/EXTERNAL BLUEPRINT/variants/K006416_14_lane_gembs
BACK
SAMPLE K006416_14_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156992229 |
1041598435 |
90.03 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156992229 |
100% |
1144878557 |
98.95 % |
12113672 |
1.05 % |
| |
|
|
|
|
|
|
| Passed |
1042504005 |
90.10 % |
1039210827 |
90.77 % |
3293178 |
0.32 % |
| Filtered |
114488224 |
9.90 % |
105667730 |
9.23 % |
8820494 |
0.85 % |
| |
|
|
|
|
|
|
| q20 |
79917304 |
69.80 % |
79182123 |
74.94 % |
735181 |
8.33 % |
| q20,mq40 |
12845595 |
11.22 % |
12733407 |
12.05 % |
112188 |
1.27 % |
| q20,qd2 |
12346900 |
10.78 % |
4911176 |
4.65 % |
7435724 |
84.30 % |
| mq40 |
3737692 |
3.26 % |
3541088 |
3.35 % |
196604 |
2.23 % |
| q20,qd2,mq40 |
3142166 |
2.74 % |
2948281 |
2.79 % |
193885 |
2.20 % |
| qd2 |
2450144 |
2.14 % |
2312640 |
2.19 % |
137504 |
1.56 % |
| qd2,mq40 |
47125 |
0.04 % |
39015 |
0.04 % |
8110 |
0.09 % |
| qd2,fs60,mq40 |
598 |
0.00 % |
0 |
0.00 % |
598 |
0.01 % |
| fs60,mq40 |
327 |
0.00 % |
0 |
0.00 % |
327 |
0.00 % |
| fs60 |
136 |
0.00 % |
0 |
0.00 % |
136 |
0.00 % |
| qd2,fs60 |
133 |
0.00 % |
0 |
0.00 % |
133 |
0.00 % |
| q20,qd2,fs60,mq40 |
73 |
0.00 % |
0 |
0.00 % |
73 |
0.00 % |
| q20,qd2,fs60 |
31 |
0.00 % |
0 |
0.00 % |
31 |
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 |
4463464 |
32.09 % |
| Transition |
G>A |
All |
954929 |
6.87 % |
| Transition |
T>C |
All |
4424482 |
31.81 % |
| Transition |
C>T |
All |
959355 |
6.90 % |
| Transversion |
A>C |
All |
227327 |
1.63 % |
| Transversion |
C>A |
All |
656813 |
4.72 % |
| Transversion |
T>G |
All |
229169 |
1.65 % |
| Transversion |
G>T |
All |
647808 |
4.66 % |
| Transversion |
A>T |
All |
461256 |
3.32 % |
| Transversion |
T>A |
All |
461606 |
3.32 % |
| Transversion |
C>G |
All |
210211 |
1.51 % |
| Transversion |
G>C |
All |
211288 |
1.52 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
640244 |
17.42 % |
| Transition |
G>A |
Passed |
589681 |
16.04 % |
| Transition |
T>C |
Passed |
641977 |
17.47 % |
| Transition |
C>T |
Passed |
593851 |
16.16 % |
| Transversion |
A>C |
Passed |
154562 |
4.20 % |
| Transversion |
C>A |
Passed |
160007 |
4.35 % |
| Transversion |
T>G |
Passed |
155243 |
4.22 % |
| Transversion |
G>T |
Passed |
160304 |
4.36 % |
| Transversion |
A>T |
Passed |
136697 |
3.72 % |
| Transversion |
T>A |
Passed |
136614 |
3.72 % |
| Transversion |
C>G |
Passed |
152963 |
4.16 % |
| Transversion |
G>C |
Passed |
153567 |
4.18 % |
| |
|
|
|
|
| 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 |
3.48 |
10802230 |
3105478 |
| Passed |
2.04 |
2465753 |
1209957 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |