/EXTERNAL DEEP/variants/K006051_K006052_K006053_K006054_K006122_5_lane_gembs
BACK
SAMPLE K006051_K006052_K006053_K006054_K006122_5_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1172496923 |
1001176804 |
85.39 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1172496923 |
100% |
1139098174 |
97.15 % |
33398749 |
2.85 % |
| |
|
|
|
|
|
|
| Passed |
1003917387 |
85.62 % |
996969197 |
87.52 % |
6948190 |
0.69 % |
| Filtered |
168579536 |
14.38 % |
142128977 |
12.48 % |
26450559 |
2.63 % |
| |
|
|
|
|
|
|
| q20 |
119721680 |
71.02 % |
116512403 |
81.98 % |
3209277 |
12.13 % |
| q20,qd2 |
30244016 |
17.94 % |
8450626 |
5.95 % |
21793390 |
82.39 % |
| q20,mq40 |
9372632 |
5.56 % |
9203641 |
6.48 % |
168991 |
0.64 % |
| qd2 |
4824881 |
2.86 % |
4002934 |
2.82 % |
821947 |
3.11 % |
| q20,qd2,mq40 |
3047851 |
1.81 % |
2872121 |
2.02 % |
175730 |
0.66 % |
| mq40 |
1330614 |
0.79 % |
1058696 |
0.74 % |
271918 |
1.03 % |
| qd2,mq40 |
36669 |
0.02 % |
28556 |
0.02 % |
8113 |
0.03 % |
| qd2,fs60,mq40 |
548 |
0.00 % |
0 |
0.00 % |
548 |
0.00 % |
| fs60,mq40 |
224 |
0.00 % |
0 |
0.00 % |
224 |
0.00 % |
| qd2,fs60 |
169 |
0.00 % |
0 |
0.00 % |
169 |
0.00 % |
| fs60 |
131 |
0.00 % |
0 |
0.00 % |
131 |
0.00 % |
| q20,qd2,fs60,mq40 |
60 |
0.00 % |
0 |
0.00 % |
60 |
0.00 % |
| q20,qd2,fs60 |
57 |
0.00 % |
0 |
0.00 % |
57 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
13396362 |
38.01 % |
| Transition |
G>A |
All |
2145419 |
6.09 % |
| Transition |
T>C |
All |
14081510 |
39.95 % |
| Transition |
C>T |
All |
1694759 |
4.81 % |
| Transversion |
A>C |
All |
278508 |
0.79 % |
| Transversion |
C>A |
All |
810740 |
2.30 % |
| Transversion |
T>G |
All |
314849 |
0.89 % |
| Transversion |
G>T |
All |
803056 |
2.28 % |
| Transversion |
A>T |
All |
558295 |
1.58 % |
| Transversion |
T>A |
All |
583959 |
1.66 % |
| Transversion |
C>G |
All |
292607 |
0.83 % |
| Transversion |
G>C |
All |
285858 |
0.81 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1224744 |
23.02 % |
| Transition |
G>A |
Passed |
654758 |
12.31 % |
| Transition |
T>C |
Passed |
1543684 |
29.02 % |
| Transition |
C>T |
Passed |
622102 |
11.69 % |
| Transversion |
A>C |
Passed |
155987 |
2.93 % |
| Transversion |
C>A |
Passed |
178363 |
3.35 % |
| Transversion |
T>G |
Passed |
162349 |
3.05 % |
| Transversion |
G>T |
Passed |
172381 |
3.24 % |
| Transversion |
A>T |
Passed |
139989 |
2.63 % |
| Transversion |
T>A |
Passed |
148199 |
2.79 % |
| Transversion |
C>G |
Passed |
159601 |
3.00 % |
| Transversion |
G>C |
Passed |
157974 |
2.97 % |
| |
|
|
|
|
| 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 |
7.97 |
31318050 |
3927872 |
| Passed |
3.17 |
4045288 |
1274843 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |