/EXTERNAL BLUEPRINT/variants/K011894_K011895_K011896_K011897_K011898_K011927_K011928_7_lane_gembs
BACK
SAMPLE K011894_K011895_K011896_K011897_K011898_K011927_K011928_7_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
637106347 |
398008 |
0.06 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
637106347 |
100% |
631414955 |
99.11 % |
5691392 |
0.89 % |
| |
|
|
|
|
|
|
| Passed |
3604902 |
0.57 % |
332064 |
0.05 % |
3272838 |
90.79 % |
| Filtered |
633501445 |
99.43 % |
631082891 |
99.95 % |
2418554 |
67.09 % |
| |
|
|
|
|
|
|
| q20 |
492621196 |
77.76 % |
490780687 |
77.77 % |
1840509 |
76.10 % |
| q20,qd2 |
85357864 |
13.47 % |
85082268 |
13.48 % |
275596 |
11.40 % |
| q20,mq40 |
41832555 |
6.60 % |
41712993 |
6.61 % |
119562 |
4.94 % |
| q20,qd2,mq40 |
13499737 |
2.13 % |
13480370 |
2.14 % |
19367 |
0.80 % |
| mq40 |
186074 |
0.03 % |
22738 |
0.00 % |
163336 |
6.75 % |
| qd2 |
3429 |
0.00 % |
3356 |
0.00 % |
73 |
0.00 % |
| qd2,mq40 |
572 |
0.00 % |
479 |
0.00 % |
93 |
0.00 % |
| qd2,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 % |
| q20,qd2,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 |
2236500 |
22.08 % |
| Transition |
G>A |
All |
774997 |
7.65 % |
| Transition |
T>C |
All |
2805850 |
27.70 % |
| Transition |
C>T |
All |
405183 |
4.00 % |
| Transversion |
A>C |
All |
404391 |
3.99 % |
| Transversion |
C>A |
All |
593543 |
5.86 % |
| Transversion |
T>G |
All |
434764 |
4.29 % |
| Transversion |
G>T |
All |
555494 |
5.48 % |
| Transversion |
A>T |
All |
492535 |
4.86 % |
| Transversion |
T>A |
All |
658399 |
6.50 % |
| Transversion |
C>G |
All |
353606 |
3.49 % |
| Transversion |
G>C |
All |
413371 |
4.08 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
9821 |
15.01 % |
| Transition |
G>A |
Passed |
8890 |
13.59 % |
| Transition |
T>C |
Passed |
14181 |
21.68 % |
| Transition |
C>T |
Passed |
3983 |
6.09 % |
| Transversion |
A>C |
Passed |
3289 |
5.03 % |
| Transversion |
C>A |
Passed |
4382 |
6.70 % |
| Transversion |
T>G |
Passed |
3495 |
5.34 % |
| Transversion |
G>T |
Passed |
2833 |
4.33 % |
| Transversion |
A>T |
Passed |
1783 |
2.73 % |
| Transversion |
T>A |
Passed |
3955 |
6.05 % |
| Transversion |
C>G |
Passed |
3874 |
5.92 % |
| Transversion |
G>C |
Passed |
4924 |
7.53 % |
| |
|
|
|
|
| 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 |
1.59 |
6222530 |
3906103 |
| Passed |
1.29 |
36875 |
28535 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |