/EXTERNAL DEEP/variants/K006104_K006105_K006106_3_lane_gembs
BACK
SAMPLE K006104_K006105_K006106_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1172918486 |
822978579 |
70.17 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1172918486 |
100% |
1136649551 |
96.91 % |
36268935 |
3.09 % |
| |
|
|
|
|
|
|
| Passed |
828791363 |
70.66 % |
817572644 |
71.93 % |
11218719 |
1.35 % |
| Filtered |
344127123 |
29.34 % |
319076907 |
28.07 % |
25050216 |
3.02 % |
| |
|
|
|
|
|
|
| q20 |
296868683 |
86.27 % |
290352063 |
91.00 % |
6516620 |
26.01 % |
| q20,qd2 |
28066092 |
8.16 % |
10611919 |
3.33 % |
17454173 |
69.68 % |
| q20,mq40 |
9605721 |
2.79 % |
9415521 |
2.95 % |
190200 |
0.76 % |
| qd2 |
5348310 |
1.55 % |
4877533 |
1.53 % |
470777 |
1.88 % |
| q20,qd2,mq40 |
2944519 |
0.86 % |
2779063 |
0.87 % |
165456 |
0.66 % |
| mq40 |
1242081 |
0.36 % |
1000396 |
0.31 % |
241685 |
0.96 % |
| qd2,mq40 |
49402 |
0.01 % |
40412 |
0.01 % |
8990 |
0.04 % |
| qd2,fs60,mq40 |
846 |
0.00 % |
0 |
0.00 % |
846 |
0.00 % |
| qd2,fs60 |
540 |
0.00 % |
0 |
0.00 % |
540 |
0.00 % |
| fs60,mq40 |
329 |
0.00 % |
0 |
0.00 % |
329 |
0.00 % |
| fs60 |
303 |
0.00 % |
0 |
0.00 % |
303 |
0.00 % |
| q20,qd2,fs60 |
167 |
0.00 % |
0 |
0.00 % |
167 |
0.00 % |
| q20,qd2,fs60,mq40 |
130 |
0.00 % |
0 |
0.00 % |
130 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
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 |
12542992 |
33.49 % |
| Transition |
G>A |
All |
2603927 |
6.95 % |
| Transition |
T>C |
All |
14449193 |
38.59 % |
| Transition |
C>T |
All |
1960533 |
5.24 % |
| Transversion |
A>C |
All |
474135 |
1.27 % |
| Transversion |
C>A |
All |
1236862 |
3.30 % |
| Transversion |
T>G |
All |
544633 |
1.45 % |
| Transversion |
G>T |
All |
1169792 |
3.12 % |
| Transversion |
A>T |
All |
781350 |
2.09 % |
| Transversion |
T>A |
All |
846105 |
2.26 % |
| Transversion |
C>G |
All |
425127 |
1.14 % |
| Transversion |
G>C |
All |
412832 |
1.10 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1118543 |
19.45 % |
| Transition |
G>A |
Passed |
705151 |
12.26 % |
| Transition |
T>C |
Passed |
1716494 |
29.85 % |
| Transition |
C>T |
Passed |
640359 |
11.13 % |
| Transversion |
A>C |
Passed |
185088 |
3.22 % |
| Transversion |
C>A |
Passed |
244240 |
4.25 % |
| Transversion |
T>G |
Passed |
196804 |
3.42 % |
| Transversion |
G>T |
Passed |
226133 |
3.93 % |
| Transversion |
A>T |
Passed |
156135 |
2.71 % |
| Transversion |
T>A |
Passed |
173068 |
3.01 % |
| Transversion |
C>G |
Passed |
195682 |
3.40 % |
| Transversion |
G>C |
Passed |
193613 |
3.37 % |
| |
|
|
|
|
| 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 |
5.36 |
31556645 |
5890836 |
| Passed |
2.66 |
4180547 |
1570763 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |