/EXTERNAL DEEP/variants/K008987_K008988_K008989_3_lane_gembs
BACK
SAMPLE K008987_K008988_K008989_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1171827655 |
714936292 |
61.01 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1171827655 |
100% |
1140406204 |
97.32 % |
31421451 |
2.68 % |
| |
|
|
|
|
|
|
| Passed |
720318057 |
61.47 % |
711287867 |
62.37 % |
9030190 |
1.25 % |
| Filtered |
451509598 |
38.53 % |
429118337 |
37.63 % |
22391261 |
3.11 % |
| |
|
|
|
|
|
|
| q20 |
409807265 |
90.76 % |
402883311 |
93.89 % |
6923954 |
30.92 % |
| q20,qd2 |
24539580 |
5.44 % |
9904281 |
2.31 % |
14635299 |
65.36 % |
| q20,mq40 |
9849950 |
2.18 % |
9662677 |
2.25 % |
187273 |
0.84 % |
| q20,qd2,mq40 |
3085077 |
0.68 % |
2935790 |
0.68 % |
149287 |
0.67 % |
| qd2 |
3059409 |
0.68 % |
2790858 |
0.65 % |
268551 |
1.20 % |
| mq40 |
1127849 |
0.25 % |
910157 |
0.21 % |
217692 |
0.97 % |
| qd2,mq40 |
38599 |
0.01 % |
31263 |
0.01 % |
7336 |
0.03 % |
| qd2,fs60,mq40 |
728 |
0.00 % |
0 |
0.00 % |
728 |
0.00 % |
| qd2,fs60 |
368 |
0.00 % |
0 |
0.00 % |
368 |
0.00 % |
| fs60,mq40 |
263 |
0.00 % |
0 |
0.00 % |
263 |
0.00 % |
| fs60 |
225 |
0.00 % |
0 |
0.00 % |
225 |
0.00 % |
| q20,qd2,fs60,mq40 |
150 |
0.00 % |
0 |
0.00 % |
150 |
0.00 % |
| q20,qd2,fs60 |
134 |
0.00 % |
0 |
0.00 % |
134 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
10755316 |
32.22 % |
| Transition |
G>A |
All |
2426843 |
7.27 % |
| Transition |
T>C |
All |
12324848 |
36.92 % |
| Transition |
C>T |
All |
1756998 |
5.26 % |
| Transversion |
A>C |
All |
605255 |
1.81 % |
| Transversion |
C>A |
All |
1108827 |
3.32 % |
| Transversion |
T>G |
All |
696019 |
2.08 % |
| Transversion |
G>T |
All |
1020909 |
3.06 % |
| Transversion |
A>T |
All |
745918 |
2.23 % |
| Transversion |
T>A |
All |
849871 |
2.55 % |
| Transversion |
C>G |
All |
558693 |
1.67 % |
| Transversion |
G>C |
All |
534900 |
1.60 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
866233 |
19.45 % |
| Transition |
G>A |
Passed |
544887 |
12.24 % |
| Transition |
T>C |
Passed |
1348282 |
30.28 % |
| Transition |
C>T |
Passed |
481091 |
10.80 % |
| Transversion |
A>C |
Passed |
159684 |
3.59 % |
| Transversion |
C>A |
Passed |
165267 |
3.71 % |
| Transversion |
T>G |
Passed |
177630 |
3.99 % |
| Transversion |
G>T |
Passed |
147245 |
3.31 % |
| Transversion |
A>T |
Passed |
124121 |
2.79 % |
| Transversion |
T>A |
Passed |
146025 |
3.28 % |
| Transversion |
C>G |
Passed |
147690 |
3.32 % |
| Transversion |
G>C |
Passed |
144833 |
3.25 % |
| |
|
|
|
|
| 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 |
4.45 |
27264005 |
6120392 |
| Passed |
2.67 |
3240493 |
1212495 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |