/EXTERNAL Roadmap/variants/K006507_K006508_K006509_K006510_K006511_K006512_6_lane_gembs
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SAMPLE K006507_K006508_K006509_K006510_K006511_K006512_6_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1158323471 |
854526602 |
73.77 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1158323471 |
100% |
1137435232 |
98.20 % |
20888239 |
1.80 % |
| |
|
|
|
|
|
|
| Passed |
856349427 |
73.93 % |
851562583 |
74.87 % |
4786844 |
0.56 % |
| Filtered |
301974044 |
26.07 % |
285872649 |
25.13 % |
16101395 |
1.88 % |
| |
|
|
|
|
|
|
| q20 |
174989846 |
57.95 % |
170552582 |
59.66 % |
4437264 |
27.56 % |
| mq40 |
62305184 |
20.63 % |
61155280 |
21.39 % |
1149904 |
7.14 % |
| q20,mq40 |
42526013 |
14.08 % |
41491335 |
14.51 % |
1034678 |
6.43 % |
| q20,qd2 |
11968863 |
3.96 % |
4341840 |
1.52 % |
7627023 |
47.37 % |
| q20,qd2,mq40 |
5525237 |
1.83 % |
4145571 |
1.45 % |
1379666 |
8.57 % |
| qd2 |
4051584 |
1.34 % |
3694754 |
1.29 % |
356830 |
2.22 % |
| qd2,mq40 |
580791 |
0.19 % |
491287 |
0.17 % |
89504 |
0.56 % |
| fs60,mq40 |
11415 |
0.00 % |
0 |
0.00 % |
11415 |
0.07 % |
| fs60 |
11248 |
0.00 % |
0 |
0.00 % |
11248 |
0.07 % |
| qd2,fs60 |
1908 |
0.00 % |
0 |
0.00 % |
1908 |
0.01 % |
| q20,qd2,fs60 |
820 |
0.00 % |
0 |
0.00 % |
820 |
0.01 % |
| qd2,fs60,mq40 |
474 |
0.00 % |
0 |
0.00 % |
474 |
0.00 % |
| q20,qd2,fs60,mq40 |
340 |
0.00 % |
0 |
0.00 % |
340 |
0.00 % |
| q20,fs60 |
221 |
0.00 % |
0 |
0.00 % |
221 |
0.00 % |
| q20,fs60,mq40 |
100 |
0.00 % |
0 |
0.00 % |
100 |
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 |
7293122 |
32.01 % |
| Transition |
G>A |
All |
1301586 |
5.71 % |
| Transition |
T>C |
All |
7396856 |
32.46 % |
| Transition |
C>T |
All |
1242506 |
5.45 % |
| Transversion |
A>C |
All |
912741 |
4.01 % |
| Transversion |
C>A |
All |
494281 |
2.17 % |
| Transversion |
T>G |
All |
1087669 |
4.77 % |
| Transversion |
G>T |
All |
503601 |
2.21 % |
| Transversion |
A>T |
All |
645900 |
2.83 % |
| Transversion |
T>A |
All |
616930 |
2.71 % |
| Transversion |
C>G |
All |
689465 |
3.03 % |
| Transversion |
G>C |
All |
599626 |
2.63 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
693963 |
18.12 % |
| Transition |
G>A |
Passed |
432056 |
11.28 % |
| Transition |
T>C |
Passed |
718910 |
18.78 % |
| Transition |
C>T |
Passed |
440218 |
11.50 % |
| Transversion |
A>C |
Passed |
297761 |
7.78 % |
| Transversion |
C>A |
Passed |
109194 |
2.85 % |
| Transversion |
T>G |
Passed |
363048 |
9.48 % |
| Transversion |
G>T |
Passed |
110254 |
2.88 % |
| Transversion |
A>T |
Passed |
94106 |
2.46 % |
| Transversion |
T>A |
Passed |
94000 |
2.45 % |
| Transversion |
C>G |
Passed |
252590 |
6.60 % |
| Transversion |
G>C |
Passed |
222858 |
5.82 % |
| |
|
|
|
|
| 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 |
3.11 |
17234070 |
5550213 |
| Passed |
1.48 |
2285147 |
1543811 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |