/EXTERNAL Roadmap/variants/K006489_1_lane_gembs
BACK
SAMPLE K006489_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1163461101 |
429208014 |
36.89 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1163461101 |
100% |
1125169922 |
96.71 % |
38291179 |
3.29 % |
| |
|
|
|
|
|
|
| Passed |
434706852 |
37.36 % |
427151117 |
37.96 % |
7555735 |
1.74 % |
| Filtered |
728754249 |
62.64 % |
698018805 |
62.04 % |
30735444 |
7.07 % |
| |
|
|
|
|
|
|
| q20 |
642234430 |
88.13 % |
629040239 |
90.12 % |
13194191 |
42.93 % |
| q20,qd2 |
40000652 |
5.49 % |
23590038 |
3.38 % |
16410614 |
53.39 % |
| q20,mq40 |
31787416 |
4.36 % |
31388033 |
4.50 % |
399383 |
1.30 % |
| q20,qd2,mq40 |
6774317 |
0.93 % |
6467836 |
0.93 % |
306481 |
1.00 % |
| qd2 |
5107904 |
0.70 % |
5007640 |
0.72 % |
100264 |
0.33 % |
| mq40 |
2793183 |
0.38 % |
2478583 |
0.36 % |
314600 |
1.02 % |
| qd2,mq40 |
55082 |
0.01 % |
46436 |
0.01 % |
8646 |
0.03 % |
| qd2,fs60,mq40 |
538 |
0.00 % |
0 |
0.00 % |
538 |
0.00 % |
| qd2,fs60 |
200 |
0.00 % |
0 |
0.00 % |
200 |
0.00 % |
| fs60,mq40 |
194 |
0.00 % |
0 |
0.00 % |
194 |
0.00 % |
| fs60 |
143 |
0.00 % |
0 |
0.00 % |
143 |
0.00 % |
| q20,qd2,fs60,mq40 |
120 |
0.00 % |
0 |
0.00 % |
120 |
0.00 % |
| q20,qd2,fs60 |
70 |
0.00 % |
0 |
0.00 % |
70 |
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 |
17009325 |
42.02 % |
| Transition |
G>A |
All |
2039719 |
5.04 % |
| Transition |
T>C |
All |
7048406 |
17.41 % |
| Transition |
C>T |
All |
2352796 |
5.81 % |
| Transversion |
A>C |
All |
969812 |
2.40 % |
| Transversion |
C>A |
All |
2283225 |
5.64 % |
| Transversion |
T>G |
All |
1626414 |
4.02 % |
| Transversion |
G>T |
All |
1958659 |
4.84 % |
| Transversion |
A>T |
All |
1210897 |
2.99 % |
| Transversion |
T>A |
All |
1734905 |
4.29 % |
| Transversion |
C>G |
All |
1353357 |
3.34 % |
| Transversion |
G>C |
All |
892620 |
2.21 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
821012 |
32.19 % |
| Transition |
G>A |
Passed |
293081 |
11.49 % |
| Transition |
T>C |
Passed |
367123 |
14.39 % |
| Transition |
C>T |
Passed |
310515 |
12.18 % |
| Transversion |
A>C |
Passed |
90733 |
3.56 % |
| Transversion |
C>A |
Passed |
93585 |
3.67 % |
| Transversion |
T>G |
Passed |
116702 |
4.58 % |
| Transversion |
G>T |
Passed |
94455 |
3.70 % |
| Transversion |
A>T |
Passed |
81335 |
3.19 % |
| Transversion |
T>A |
Passed |
82121 |
3.22 % |
| Transversion |
C>G |
Passed |
107856 |
4.23 % |
| Transversion |
G>C |
Passed |
91851 |
3.60 % |
| |
|
|
|
|
| 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 |
2.36 |
28450246 |
12029889 |
| Passed |
2.36 |
1791731 |
758638 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |