/EXTERNAL DEEP/variants/K006038_K006039_K006040_K006041_K006042_K006043_K006044_7_lane_gembs
BACK
SAMPLE K006038_K006039_K006040_K006041_K006042_K006043_K006044_7_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1173207734 |
836803827 |
71.33 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1173207734 |
100% |
1137090026 |
96.92 % |
36117708 |
3.08 % |
| |
|
|
|
|
|
|
| Passed |
842085662 |
71.78 % |
831984657 |
73.17 % |
10101005 |
1.20 % |
| Filtered |
331122072 |
28.22 % |
305105369 |
26.83 % |
26016703 |
3.09 % |
| |
|
|
|
|
|
|
| q20 |
284096448 |
85.80 % |
277119437 |
90.83 % |
6977011 |
26.82 % |
| q20,qd2 |
27499071 |
8.30 % |
9690710 |
3.18 % |
17808361 |
68.45 % |
| q20,mq40 |
9971417 |
3.01 % |
9768269 |
3.20 % |
203148 |
0.78 % |
| qd2 |
5111177 |
1.54 % |
4544362 |
1.49 % |
566815 |
2.18 % |
| q20,qd2,mq40 |
3136105 |
0.95 % |
2953373 |
0.97 % |
182732 |
0.70 % |
| mq40 |
1249931 |
0.38 % |
983888 |
0.32 % |
266043 |
1.02 % |
| qd2,mq40 |
54840 |
0.02 % |
45330 |
0.01 % |
9510 |
0.04 % |
| qd2,fs60,mq40 |
1002 |
0.00 % |
0 |
0.00 % |
1002 |
0.00 % |
| qd2,fs60 |
585 |
0.00 % |
0 |
0.00 % |
585 |
0.00 % |
| fs60 |
497 |
0.00 % |
0 |
0.00 % |
497 |
0.00 % |
| q20,qd2,fs60 |
378 |
0.00 % |
0 |
0.00 % |
378 |
0.00 % |
| fs60,mq40 |
359 |
0.00 % |
0 |
0.00 % |
359 |
0.00 % |
| q20,qd2,fs60,mq40 |
259 |
0.00 % |
0 |
0.00 % |
259 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
14082883 |
36.95 % |
| Transition |
G>A |
All |
2639322 |
6.93 % |
| Transition |
T>C |
All |
14480464 |
38.00 % |
| Transition |
C>T |
All |
1983829 |
5.21 % |
| Transversion |
A>C |
All |
375787 |
0.99 % |
| Transversion |
C>A |
All |
1001988 |
2.63 % |
| Transversion |
T>G |
All |
474157 |
1.24 % |
| Transversion |
G>T |
All |
905811 |
2.38 % |
| Transversion |
A>T |
All |
629391 |
1.65 % |
| Transversion |
T>A |
All |
740689 |
1.94 % |
| Transversion |
C>G |
All |
414639 |
1.09 % |
| Transversion |
G>C |
All |
381301 |
1.00 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1420805 |
24.94 % |
| Transition |
G>A |
Passed |
658159 |
11.55 % |
| Transition |
T>C |
Passed |
1765933 |
31.00 % |
| Transition |
C>T |
Passed |
551720 |
9.68 % |
| Transversion |
A>C |
Passed |
151934 |
2.67 % |
| Transversion |
C>A |
Passed |
191871 |
3.37 % |
| Transversion |
T>G |
Passed |
172525 |
3.03 % |
| Transversion |
G>T |
Passed |
171479 |
3.01 % |
| Transversion |
A>T |
Passed |
131790 |
2.31 % |
| Transversion |
T>A |
Passed |
157561 |
2.77 % |
| Transversion |
C>G |
Passed |
164060 |
2.88 % |
| Transversion |
G>C |
Passed |
159065 |
2.79 % |
| |
|
|
|
|
| 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 |
6.74 |
33186498 |
4923763 |
| Passed |
3.38 |
4396617 |
1300285 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |