/EXTERNAL DEEP/variants/K006109_K006110_K006111_K006112_K006113_K006114_6_lane_gembs
BACK
SAMPLE K006109_K006110_K006111_K006112_K006113_K006114_6_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1174209919 |
791719878 |
67.43 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1174209919 |
100% |
1136661247 |
96.80 % |
37548672 |
3.20 % |
| |
|
|
|
|
|
|
| Passed |
796570860 |
67.84 % |
785759891 |
69.13 % |
10810969 |
1.36 % |
| Filtered |
377639059 |
32.16 % |
350901356 |
30.87 % |
26737703 |
3.36 % |
| |
|
|
|
|
|
|
| q20 |
321470243 |
85.13 % |
315146580 |
89.81 % |
6323663 |
23.65 % |
| q20,qd2 |
31438427 |
8.32 % |
12455447 |
3.55 % |
18982980 |
71.00 % |
| q20,mq40 |
13766636 |
3.65 % |
13468348 |
3.84 % |
298288 |
1.12 % |
| qd2 |
5447039 |
1.44 % |
4964162 |
1.41 % |
482877 |
1.81 % |
| q20,qd2,mq40 |
3714597 |
0.98 % |
3428317 |
0.98 % |
286280 |
1.07 % |
| mq40 |
1749605 |
0.46 % |
1396655 |
0.40 % |
352950 |
1.32 % |
| qd2,mq40 |
50633 |
0.01 % |
41847 |
0.01 % |
8786 |
0.03 % |
| qd2,fs60,mq40 |
730 |
0.00 % |
0 |
0.00 % |
730 |
0.00 % |
| qd2,fs60 |
346 |
0.00 % |
0 |
0.00 % |
346 |
0.00 % |
| fs60,mq40 |
279 |
0.00 % |
0 |
0.00 % |
279 |
0.00 % |
| fs60 |
241 |
0.00 % |
0 |
0.00 % |
241 |
0.00 % |
| q20,qd2,fs60 |
141 |
0.00 % |
0 |
0.00 % |
141 |
0.00 % |
| q20,qd2,fs60,mq40 |
138 |
0.00 % |
0 |
0.00 % |
138 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
12754190 |
32.84 % |
| Transition |
G>A |
All |
2659258 |
6.85 % |
| Transition |
T>C |
All |
13469942 |
34.68 % |
| Transition |
C>T |
All |
2161977 |
5.57 % |
| Transversion |
A>C |
All |
578138 |
1.49 % |
| Transversion |
C>A |
All |
1690084 |
4.35 % |
| Transversion |
T>G |
All |
647408 |
1.67 % |
| Transversion |
G>T |
All |
1651689 |
4.25 % |
| Transversion |
A>T |
All |
916558 |
2.36 % |
| Transversion |
T>A |
All |
996065 |
2.56 % |
| Transversion |
C>G |
All |
665217 |
1.71 % |
| Transversion |
G>C |
All |
648190 |
1.67 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1391212 |
21.81 % |
| Transition |
G>A |
Passed |
770359 |
12.08 % |
| Transition |
T>C |
Passed |
1690119 |
26.50 % |
| Transition |
C>T |
Passed |
672336 |
10.54 % |
| Transversion |
A>C |
Passed |
211928 |
3.32 % |
| Transversion |
C>A |
Passed |
293309 |
4.60 % |
| Transversion |
T>G |
Passed |
228441 |
3.58 % |
| Transversion |
G>T |
Passed |
263617 |
4.13 % |
| Transversion |
A>T |
Passed |
179375 |
2.81 % |
| Transversion |
T>A |
Passed |
210609 |
3.30 % |
| Transversion |
C>G |
Passed |
233845 |
3.67 % |
| Transversion |
G>C |
Passed |
232713 |
3.65 % |
| |
|
|
|
|
| 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 |
3.98 |
31045367 |
7793349 |
| Passed |
2.44 |
4524026 |
1853837 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |