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 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,191,865 |
G→A |
21.3% |
A116T (GCC→ACC) |
yqiK → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,191,865 | 0 | G | A | 21.3%
| 100.6
/ 21.4
| 47 | A116T (GCC→ACC) | yqiK | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (11/26); new base A (5/5); total (16/31) |
| Fisher's exact test for biased strand distribution p-value = 2.74e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.82e-01 |
CGCGTCGATGTAGTAGTCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATAAATTTGTC > W3110S.gb/3191799‑3191933
|
cgcgTCGATGTAGTAGTCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGcc > 1:1461119/1‑69 (MQ=255)
cgcgTCGATGTAGTAGTCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGcc > 1:816048/1‑69 (MQ=255)
cgcgTCGATGTAGTAGTCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGcc > 1:3993110/1‑69 (MQ=255)
cgcgTCGATGTAGTAGTCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCa < 1:610649/71‑1 (MQ=255)
gTCGATGTAGTAGTCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTACCCa > 1:376074/1‑68 (MQ=255)
gATGTAGTAGTCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGc < 1:1784926/70‑1 (MQ=255)
gATGTAGTAGTAGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGc < 1:675779/70‑1 (MQ=255)
gtagtagtaGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTACCCAGACGCTggg > 1:3226828/1‑71 (MQ=255)
gtagtaGTCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTgg < 1:1088359/70‑1 (MQ=255)
gtagtaGTCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTgg < 1:3294002/70‑1 (MQ=255)
agtagtCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTgggg > 1:4300460/1‑70 (MQ=255)
gtagtCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACg > 1:3874450/1‑63 (MQ=255)
gtagtCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGc < 1:1981953/70‑1 (MQ=255)
gtagtCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTACCCAGACGCTGGGGc < 1:3277049/70‑1 (MQ=255)
gtagtCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTACCCAGACGCTGGGGCa < 1:3868254/71‑1 (MQ=255)
tCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGc < 1:2666343/71‑1 (MQ=255)
tCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTACCCAGACGCTgg < 1:2001825/63‑1 (MQ=255)
tctttGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTg > 1:3980518/1‑71 (MQ=255)
tctttGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTg > 1:751533/1‑71 (MQ=255)
tgtgCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTc < 1:4554505/69‑1 (MQ=255)
cGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTACCCAGACGCTGGGGCAACGCACCCTGTCGCCTGa < 1:2976699/71‑1 (MQ=255)
ggTAAAACCTTCAGTAGAAGGGATTGCCACCGCTACCCAGACGCTGGGGCAAc > 1:967301/1‑53 (MQ=255)
aaaCCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACt > 1:389763/1‑70 (MQ=255)
aaaCCTTCAGTAGAAGGGATTGCCACCGCTACCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACt > 1:3045096/1‑70 (MQ=255)
aCCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAAAGCACCCTGTCGCCTGAAGACTTAc < 1:4128900/71‑1 (MQ=255)
ccTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACg < 1:3151882/71‑1 (MQ=255)
ccTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACg < 1:1141063/71‑1 (MQ=255)
cTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACg < 1:2353216/70‑1 (MQ=255)
cAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTa < 1:4089068/69‑1 (MQ=255)
cAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTa < 1:2935726/69‑1 (MQ=255)
cAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTa < 1:1999755/69‑1 (MQ=255)
cAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATg > 1:701639/1‑71 (MQ=255)
gTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATgtt < 1:2944068/71‑1 (MQ=255)
gTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATgtt < 1:1931254/71‑1 (MQ=255)
gAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGAc > 1:2682107/1‑57 (MQ=255)
gAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACg < 1:4317106/62‑1 (MQ=255)
aGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATgttggttg < 1:2109931/71‑1 (MQ=255)
gATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATgttggttg > 1:208386/1‑68 (MQ=255)
aTTGCCACCGCTACCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATgt > 1:1648307/1‑61 (MQ=255)
ttGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTa < 1:639660/53‑1 (MQ=255)
ccACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATaaa < 1:534652/71‑1 (MQ=255)
ccGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATAAAttt < 1:583917/71‑1 (MQ=255)
cGCTACCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATAAAttt < 1:4495171/70‑1 (MQ=255)
cTGCCCAGACGCTGGGTCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATAAATTTGTc < 1:77642/71‑1 (MQ=255)
cTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATg < 1:577088/50‑1 (MQ=255)
cTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATAAATTTGTc < 1:4569961/71‑1 (MQ=255)
cTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATAAATTTGTc < 1:3596163/71‑1 (MQ=255)
|
CGCGTCGATGTAGTAGTCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATAAATTTGTC > W3110S.gb/3191799‑3191933
|
| 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
