/EXTERNAL BLUEPRINT/variants/K010490_K010491_2_lane_gembs
BACK
SAMPLE K010490_K010491_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1049324763 |
421593925 |
40.18 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1049324763 |
100% |
1033811563 |
98.52 % |
15513200 |
1.48 % |
| |
|
|
|
|
|
|
| Passed |
423764134 |
40.38 % |
420699823 |
40.69 % |
3064311 |
0.72 % |
| Filtered |
625560629 |
59.62 % |
613111740 |
59.31 % |
12448889 |
2.94 % |
| |
|
|
|
|
|
|
| q20 |
517151990 |
82.67 % |
514221299 |
83.87 % |
2930691 |
23.54 % |
| q20,qd2 |
59826516 |
9.56 % |
50834734 |
8.29 % |
8991782 |
72.23 % |
| qd2 |
24493116 |
3.92 % |
24379044 |
3.98 % |
114072 |
0.92 % |
| q20,mq40 |
15019508 |
2.40 % |
14932491 |
2.44 % |
87017 |
0.70 % |
| mq40 |
5356148 |
0.86 % |
5203154 |
0.85 % |
152994 |
1.23 % |
| q20,qd2,mq40 |
3571041 |
0.57 % |
3435142 |
0.56 % |
135899 |
1.09 % |
| qd2,mq40 |
121144 |
0.02 % |
105876 |
0.02 % |
15268 |
0.12 % |
| qd2,fs60 |
7980 |
0.00 % |
0 |
0.00 % |
7980 |
0.06 % |
| q20,qd2,fs60 |
5808 |
0.00 % |
0 |
0.00 % |
5808 |
0.05 % |
| qd2,fs60,mq40 |
3203 |
0.00 % |
0 |
0.00 % |
3203 |
0.03 % |
| fs60 |
2144 |
0.00 % |
0 |
0.00 % |
2144 |
0.02 % |
| q20,qd2,fs60,mq40 |
1159 |
0.00 % |
0 |
0.00 % |
1159 |
0.01 % |
| fs60,mq40 |
867 |
0.00 % |
0 |
0.00 % |
867 |
0.01 % |
| q20,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
3465192 |
12.42 % |
| Transition |
G>A |
All |
9304652 |
33.36 % |
| Transition |
T>C |
All |
3015111 |
10.81 % |
| Transition |
C>T |
All |
9197123 |
32.97 % |
| Transversion |
A>C |
All |
260759 |
0.93 % |
| Transversion |
C>A |
All |
498368 |
1.79 % |
| Transversion |
T>G |
All |
303264 |
1.09 % |
| Transversion |
G>T |
All |
470486 |
1.69 % |
| Transversion |
A>T |
All |
446326 |
1.60 % |
| Transversion |
T>A |
All |
468468 |
1.68 % |
| Transversion |
C>G |
All |
242120 |
0.87 % |
| Transversion |
G>C |
All |
220561 |
0.79 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
254639 |
19.77 % |
| Transition |
G>A |
Passed |
220220 |
17.09 % |
| Transition |
T>C |
Passed |
252616 |
19.61 % |
| Transition |
C>T |
Passed |
219235 |
17.02 % |
| Transversion |
A>C |
Passed |
45360 |
3.52 % |
| Transversion |
C>A |
Passed |
39547 |
3.07 % |
| Transversion |
T>G |
Passed |
45064 |
3.50 % |
| Transversion |
G>T |
Passed |
40074 |
3.11 % |
| Transversion |
A>T |
Passed |
24831 |
1.93 % |
| Transversion |
T>A |
Passed |
24313 |
1.89 % |
| Transversion |
C>G |
Passed |
61113 |
4.74 % |
| Transversion |
G>C |
Passed |
61210 |
4.75 % |
| |
|
|
|
|
| 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 |
8.58 |
24982078 |
2910352 |
| Passed |
2.77 |
946710 |
341512 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |