/EXTERNAL Roadmap/variants/K006513_K006514_K006515_3_lane_gembs
BACK
SAMPLE K006513_K006514_K006515_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1155907027 |
1069872645 |
92.56 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1155907027 |
100% |
1148718076 |
99.38 % |
7188951 |
0.62 % |
| |
|
|
|
|
|
|
| Passed |
1070054547 |
92.57 % |
1067109423 |
92.90 % |
2945124 |
0.28 % |
| Filtered |
85852480 |
7.43 % |
81608653 |
7.10 % |
4243827 |
0.40 % |
| |
|
|
|
|
|
|
| mq40 |
42791804 |
49.84 % |
42242009 |
51.76 % |
549795 |
12.96 % |
| q20,mq40 |
18821833 |
21.92 % |
18601031 |
22.79 % |
220802 |
5.20 % |
| q20 |
16809301 |
19.58 % |
16539485 |
20.27 % |
269816 |
6.36 % |
| q20,qd2 |
2940304 |
3.42 % |
760324 |
0.93 % |
2179980 |
51.37 % |
| q20,qd2,mq40 |
2403248 |
2.80 % |
1802159 |
2.21 % |
601089 |
14.16 % |
| qd2 |
1750164 |
2.04 % |
1467777 |
1.80 % |
282387 |
6.65 % |
| qd2,mq40 |
249717 |
0.29 % |
195868 |
0.24 % |
53849 |
1.27 % |
| q20,qd2,fs60 |
38929 |
0.05 % |
0 |
0.00 % |
38929 |
0.92 % |
| fs60 |
25566 |
0.03 % |
0 |
0.00 % |
25566 |
0.60 % |
| q20,fs60 |
10866 |
0.01 % |
0 |
0.00 % |
10866 |
0.26 % |
| fs60,mq40 |
7358 |
0.01 % |
0 |
0.00 % |
7358 |
0.17 % |
| qd2,fs60 |
2073 |
0.00 % |
0 |
0.00 % |
2073 |
0.05 % |
| q20,qd2,fs60,mq40 |
810 |
0.00 % |
0 |
0.00 % |
810 |
0.02 % |
| qd2,fs60,mq40 |
353 |
0.00 % |
0 |
0.00 % |
353 |
0.01 % |
| q20,fs60,mq40 |
154 |
0.00 % |
0 |
0.00 % |
154 |
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 |
2214033 |
25.40 % |
| Transition |
G>A |
All |
939334 |
10.78 % |
| Transition |
T>C |
All |
2228584 |
25.57 % |
| Transition |
C>T |
All |
955837 |
10.97 % |
| Transversion |
A>C |
All |
228195 |
2.62 % |
| Transversion |
C>A |
All |
391732 |
4.49 % |
| Transversion |
T>G |
All |
229600 |
2.63 % |
| Transversion |
G>T |
All |
395637 |
4.54 % |
| Transversion |
A>T |
All |
353826 |
4.06 % |
| Transversion |
T>A |
All |
343139 |
3.94 % |
| Transversion |
C>G |
All |
216415 |
2.48 % |
| Transversion |
G>C |
All |
220193 |
2.53 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
727661 |
18.22 % |
| Transition |
G>A |
Passed |
630973 |
15.80 % |
| Transition |
T>C |
Passed |
744433 |
18.64 % |
| Transition |
C>T |
Passed |
641762 |
16.07 % |
| Transversion |
A>C |
Passed |
161680 |
4.05 % |
| Transversion |
C>A |
Passed |
158601 |
3.97 % |
| Transversion |
T>G |
Passed |
161653 |
4.05 % |
| Transversion |
G>T |
Passed |
160077 |
4.01 % |
| Transversion |
A>T |
Passed |
144515 |
3.62 % |
| Transversion |
T>A |
Passed |
143703 |
3.60 % |
| Transversion |
C>G |
Passed |
158229 |
3.96 % |
| Transversion |
G>C |
Passed |
160003 |
4.01 % |
| |
|
|
|
|
| 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 |
2.66 |
6337788 |
2378737 |
| Passed |
2.20 |
2744829 |
1248461 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |