/EXTERNAL KNIH/variants/K006236_1_lane_gembs
BACK
SAMPLE K006236_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1199019120 |
829172779 |
69.15 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1199019120 |
100% |
1140198098 |
95.09 % |
58821022 |
4.91 % |
| |
|
|
|
|
|
|
| Passed |
838797253 |
69.96 % |
818776249 |
71.81 % |
20021004 |
2.39 % |
| Filtered |
360221867 |
30.04 % |
321421849 |
28.19 % |
38800018 |
4.63 % |
| |
|
|
|
|
|
|
| q20 |
298919837 |
82.98 % |
287431143 |
89.42 % |
11488694 |
29.61 % |
| q20,qd2 |
40394581 |
11.21 % |
15706304 |
4.89 % |
24688277 |
63.63 % |
| qd2 |
13004600 |
3.61 % |
10869083 |
3.38 % |
2135517 |
5.50 % |
| q20,mq40 |
5024406 |
1.39 % |
4861456 |
1.51 % |
162950 |
0.42 % |
| q20,qd2,mq40 |
2108042 |
0.59 % |
1993475 |
0.62 % |
114567 |
0.30 % |
| mq40 |
733129 |
0.20 % |
539602 |
0.17 % |
193527 |
0.50 % |
| qd2,mq40 |
27578 |
0.01 % |
20786 |
0.01 % |
6792 |
0.02 % |
| fs60 |
5444 |
0.00 % |
0 |
0.00 % |
5444 |
0.01 % |
| q20,qd2,fs60 |
2821 |
0.00 % |
0 |
0.00 % |
2821 |
0.01 % |
| qd2,fs60 |
907 |
0.00 % |
0 |
0.00 % |
907 |
0.00 % |
| fs60,mq40 |
186 |
0.00 % |
0 |
0.00 % |
186 |
0.00 % |
| q20,fs60 |
154 |
0.00 % |
0 |
0.00 % |
154 |
0.00 % |
| qd2,fs60,mq40 |
144 |
0.00 % |
0 |
0.00 % |
144 |
0.00 % |
| q20,qd2,fs60,mq40 |
38 |
0.00 % |
0 |
0.00 % |
38 |
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 |
19849766 |
32.50 % |
| Transition |
G>A |
All |
4593683 |
7.52 % |
| Transition |
T>C |
All |
23274667 |
38.10 % |
| Transition |
C>T |
All |
3274812 |
5.36 % |
| Transversion |
A>C |
All |
1128125 |
1.85 % |
| Transversion |
C>A |
All |
1651577 |
2.70 % |
| Transversion |
T>G |
All |
1237142 |
2.03 % |
| Transversion |
G>T |
All |
1561557 |
2.56 % |
| Transversion |
A>T |
All |
1406957 |
2.30 % |
| Transversion |
T>A |
All |
1557568 |
2.55 % |
| Transversion |
C>G |
All |
782815 |
1.28 % |
| Transversion |
G>C |
All |
766621 |
1.26 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2734578 |
24.17 % |
| Transition |
G>A |
Passed |
994441 |
8.79 % |
| Transition |
T>C |
Passed |
4995647 |
44.15 % |
| Transition |
C>T |
Passed |
741128 |
6.55 % |
| Transversion |
A>C |
Passed |
231403 |
2.05 % |
| Transversion |
C>A |
Passed |
277693 |
2.45 % |
| Transversion |
T>G |
Passed |
250712 |
2.22 % |
| Transversion |
G>T |
Passed |
224420 |
1.98 % |
| Transversion |
A>T |
Passed |
179816 |
1.59 % |
| Transversion |
T>A |
Passed |
232586 |
2.06 % |
| Transversion |
C>G |
Passed |
228093 |
2.02 % |
| Transversion |
G>C |
Passed |
224876 |
1.99 % |
| |
|
|
|
|
| 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 |
5.05 |
50992928 |
10092362 |
| Passed |
5.12 |
9465794 |
1849599 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |