/EXTERNAL KNIH/variants/K006230_1_lane_gembs
BACK
SAMPLE K006230_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1155074701 |
1064051743 |
92.12 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1155074701 |
100% |
1141802346 |
98.85 % |
13272355 |
1.15 % |
| |
|
|
|
|
|
|
| Passed |
1065090244 |
92.21 % |
1061502755 |
92.97 % |
3587489 |
0.34 % |
| Filtered |
89984457 |
7.79 % |
80299591 |
7.03 % |
9684866 |
0.91 % |
| |
|
|
|
|
|
|
| q20 |
52105865 |
57.91 % |
51284305 |
63.87 % |
821560 |
8.48 % |
| q20,mq40 |
14123589 |
15.70 % |
13964663 |
17.39 % |
158926 |
1.64 % |
| q20,qd2 |
10150616 |
11.28 % |
2498459 |
3.11 % |
7652157 |
79.01 % |
| mq40 |
7969470 |
8.86 % |
7648762 |
9.53 % |
320708 |
3.31 % |
| q20,qd2,mq40 |
3048232 |
3.39 % |
2782548 |
3.47 % |
265684 |
2.74 % |
| qd2 |
2508800 |
2.79 % |
2059271 |
2.56 % |
449529 |
4.64 % |
| qd2,mq40 |
74608 |
0.08 % |
61583 |
0.08 % |
13025 |
0.13 % |
| qd2,fs60,mq40 |
1225 |
0.00 % |
0 |
0.00 % |
1225 |
0.01 % |
| fs60 |
611 |
0.00 % |
0 |
0.00 % |
611 |
0.01 % |
| fs60,mq40 |
532 |
0.00 % |
0 |
0.00 % |
532 |
0.01 % |
| qd2,fs60 |
413 |
0.00 % |
0 |
0.00 % |
413 |
0.00 % |
| q20,qd2,fs60 |
354 |
0.00 % |
0 |
0.00 % |
354 |
0.00 % |
| q20,qd2,fs60,mq40 |
138 |
0.00 % |
0 |
0.00 % |
138 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
5567085 |
36.88 % |
| Transition |
G>A |
All |
869717 |
5.76 % |
| Transition |
T>C |
All |
5536988 |
36.68 % |
| Transition |
C>T |
All |
873201 |
5.79 % |
| Transversion |
A>C |
All |
234158 |
1.55 % |
| Transversion |
C>A |
All |
366418 |
2.43 % |
| Transversion |
T>G |
All |
236422 |
1.57 % |
| Transversion |
G>T |
All |
363583 |
2.41 % |
| Transversion |
A>T |
All |
313058 |
2.07 % |
| Transversion |
T>A |
All |
305131 |
2.02 % |
| Transversion |
C>G |
All |
214500 |
1.42 % |
| Transversion |
G>C |
All |
213639 |
1.42 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
749511 |
19.32 % |
| Transition |
G>A |
Passed |
594099 |
15.31 % |
| Transition |
T>C |
Passed |
751417 |
19.37 % |
| Transition |
C>T |
Passed |
597321 |
15.40 % |
| Transversion |
A>C |
Passed |
152877 |
3.94 % |
| Transversion |
C>A |
Passed |
154297 |
3.98 % |
| Transversion |
T>G |
Passed |
153103 |
3.95 % |
| Transversion |
G>T |
Passed |
154666 |
3.99 % |
| Transversion |
A>T |
Passed |
133478 |
3.44 % |
| Transversion |
T>A |
Passed |
133727 |
3.45 % |
| Transversion |
C>G |
Passed |
152529 |
3.93 % |
| Transversion |
G>C |
Passed |
152582 |
3.93 % |
| |
|
|
|
|
| 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 |
5.72 |
12846991 |
2246909 |
| Passed |
2.27 |
2692348 |
1187259 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |