/EXTERNAL BLUEPRINT/variants/K006335_6_lane_gembs
BACK
SAMPLE K006335_6_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1155983393 |
910611334 |
78.77 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1155983393 |
100% |
1141411922 |
98.74 % |
14571471 |
1.26 % |
| |
|
|
|
|
|
|
| Passed |
912272292 |
78.92 % |
907348047 |
79.49 % |
4924245 |
0.54 % |
| Filtered |
243711101 |
21.08 % |
234063875 |
20.51 % |
9647226 |
1.06 % |
| |
|
|
|
|
|
|
| q20 |
196615456 |
80.68 % |
195237443 |
83.41 % |
1378013 |
14.28 % |
| q20,qd2 |
17983242 |
7.38 % |
10782863 |
4.61 % |
7200379 |
74.64 % |
| q20,mq40 |
12924985 |
5.30 % |
12793263 |
5.47 % |
131722 |
1.37 % |
| mq40 |
8719993 |
3.58 % |
8472804 |
3.62 % |
247189 |
2.56 % |
| qd2 |
4547475 |
1.87 % |
4148526 |
1.77 % |
398949 |
4.14 % |
| q20,qd2,mq40 |
2794792 |
1.15 % |
2527147 |
1.08 % |
267645 |
2.77 % |
| qd2,mq40 |
118577 |
0.05 % |
101829 |
0.04 % |
16748 |
0.17 % |
| q20,qd2,fs60 |
2730 |
0.00 % |
0 |
0.00 % |
2730 |
0.03 % |
| qd2,fs60,mq40 |
1304 |
0.00 % |
0 |
0.00 % |
1304 |
0.01 % |
| fs60 |
946 |
0.00 % |
0 |
0.00 % |
946 |
0.01 % |
| qd2,fs60 |
727 |
0.00 % |
0 |
0.00 % |
727 |
0.01 % |
| fs60,mq40 |
574 |
0.00 % |
0 |
0.00 % |
574 |
0.01 % |
| q20,qd2,fs60,mq40 |
294 |
0.00 % |
0 |
0.00 % |
294 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
3738630 |
23.86 % |
| Transition |
G>A |
All |
2496333 |
15.93 % |
| Transition |
T>C |
All |
3614727 |
23.07 % |
| Transition |
C>T |
All |
2434210 |
15.54 % |
| Transversion |
A>C |
All |
279902 |
1.79 % |
| Transversion |
C>A |
All |
694494 |
4.43 % |
| Transversion |
T>G |
All |
286809 |
1.83 % |
| Transversion |
G>T |
All |
694064 |
4.43 % |
| Transversion |
A>T |
All |
456792 |
2.92 % |
| Transversion |
T>A |
All |
451658 |
2.88 % |
| Transversion |
C>G |
All |
262054 |
1.67 % |
| Transversion |
G>C |
All |
258528 |
1.65 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
631081 |
17.38 % |
| Transition |
G>A |
Passed |
605406 |
16.67 % |
| Transition |
T>C |
Passed |
629162 |
17.32 % |
| Transition |
C>T |
Passed |
607218 |
16.72 % |
| Transversion |
A>C |
Passed |
148232 |
4.08 % |
| Transversion |
C>A |
Passed |
150685 |
4.15 % |
| Transversion |
T>G |
Passed |
148518 |
4.09 % |
| Transversion |
G>T |
Passed |
150664 |
4.15 % |
| Transversion |
A>T |
Passed |
115909 |
3.19 % |
| Transversion |
T>A |
Passed |
115664 |
3.18 % |
| Transversion |
C>G |
Passed |
164238 |
4.52 % |
| Transversion |
G>C |
Passed |
164920 |
4.54 % |
| |
|
|
|
|
| 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 |
3.63 |
12283900 |
3384301 |
| Passed |
2.13 |
2472867 |
1158830 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |