/EXTERNAL Roadmap/variants/K006493_K006494_K006495_K006496_4_lane_gembs
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SAMPLE K006493_K006494_K006495_K006496_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157653257 |
1084491334 |
93.68 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157653257 |
100% |
1149532904 |
99.30 % |
8120353 |
0.70 % |
| |
|
|
|
|
|
|
| Passed |
1084557052 |
93.69 % |
1079774875 |
93.93 % |
4782177 |
0.44 % |
| Filtered |
73096205 |
6.31 % |
69758029 |
6.07 % |
3338176 |
0.31 % |
| |
|
|
|
|
|
|
| mq40 |
48608792 |
66.50 % |
48030083 |
68.85 % |
578709 |
17.34 % |
| q20,mq40 |
13442671 |
18.39 % |
13245667 |
18.99 % |
197004 |
5.90 % |
| q20 |
5155033 |
7.05 % |
5033464 |
7.22 % |
121569 |
3.64 % |
| q20,qd2,mq40 |
2195361 |
3.00 % |
1579621 |
2.26 % |
615740 |
18.45 % |
| q20,qd2 |
1476799 |
2.02 % |
532493 |
0.76 % |
944306 |
28.29 % |
| qd2 |
1402822 |
1.92 % |
990334 |
1.42 % |
412488 |
12.36 % |
| qd2,mq40 |
447249 |
0.61 % |
346367 |
0.50 % |
100882 |
3.02 % |
| fs60 |
187641 |
0.26 % |
0 |
0.00 % |
187641 |
5.62 % |
| q20,qd2,fs60 |
108429 |
0.15 % |
0 |
0.00 % |
108429 |
3.25 % |
| fs60,mq40 |
30587 |
0.04 % |
0 |
0.00 % |
30587 |
0.92 % |
| qd2,fs60 |
16707 |
0.02 % |
0 |
0.00 % |
16707 |
0.50 % |
| q20,fs60 |
15718 |
0.02 % |
0 |
0.00 % |
15718 |
0.47 % |
| qd2,fs60,mq40 |
5149 |
0.01 % |
0 |
0.00 % |
5149 |
0.15 % |
| q20,qd2,fs60,mq40 |
2987 |
0.00 % |
0 |
0.00 % |
2987 |
0.09 % |
| q20,fs60,mq40 |
260 |
0.00 % |
0 |
0.00 % |
260 |
0.01 % |
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 |
1787016 |
19.95 % |
| Transition |
G>A |
All |
1296156 |
14.47 % |
| Transition |
T>C |
All |
1787396 |
19.96 % |
| Transition |
C>T |
All |
1302319 |
14.54 % |
| Transversion |
A>C |
All |
293694 |
3.28 % |
| Transversion |
C>A |
All |
420059 |
4.69 % |
| Transversion |
T>G |
All |
296199 |
3.31 % |
| Transversion |
G>T |
All |
425874 |
4.76 % |
| Transversion |
A>T |
All |
388035 |
4.33 % |
| Transversion |
T>A |
All |
378034 |
4.22 % |
| Transversion |
C>G |
All |
288889 |
3.23 % |
| Transversion |
G>C |
All |
291640 |
3.26 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
902832 |
16.81 % |
| Transition |
G>A |
Passed |
876541 |
16.32 % |
| Transition |
T>C |
Passed |
919226 |
17.12 % |
| Transition |
C>T |
Passed |
894614 |
16.66 % |
| Transversion |
A>C |
Passed |
225913 |
4.21 % |
| Transversion |
C>A |
Passed |
231005 |
4.30 % |
| Transversion |
T>G |
Passed |
223746 |
4.17 % |
| Transversion |
G>T |
Passed |
229386 |
4.27 % |
| Transversion |
A>T |
Passed |
205456 |
3.83 % |
| Transversion |
T>A |
Passed |
204203 |
3.80 % |
| Transversion |
C>G |
Passed |
227985 |
4.24 % |
| Transversion |
G>C |
Passed |
229889 |
4.28 % |
| |
|
|
|
|
| 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 |
2.22 |
6172887 |
2782424 |
| Passed |
2.02 |
3593213 |
1777583 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |