/EXTERNAL DEEP/variants/K006081_K006082_K006083_3_lane_gembs
BACK
SAMPLE K006081_K006082_K006083_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1169477953 |
886591609 |
75.81 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1169477953 |
100% |
1141985786 |
97.65 % |
27492167 |
2.35 % |
| |
|
|
|
|
|
|
| Passed |
890006194 |
76.10 % |
882560581 |
77.28 % |
7445613 |
0.84 % |
| Filtered |
279471759 |
23.90 % |
259425205 |
22.72 % |
20046554 |
2.25 % |
| |
|
|
|
|
|
|
| q20 |
238864763 |
85.47 % |
234386014 |
90.35 % |
4478749 |
22.34 % |
| q20,qd2 |
23782553 |
8.51 % |
9055858 |
3.49 % |
14726695 |
73.46 % |
| q20,mq40 |
8846029 |
3.17 % |
8714030 |
3.36 % |
131999 |
0.66 % |
| qd2 |
4123494 |
1.48 % |
3747649 |
1.44 % |
375845 |
1.87 % |
| q20,qd2,mq40 |
2726859 |
0.98 % |
2603949 |
1.00 % |
122910 |
0.61 % |
| mq40 |
1092496 |
0.39 % |
891109 |
0.34 % |
201387 |
1.00 % |
| qd2,mq40 |
34018 |
0.01 % |
26596 |
0.01 % |
7422 |
0.04 % |
| qd2,fs60,mq40 |
623 |
0.00 % |
0 |
0.00 % |
623 |
0.00 % |
| qd2,fs60 |
330 |
0.00 % |
0 |
0.00 % |
330 |
0.00 % |
| fs60,mq40 |
260 |
0.00 % |
0 |
0.00 % |
260 |
0.00 % |
| fs60 |
232 |
0.00 % |
0 |
0.00 % |
232 |
0.00 % |
| q20,qd2,fs60 |
51 |
0.00 % |
0 |
0.00 % |
51 |
0.00 % |
| q20,qd2,fs60,mq40 |
51 |
0.00 % |
0 |
0.00 % |
51 |
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 |
9405850 |
32.11 % |
| Transition |
G>A |
All |
2373402 |
8.10 % |
| Transition |
T>C |
All |
11207090 |
38.26 % |
| Transition |
C>T |
All |
1692208 |
5.78 % |
| Transversion |
A>C |
All |
327852 |
1.12 % |
| Transversion |
C>A |
All |
925413 |
3.16 % |
| Transversion |
T>G |
All |
397241 |
1.36 % |
| Transversion |
G>T |
All |
870099 |
2.97 % |
| Transversion |
A>T |
All |
639341 |
2.18 % |
| Transversion |
T>A |
All |
714383 |
2.44 % |
| Transversion |
C>G |
All |
375236 |
1.28 % |
| Transversion |
G>C |
All |
364548 |
1.24 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
973436 |
19.33 % |
| Transition |
G>A |
Passed |
634005 |
12.59 % |
| Transition |
T>C |
Passed |
1586092 |
31.49 % |
| Transition |
C>T |
Passed |
566098 |
11.24 % |
| Transversion |
A>C |
Passed |
152761 |
3.03 % |
| Transversion |
C>A |
Passed |
182012 |
3.61 % |
| Transversion |
T>G |
Passed |
166786 |
3.31 % |
| Transversion |
G>T |
Passed |
165520 |
3.29 % |
| Transversion |
A>T |
Passed |
139053 |
2.76 % |
| Transversion |
T>A |
Passed |
156963 |
3.12 % |
| Transversion |
C>G |
Passed |
158205 |
3.14 % |
| Transversion |
G>C |
Passed |
156153 |
3.10 % |
| |
|
|
|
|
| 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 |
5.35 |
24678550 |
4614113 |
| Passed |
2.94 |
3759631 |
1277453 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |