/EXTERNAL DEEP/variants/K006063_K006064_K006065_K006066_4_lane_gembs
BACK
SAMPLE K006063_K006064_K006065_K006066_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1166762963 |
986701843 |
84.57 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1166762963 |
100% |
1145720061 |
98.20 % |
21042902 |
1.80 % |
| |
|
|
|
|
|
|
| Passed |
988851818 |
84.75 % |
982985322 |
85.80 % |
5866496 |
0.59 % |
| Filtered |
177911145 |
15.25 % |
162734739 |
14.20 % |
15176406 |
1.53 % |
| |
|
|
|
|
|
|
| q20 |
142209516 |
79.93 % |
139653766 |
85.82 % |
2555750 |
16.84 % |
| q20,qd2 |
18541548 |
10.42 % |
6924793 |
4.26 % |
11616755 |
76.54 % |
| q20,mq40 |
8939406 |
5.02 % |
8805458 |
5.41 % |
133948 |
0.88 % |
| qd2 |
4058487 |
2.28 % |
3567629 |
2.19 % |
490858 |
3.23 % |
| q20,qd2,mq40 |
2661832 |
1.50 % |
2522392 |
1.55 % |
139440 |
0.92 % |
| mq40 |
1456272 |
0.82 % |
1227686 |
0.75 % |
228586 |
1.51 % |
| qd2,mq40 |
41925 |
0.02 % |
33015 |
0.02 % |
8910 |
0.06 % |
| qd2,fs60,mq40 |
863 |
0.00 % |
0 |
0.00 % |
863 |
0.01 % |
| qd2,fs60 |
483 |
0.00 % |
0 |
0.00 % |
483 |
0.00 % |
| fs60 |
330 |
0.00 % |
0 |
0.00 % |
330 |
0.00 % |
| fs60,mq40 |
328 |
0.00 % |
0 |
0.00 % |
328 |
0.00 % |
| q20,qd2,fs60 |
86 |
0.00 % |
0 |
0.00 % |
86 |
0.00 % |
| q20,qd2,fs60,mq40 |
69 |
0.00 % |
0 |
0.00 % |
69 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
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 |
7351074 |
32.17 % |
| Transition |
G>A |
All |
1963165 |
8.59 % |
| Transition |
T>C |
All |
8463403 |
37.04 % |
| Transition |
C>T |
All |
1410632 |
6.17 % |
| Transversion |
A>C |
All |
275771 |
1.21 % |
| Transversion |
C>A |
All |
709733 |
3.11 % |
| Transversion |
T>G |
All |
332250 |
1.45 % |
| Transversion |
G>T |
All |
659918 |
2.89 % |
| Transversion |
A>T |
All |
504518 |
2.21 % |
| Transversion |
T>A |
All |
560407 |
2.45 % |
| Transversion |
C>G |
All |
315139 |
1.38 % |
| Transversion |
G>C |
All |
302808 |
1.33 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
950335 |
19.50 % |
| Transition |
G>A |
Passed |
675494 |
13.86 % |
| Transition |
T>C |
Passed |
1319792 |
27.08 % |
| Transition |
C>T |
Passed |
609414 |
12.51 % |
| Transversion |
A>C |
Passed |
157314 |
3.23 % |
| Transversion |
C>A |
Passed |
187680 |
3.85 % |
| Transversion |
T>G |
Passed |
168661 |
3.46 % |
| Transversion |
G>T |
Passed |
170291 |
3.49 % |
| Transversion |
A>T |
Passed |
146897 |
3.01 % |
| Transversion |
T>A |
Passed |
162236 |
3.33 % |
| Transversion |
C>G |
Passed |
163688 |
3.36 % |
| Transversion |
G>C |
Passed |
160998 |
3.30 % |
| |
|
|
|
|
| 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 |
5.24 |
19188274 |
3660544 |
| Passed |
2.70 |
3555035 |
1317765 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |