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 |
|
A93 F1 I1 R1
|
15 |
55.4 |
3682408 |
94.4% |
3476193 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
2,298,651 |
Δ1 bp |
coding (432/1359 nt) |
glpT ← |
sn‑glycerol‑3‑phosphate transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 2,298,651 | 0 | A | . | 93.5%
| 129.2
/ 4.0
| 31 | coding (432/1359 nt) | glpT | sn‑glycerol‑3‑phosphate transporter |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base . (12/17); total (13/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.04e-01 |
CCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACC > REL606/2298580‑2298720
|
ccGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCAT‑GTACg < 1:437285/76‑1 (MQ=255)
cGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCAT‑GTACGACca < 1:1276543/76‑1 (MQ=255)
gTTGTGCGCATAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCAT‑GTACGACcac < 2:1270942/76‑1 (MQ=255)
ttGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACcac < 1:1053917/76‑1 (MQ=255)
ttGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCAT‑GTACGACcaca < 1:638408/76‑1 (MQ=255)
tgtgCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCCT‑GTACGACCacac < 1:1222795/76‑1 (MQ=255)
gtgCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCAT‑GTACGACCACAcg > 1:1529418/1‑76 (MQ=255)
tgCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCAT‑GTACGACCACAcgg > 1:804057/1‑76 (MQ=255)
ggcgcACCGCTCCCCGCCGACACAACGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCAT‑GTACGACCACTcga < 2:1478723/75‑2 (MQ=255)
gcgcACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCAT‑GTACGACCACAcggc < 1:394393/76‑1 (MQ=255)
gcACACTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCAT‑GTACGACCACAcggcgg < 2:1813775/76‑1 (MQ=255)
aGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCAT‑GTACGACCACACGGCGGCCAc < 2:1321849/76‑1 (MQ=255)
ttCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCAT‑GTACGACCACACGGCGGCCAccc > 2:1472258/1‑76 (MQ=255)
tCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCAT‑GTACGACCACACGGCGGCCAcccc < 1:615444/76‑1 (MQ=255)
ccACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCAT‑GTACGACCACACGGCGGCCACCCCa > 2:722378/1‑76 (MQ=255)
cacTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCAT‑GTACGACCACACGGCGGCCACCCCATcc > 2:513345/1‑76 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCAT‑GTACGACCACACGGCGGCCACCCCATCCCCTg < 2:470824/76‑1 (MQ=255)
caATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCAT‑GTACGACCACACGGCGGCCACCCCATCCCCTGGgac > 1:1705021/1‑76 (MQ=255)
aTGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCAT‑GTACGACCACACGGCGGCCACCCCATCCCCTGGaacca < 1:526081/76‑1 (MQ=255)
tGCCGCCACGTTCTNTCTGCGACCACCAGTGCACCAT‑GTACGACCACACGGCGGCCACCCCATCCCCTGGaaccaa > 1:994701/1‑76 (MQ=255)
gccgccACGTTCTTTCTGCGACCACCAGTGCACCAT‑GTACGACCACACGGCGGCCACCCCATCCCCCGGaacccac > 1:1152992/1‑76 (MQ=255)
ccgccACGTTCTTTCTGCGACCACCAGTGCACCAT‑GTACGACCACACGGCGGCCACCCCATCCCCTGGaaccaacc < 2:384412/76‑1 (MQ=255)
gTTCTTTCTGCGACCACCAGTGCACCAT‑GTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAgg < 2:674481/76‑1 (MQ=255)
ttctGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGaaca > 1:1117796/1‑76 (MQ=255)
ttctGCGACCACCAGTGCACCAT‑GTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGaacaa < 1:200123/76‑1 (MQ=255)
tgctGCGACCACCAGTGCGCCAT‑GTCCGACCACACGGCGGCCTCCCCATCCCCTGGAACCAACCGCAGAGGaacaa < 2:196995/74‑1 (MQ=255)
gcgcCCACCAGTGCACCAT‑GTACGACCACACGGCGTCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGt < 1:512941/76‑1 (MQ=255)
cGACCACCAGTGCACCAT‑GTACGACCACACGGCGGCCACCCCCTCCCCTGGAACCAACCGCAGAGGAACAACAgaa > 2:348532/1‑74 (MQ=255)
gACCACCAGTGCACCAT‑GTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTAc > 1:1308743/1‑76 (MQ=255)
accaccAGTGCACCAT‑GTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACa < 2:349434/76‑1 (MQ=255)
caGTGCACCAT‑GTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACAt < 1:347483/76‑1 (MQ=255)
gTGCATCAT‑GTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCa < 2:1817038/76‑1 (MQ=255)
gTGCACCAT‑GTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCa > 1:1400762/1‑76 (MQ=255)
tGCACCAT‑GTACGNCCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCAc > 1:1234184/1‑76 (MQ=255)
gCACCAT‑GTACGGCCACACGGCGCCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCAcc < 2:921868/76‑1 (MQ=255)
|
CCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACC > REL606/2298580‑2298720
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
