTAc < 1:3539650/71‑1 (MQ=255)
cGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGttt < 1:3228354/71‑1 (MQ=255)
gCCATTACCCTCTCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTa < 1:2592614/71‑1 (MQ=255)
ccATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTaa > 1:3032478/1‑71 (MQ=255)
cATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAAt < 1:4135751/71‑1 (MQ=255)
cATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAAt > 1:3238746/1‑71 (MQ=255)
aTTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAAtg > 1:849037/1‑71 (MQ=255)
aTTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAAtg < 1:3107298/71‑1 (MQ=255)
ttACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAAtgt < 1:2243096/71‑1 (MQ=255)
tACCCTCGCTAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTa > 1:1826412/1‑66 (MQ=255)
aCCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTgg > 1:131246/1‑71 (MQ=255)
ccTCGCCAACAACATCAGCACGCATAATAAAGGTACTGtt < 1:698528/40‑1 (MQ=255)
ccTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCa < 1:1660150/71‑1 (MQ=255)
tCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTAc < 1:1187884/56‑1 (MQ=255)
cGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAAtg < 1:648229/63‑1 (MQ=255)
cGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCAAAt > 1:2992511/1‑71 (MQ=255)
gCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCaaa < 1:1580167/69‑1 (MQ=255)
gCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCAAAt < 1:2516255/70‑1 (MQ=255)
caacaaCATCAGCACGCATAATAAAGGTACTGTTACCGCTCa < 1:4565572/42‑1 (MQ=255)
caacaaCATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCAAAtgtg < 1:3898544/71‑1 (MQ=255)
|
CGTGATTACCAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCAAATGTG > W3110S.gb/1255849‑1255988
|
| 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
