/cemt/variants/A70097_2_lane_gembs
BACK
SAMPLE A70097_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1171241372 |
1050834309 |
89.72 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1171241372 |
100% |
1152318964 |
98.38 % |
18922408 |
1.62 % |
| |
|
|
|
|
|
|
| Passed |
1052902566 |
89.90 % |
1047684221 |
90.92 % |
5218345 |
0.50 % |
| Filtered |
118338806 |
10.10 % |
104634743 |
9.08 % |
13704063 |
1.30 % |
| |
|
|
|
|
|
|
| q20 |
86786776 |
73.34 % |
86086043 |
82.27 % |
700733 |
5.11 % |
| q20,qd2 |
15051891 |
12.72 % |
2957382 |
2.83 % |
12094509 |
88.25 % |
| q20,mq40 |
10040170 |
8.48 % |
9950992 |
9.51 % |
89178 |
0.65 % |
| mq40 |
2553146 |
2.16 % |
2318038 |
2.22 % |
235108 |
1.72 % |
| q20,qd2,mq40 |
2420264 |
2.05 % |
2288764 |
2.19 % |
131500 |
0.96 % |
| qd2 |
1439556 |
1.22 % |
997539 |
0.95 % |
442017 |
3.23 % |
| qd2,mq40 |
45299 |
0.04 % |
35985 |
0.03 % |
9314 |
0.07 % |
| qd2,fs60,mq40 |
754 |
0.00 % |
0 |
0.00 % |
754 |
0.01 % |
| qd2,fs60 |
394 |
0.00 % |
0 |
0.00 % |
394 |
0.00 % |
| fs60,mq40 |
256 |
0.00 % |
0 |
0.00 % |
256 |
0.00 % |
| fs60 |
180 |
0.00 % |
0 |
0.00 % |
180 |
0.00 % |
| q20,qd2,fs60,mq40 |
59 |
0.00 % |
0 |
0.00 % |
59 |
0.00 % |
| q20,qd2,fs60 |
58 |
0.00 % |
0 |
0.00 % |
58 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60 |
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 |
7907173 |
38.39 % |
| Transition |
G>A |
All |
937877 |
4.55 % |
| Transition |
T>C |
All |
7997933 |
38.83 % |
| Transition |
C>T |
All |
941215 |
4.57 % |
| Transversion |
A>C |
All |
264140 |
1.28 % |
| Transversion |
C>A |
All |
441651 |
2.14 % |
| Transversion |
T>G |
All |
269091 |
1.31 % |
| Transversion |
G>T |
All |
428158 |
2.08 % |
| Transversion |
A>T |
All |
452144 |
2.20 % |
| Transversion |
T>A |
All |
461862 |
2.24 % |
| Transversion |
C>G |
All |
249015 |
1.21 % |
| Transversion |
G>C |
All |
246682 |
1.20 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
923086 |
21.09 % |
| Transition |
G>A |
Passed |
619677 |
14.16 % |
| Transition |
T>C |
Passed |
890764 |
20.35 % |
| Transition |
C>T |
Passed |
619010 |
14.14 % |
| Transversion |
A>C |
Passed |
169258 |
3.87 % |
| Transversion |
C>A |
Passed |
176922 |
4.04 % |
| Transversion |
T>G |
Passed |
169831 |
3.88 % |
| Transversion |
G>T |
Passed |
168598 |
3.85 % |
| Transversion |
A>T |
Passed |
150162 |
3.43 % |
| Transversion |
T>A |
Passed |
153673 |
3.51 % |
| Transversion |
C>G |
Passed |
168146 |
3.84 % |
| Transversion |
G>C |
Passed |
168027 |
3.84 % |
| |
|
|
|
|
| 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 |
6.32 |
17784198 |
2812743 |
| Passed |
2.30 |
3052537 |
1324617 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |