/REMC/variants/A27341_5_lane_gembs
BACK
SAMPLE A27341_5_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1167848373 |
971197849 |
83.16 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1167848373 |
100% |
1142557333 |
97.83 % |
25291040 |
2.17 % |
| |
|
|
|
|
|
|
| Passed |
973481954 |
83.36 % |
968261289 |
84.75 % |
5220665 |
0.54 % |
| Filtered |
194366419 |
16.64 % |
174296044 |
15.25 % |
20070375 |
2.06 % |
| |
|
|
|
|
|
|
| q20 |
143688095 |
73.93 % |
141544744 |
81.21 % |
2143351 |
10.68 % |
| q20,qd2 |
24730995 |
12.72 % |
7733911 |
4.44 % |
16997084 |
84.69 % |
| q20,mq40 |
15566816 |
8.01 % |
15415182 |
8.84 % |
151634 |
0.76 % |
| mq40 |
4198513 |
2.16 % |
3918966 |
2.25 % |
279547 |
1.39 % |
| q20,qd2,mq40 |
3422846 |
1.76 % |
3215785 |
1.85 % |
207061 |
1.03 % |
| qd2 |
2713977 |
1.40 % |
2432272 |
1.40 % |
281705 |
1.40 % |
| qd2,mq40 |
44351 |
0.02 % |
35184 |
0.02 % |
9167 |
0.05 % |
| qd2,fs60,mq40 |
458 |
0.00 % |
0 |
0.00 % |
458 |
0.00 % |
| fs60,mq40 |
161 |
0.00 % |
0 |
0.00 % |
161 |
0.00 % |
| qd2,fs60 |
119 |
0.00 % |
0 |
0.00 % |
119 |
0.00 % |
| q20,qd2,fs60,mq40 |
37 |
0.00 % |
0 |
0.00 % |
37 |
0.00 % |
| fs60 |
35 |
0.00 % |
0 |
0.00 % |
35 |
0.00 % |
| q20,qd2,fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
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 |
11016725 |
40.85 % |
| Transition |
G>A |
All |
1815499 |
6.73 % |
| Transition |
T>C |
All |
8308820 |
30.81 % |
| Transition |
C>T |
All |
1929859 |
7.16 % |
| Transversion |
A>C |
All |
276224 |
1.02 % |
| Transversion |
C>A |
All |
709407 |
2.63 % |
| Transversion |
T>G |
All |
350437 |
1.30 % |
| Transversion |
G>T |
All |
646083 |
2.40 % |
| Transversion |
A>T |
All |
633749 |
2.35 % |
| Transversion |
T>A |
All |
691727 |
2.57 % |
| Transversion |
C>G |
All |
320938 |
1.19 % |
| Transversion |
G>C |
All |
267933 |
0.99 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
959707 |
24.01 % |
| Transition |
G>A |
Passed |
572500 |
14.32 % |
| Transition |
T>C |
Passed |
701759 |
17.56 % |
| Transition |
C>T |
Passed |
583225 |
14.59 % |
| Transversion |
A>C |
Passed |
147343 |
3.69 % |
| Transversion |
C>A |
Passed |
152313 |
3.81 % |
| Transversion |
T>G |
Passed |
151993 |
3.80 % |
| Transversion |
G>T |
Passed |
152992 |
3.83 % |
| Transversion |
A>T |
Passed |
136143 |
3.41 % |
| Transversion |
T>A |
Passed |
136564 |
3.42 % |
| Transversion |
C>G |
Passed |
152633 |
3.82 % |
| Transversion |
G>C |
Passed |
150099 |
3.76 % |
| |
|
|
|
|
| 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 |
5.92 |
23070903 |
3896498 |
| Passed |
2.39 |
2817191 |
1180080 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |