/EXTERNAL KNIH/variants/K006251_1_lane_gembs
BACK
SAMPLE K006251_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1191973413 |
292638466 |
24.55 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1191973413 |
100% |
1100889759 |
92.36 % |
91083654 |
7.64 % |
| |
|
|
|
|
|
|
| Passed |
318329363 |
26.71 % |
284834420 |
25.87 % |
33494943 |
10.52 % |
| Filtered |
873644050 |
73.29 % |
816055339 |
74.13 % |
57588711 |
18.09 % |
| |
|
|
|
|
|
|
| q20 |
783453994 |
89.68 % |
754617398 |
92.47 % |
28836596 |
50.07 % |
| q20,qd2 |
78839966 |
9.02 % |
50807316 |
6.23 % |
28032650 |
48.68 % |
| q20,mq40 |
6276966 |
0.72 % |
6090096 |
0.75 % |
186870 |
0.32 % |
| q20,qd2,mq40 |
3199333 |
0.37 % |
3110695 |
0.38 % |
88638 |
0.15 % |
| qd2 |
1447450 |
0.17 % |
1186964 |
0.15 % |
260486 |
0.45 % |
| mq40 |
413385 |
0.05 % |
233254 |
0.03 % |
180131 |
0.31 % |
| qd2,mq40 |
12648 |
0.00 % |
9616 |
0.00 % |
3032 |
0.01 % |
| fs60 |
141 |
0.00 % |
0 |
0.00 % |
141 |
0.00 % |
| qd2,fs60 |
58 |
0.00 % |
0 |
0.00 % |
58 |
0.00 % |
| q20,qd2,fs60 |
46 |
0.00 % |
0 |
0.00 % |
46 |
0.00 % |
| fs60,mq40 |
31 |
0.00 % |
0 |
0.00 % |
31 |
0.00 % |
| qd2,fs60,mq40 |
21 |
0.00 % |
0 |
0.00 % |
21 |
0.00 % |
| q20,qd2,fs60,mq40 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
30084074 |
31.69 % |
| Transition |
G>A |
All |
3952119 |
4.16 % |
| Transition |
T>C |
All |
29690953 |
31.28 % |
| Transition |
C>T |
All |
2820335 |
2.97 % |
| Transversion |
A>C |
All |
4739012 |
4.99 % |
| Transversion |
C>A |
All |
3346174 |
3.52 % |
| Transversion |
T>G |
All |
5342942 |
5.63 % |
| Transversion |
G>T |
All |
3132813 |
3.30 % |
| Transversion |
A>T |
All |
2282583 |
2.40 % |
| Transversion |
T>A |
All |
2693704 |
2.84 % |
| Transversion |
C>G |
All |
3546594 |
3.74 % |
| Transversion |
G>C |
All |
3298093 |
3.47 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2304892 |
28.63 % |
| Transition |
G>A |
Passed |
479589 |
5.96 % |
| Transition |
T>C |
Passed |
2750468 |
34.17 % |
| Transition |
C>T |
Passed |
339248 |
4.21 % |
| Transversion |
A>C |
Passed |
440984 |
5.48 % |
| Transversion |
C>A |
Passed |
190407 |
2.37 % |
| Transversion |
T>G |
Passed |
509072 |
6.32 % |
| Transversion |
G>T |
Passed |
156200 |
1.94 % |
| Transversion |
A>T |
Passed |
94460 |
1.17 % |
| Transversion |
T>A |
Passed |
141510 |
1.76 % |
| Transversion |
C>G |
Passed |
331166 |
4.11 % |
| Transversion |
G>C |
Passed |
311845 |
3.87 % |
| |
|
|
|
|
| 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 |
2.34 |
66547481 |
28381915 |
| Passed |
2.70 |
5874197 |
2175644 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |