/EXTERNAL KNIH/variants/K006227_1_lane_gembs
BACK
SAMPLE K006227_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1158585531 |
1069327537 |
92.30 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1158585531 |
100% |
1147264152 |
99.02 % |
11321379 |
0.98 % |
| |
|
|
|
|
|
|
| Passed |
1070098141 |
92.36 % |
1066821759 |
92.99 % |
3276382 |
0.31 % |
| Filtered |
88487390 |
7.64 % |
80442393 |
7.01 % |
8044997 |
0.75 % |
| |
|
|
|
|
|
|
| q20 |
53010617 |
59.91 % |
52426972 |
65.17 % |
583645 |
7.25 % |
| q20,mq40 |
14123341 |
15.96 % |
13981692 |
17.38 % |
141649 |
1.76 % |
| q20,qd2 |
9150441 |
10.34 % |
2776813 |
3.45 % |
6373628 |
79.22 % |
| mq40 |
6648566 |
7.51 % |
6351185 |
7.90 % |
297381 |
3.70 % |
| q20,qd2,mq40 |
3137370 |
3.55 % |
2885534 |
3.59 % |
251836 |
3.13 % |
| qd2 |
2339650 |
2.64 % |
1958438 |
2.43 % |
381212 |
4.74 % |
| qd2,mq40 |
74701 |
0.08 % |
61759 |
0.08 % |
12942 |
0.16 % |
| qd2,fs60,mq40 |
1207 |
0.00 % |
0 |
0.00 % |
1207 |
0.02 % |
| fs60,mq40 |
501 |
0.00 % |
0 |
0.00 % |
501 |
0.01 % |
| fs60 |
401 |
0.00 % |
0 |
0.00 % |
401 |
0.00 % |
| qd2,fs60 |
311 |
0.00 % |
0 |
0.00 % |
311 |
0.00 % |
| q20,qd2,fs60 |
148 |
0.00 % |
0 |
0.00 % |
148 |
0.00 % |
| q20,qd2,fs60,mq40 |
128 |
0.00 % |
0 |
0.00 % |
128 |
0.00 % |
| q20,fs60,mq40 |
8 |
0.00 % |
0 |
0.00 % |
8 |
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 |
4514937 |
34.35 % |
| Transition |
G>A |
All |
879681 |
6.69 % |
| Transition |
T>C |
All |
4480161 |
34.08 % |
| Transition |
C>T |
All |
884640 |
6.73 % |
| Transversion |
A>C |
All |
224534 |
1.71 % |
| Transversion |
C>A |
All |
407082 |
3.10 % |
| Transversion |
T>G |
All |
226189 |
1.72 % |
| Transversion |
G>T |
All |
400916 |
3.05 % |
| Transversion |
A>T |
All |
355639 |
2.71 % |
| Transversion |
T>A |
All |
345707 |
2.63 % |
| Transversion |
C>G |
All |
212462 |
1.62 % |
| Transversion |
G>C |
All |
213247 |
1.62 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
712109 |
18.43 % |
| Transition |
G>A |
Passed |
608511 |
15.74 % |
| Transition |
T>C |
Passed |
713024 |
18.45 % |
| Transition |
C>T |
Passed |
613164 |
15.87 % |
| Transversion |
A>C |
Passed |
154494 |
4.00 % |
| Transversion |
C>A |
Passed |
160070 |
4.14 % |
| Transversion |
T>G |
Passed |
154673 |
4.00 % |
| Transversion |
G>T |
Passed |
160081 |
4.14 % |
| Transversion |
A>T |
Passed |
140661 |
3.64 % |
| Transversion |
T>A |
Passed |
139495 |
3.61 % |
| Transversion |
C>G |
Passed |
154110 |
3.99 % |
| Transversion |
G>C |
Passed |
154433 |
4.00 % |
| |
|
|
|
|
| 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 |
4.51 |
10759419 |
2385776 |
| Passed |
2.17 |
2646808 |
1218017 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |