/EXTERNAL ENCODE/variants/K005722_K005707_2_lane_gembs
BACK
SAMPLE K005722_K005707_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1171091392 |
1030248489 |
87.97 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1171091392 |
100% |
1160515867 |
99.10 % |
10575525 |
0.90 % |
| |
|
|
|
|
|
|
| Passed |
1031581332 |
88.09 % |
1027931002 |
88.58 % |
3650330 |
0.35 % |
| Filtered |
139510060 |
11.91 % |
132584865 |
11.42 % |
6925195 |
0.67 % |
| |
|
|
|
|
|
|
| q20 |
109788118 |
78.70 % |
108797701 |
82.06 % |
990417 |
14.30 % |
| q20,mq40 |
9948275 |
7.13 % |
9774656 |
7.37 % |
173619 |
2.51 % |
| q20,qd2 |
7289783 |
5.23 % |
2530475 |
1.91 % |
4759308 |
68.72 % |
| qd2 |
4856019 |
3.48 % |
4487701 |
3.38 % |
368318 |
5.32 % |
| mq40 |
4795511 |
3.44 % |
4441595 |
3.35 % |
353916 |
5.11 % |
| q20,qd2,mq40 |
2683987 |
1.92 % |
2436180 |
1.84 % |
247807 |
3.58 % |
| qd2,mq40 |
140305 |
0.10 % |
116557 |
0.09 % |
23748 |
0.34 % |
| fs60 |
2443 |
0.00 % |
0 |
0.00 % |
2443 |
0.04 % |
| qd2,fs60,mq40 |
2021 |
0.00 % |
0 |
0.00 % |
2021 |
0.03 % |
| qd2,fs60 |
1950 |
0.00 % |
0 |
0.00 % |
1950 |
0.03 % |
| q20,qd2,fs60 |
872 |
0.00 % |
0 |
0.00 % |
872 |
0.01 % |
| fs60,mq40 |
534 |
0.00 % |
0 |
0.00 % |
534 |
0.01 % |
| q20,qd2,fs60,mq40 |
220 |
0.00 % |
0 |
0.00 % |
220 |
0.00 % |
| q20,fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
Coverage and Quality
| Coverage Variants |
Quality Variants |
 |
 |
Filtering Criteria Distribution
| Phred scale strand bias estimated using Fisher's Exact Test. |
 |
| Allele-specific call confidence normalized by depth of sample reads supporting the allele. Variants. |
Allele-specific call confidence normalized by depth of sample reads supporting the allele. Non-Variants. |
 |
 |
| Root Mean Square of the mapping quality of reads. Variants. |
Root Mean Square of the mapping quality of reads. Non-Variants. |
 |
 |
Mutations
| Type |
Mutation |
Status |
# |
% |
| Transition |
A>G |
All |
4165719 |
32.72 % |
| Transition |
G>A |
All |
968751 |
7.61 % |
| Transition |
T>C |
All |
3763797 |
29.57 % |
| Transition |
C>T |
All |
1010399 |
7.94 % |
| Transversion |
A>C |
All |
300203 |
2.36 % |
| Transversion |
C>A |
All |
436179 |
3.43 % |
| Transversion |
T>G |
All |
318864 |
2.50 % |
| Transversion |
G>T |
All |
432032 |
3.39 % |
| Transversion |
A>T |
All |
349883 |
2.75 % |
| Transversion |
T>A |
All |
360116 |
2.83 % |
| Transversion |
C>G |
All |
318802 |
2.50 % |
| Transversion |
G>C |
All |
305004 |
2.40 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
712776 |
18.83 % |
| Transition |
G>A |
Passed |
562358 |
14.86 % |
| Transition |
T>C |
Passed |
690445 |
18.24 % |
| Transition |
C>T |
Passed |
564524 |
14.92 % |
| Transversion |
A>C |
Passed |
158074 |
4.18 % |
| Transversion |
C>A |
Passed |
170279 |
4.50 % |
| Transversion |
T>G |
Passed |
159652 |
4.22 % |
| Transversion |
G>T |
Passed |
164143 |
4.34 % |
| Transversion |
A>T |
Passed |
147183 |
3.89 % |
| Transversion |
T>A |
Passed |
149013 |
3.94 % |
| Transversion |
C>G |
Passed |
153501 |
4.06 % |
| Transversion |
G>C |
Passed |
152949 |
4.04 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPAll |
0 |
0.00 % |
| Transition |
G>A |
dbSNPAll |
0 |
0.00 % |
| Transition |
T>C |
dbSNPAll |
0 |
0.00 % |
| Transition |
C>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPAll |
0 |
0.00 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPPassed |
0 |
0.00 % |
| Transition |
G>A |
dbSNPPassed |
0 |
0.00 % |
| Transition |
T>C |
dbSNPPassed |
0 |
0.00 % |
| Transition |
C>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPPassed |
0 |
0.00 % |
| |
|
|
|
|
Ti/Tv Ratio
| Status |
Ratio |
Transitions |
Transversions |
| All |
3.51 |
9908666 |
2821083 |
| Passed |
2.02 |
2530103 |
1254794 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |