/CEMT/variants/A77954_1_lane_gembs
BACK
SAMPLE A77954_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1170646100 |
1023391590 |
87.42 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1170646100 |
100% |
1150586214 |
98.29 % |
20059886 |
1.71 % |
| |
|
|
|
|
|
|
| Passed |
1025745587 |
87.62 % |
1020041430 |
88.65 % |
5704157 |
0.56 % |
| Filtered |
144900513 |
12.38 % |
130544784 |
11.35 % |
14355729 |
1.40 % |
| |
|
|
|
|
|
|
| q20 |
109010381 |
75.23 % |
108065633 |
82.78 % |
944748 |
6.58 % |
| q20,qd2 |
17089677 |
11.79 % |
4734111 |
3.63 % |
12355566 |
86.07 % |
| q20,mq40 |
10779080 |
7.44 % |
10656480 |
8.16 % |
122600 |
0.85 % |
| qd2 |
2764411 |
1.91 % |
2281320 |
1.75 % |
483091 |
3.37 % |
| q20,qd2,mq40 |
2626385 |
1.81 % |
2460482 |
1.88 % |
165903 |
1.16 % |
| mq40 |
2581782 |
1.78 % |
2308470 |
1.77 % |
273312 |
1.90 % |
| qd2,mq40 |
47634 |
0.03 % |
38288 |
0.03 % |
9346 |
0.07 % |
| qd2,fs60,mq40 |
495 |
0.00 % |
0 |
0.00 % |
495 |
0.00 % |
| qd2,fs60 |
240 |
0.00 % |
0 |
0.00 % |
240 |
0.00 % |
| fs60,mq40 |
240 |
0.00 % |
0 |
0.00 % |
240 |
0.00 % |
| fs60 |
127 |
0.00 % |
0 |
0.00 % |
127 |
0.00 % |
| q20,qd2,fs60,mq40 |
47 |
0.00 % |
0 |
0.00 % |
47 |
0.00 % |
| q20,qd2,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
7843819 |
36.05 % |
| Transition |
G>A |
All |
983551 |
4.52 % |
| Transition |
T>C |
All |
7829436 |
35.99 % |
| Transition |
C>T |
All |
991932 |
4.56 % |
| Transversion |
A>C |
All |
331230 |
1.52 % |
| Transversion |
C>A |
All |
972671 |
4.47 % |
| Transversion |
T>G |
All |
331761 |
1.52 % |
| Transversion |
G>T |
All |
806438 |
3.71 % |
| Transversion |
A>T |
All |
527658 |
2.43 % |
| Transversion |
T>A |
All |
540734 |
2.49 % |
| Transversion |
C>G |
All |
301269 |
1.38 % |
| Transversion |
G>C |
All |
296045 |
1.36 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
858963 |
18.94 % |
| Transition |
G>A |
Passed |
603565 |
13.31 % |
| Transition |
T>C |
Passed |
825816 |
18.21 % |
| Transition |
C>T |
Passed |
601962 |
13.27 % |
| Transversion |
A>C |
Passed |
174067 |
3.84 % |
| Transversion |
C>A |
Passed |
351354 |
7.75 % |
| Transversion |
T>G |
Passed |
175615 |
3.87 % |
| Transversion |
G>T |
Passed |
283416 |
6.25 % |
| Transversion |
A>T |
Passed |
160978 |
3.55 % |
| Transversion |
T>A |
Passed |
167341 |
3.69 % |
| Transversion |
C>G |
Passed |
166578 |
3.67 % |
| Transversion |
G>C |
Passed |
165803 |
3.66 % |
| |
|
|
|
|
| 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 |
4.30 |
17648738 |
4107806 |
| Passed |
1.76 |
2890306 |
1645152 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |