Spreadsheet: 5078a02c-601d-406c-ac2d-90cf7551bcf0
Sheet: Trios

a) Trio Overlapping RP and SR detection
Counts of detected events in high coverage trio children with dereived detection sensitivities for RP and SR algorithms
NA12878
 | RP | SR | RP+SR | RP-only | SR-only | RPeff | RP se | SReff | SReffu | eff | effu
ALU | 733 | 843 | 589 | 144 | 254 | 0.716 | 0.039 | 0.813 | 0.046 | 0.947 | 0.015
L1 | 80 | 114 | 32 | 48 | 82 | 0.453 | 0.142 | 0.41 | 0.086 | 0.677 | 0.096
SVA | 11 | 7 | 2 | 9 | 5 | 0.357 | 0.3 | 0.364 | 0.378 | 0.591 | 0.309
MEI | 824 | 964 | 623 | 201 | 341 | 0.673 | 0.036 | 0.771 | 0.042 | 0.925 | 0.016
NA19240
 | RP | SR | RP+SR | RP-only | SR-only | RPeff | RPeffu | SReff | SReffu | eff | effu
ALU | 1345 | 1282 | 892 | 453 | 390 | 0.713 | 0.032 | 0.671 | 0.03 | 0.906 | 0.014
L1 | 137 | 168 | 51 | 86 | 117 | 0.49 | 0.142 | 0.382 | 0.063 | 0.684 | 0.094
SVA | 29 | 7 | 2 | 27 | 5 | 0.357 | 0.3 | 0.138 | 0.14 | 0.446 | 0.274
MEI | 1511 | 1457 | 945 | 566 | 512 | 0.676 | 0.03 | 0.638 | 0.027 | 0.883 | 0.014
Notes: | symbol | description
RP | NRP | count of loci detected by RP algorithm
SR | NSR | count of loci detected by SR algorithm
RP+SR | NSR & RP | count of loci detected by both RP and SR algorithms
RP-only | NSR & not RP | count of loci detected by RP algorithm but not SR
SR-only | NRP & not SR | count of loci detected by SR algorithm but not RP
RPeff | eRP | RP detection sensitivity based on overlaps with SR
RPeffu | se,RP | uncertainty of RP detection sensitivity propagating errors from [NAME] and Poisson sampling
SReff | eSR | SR detection sensitivity based on overlaps with RP
SReffu | se,SR | uncertainty of SR detection sensitivity propagating errors from [NAME] and Poisson sampling
eff | eRP+SR | combined RP+SR detection efficiency
effu | se,RP+SR | uncertainty of combined detection sensitivity
b) Counts of MEI variations between pairs among the trios
MEI insertions |  | CEU-YRI children |  |  |  |  |  | MEI insertions |  | CEU parents |  |  |  |  | MEI insertions |  | YRI parents
type | NA12878 | NA19240 | symdiff | corrected | uncert |  |  | type | NA12891 | NA12892 | symdiff | corrected | uncert |  | type | NA19238 | NA19239 | symdiff | corrected | uncert
Alu | 987 | 1153 | 1334 | 1335 | 77 |  |  | Alu | 684 | 664 | 542 | 473 | 72 |  | Alu | 898 | 887 | 1021 | 1000 | 70
L1 | 161 | 144 | 213 | 162 | 51 |  |  | L1 | 66 | 78 | 52 | 0 | 57 |  | L1 | 101 | 97 | 104 | 44 | 51
SVA | 16 | 28 | 26 | 12 | 19 |  |  | SVA | 8 | 6 | 8 | 3 | 9 |  | SVA | 25 | 22 | 19 | 0 | 29
total | 1164 | 1325 | 1573 | 1509 | 94 |  |  | total | 758 | 748 | 602 | 466 | 92 |  | total | 1024 | 1006 | 1144 | 1044 | 91
MEI deletions |  |  |  |  |  |  |  | MEI deletions |  |  |  |  |  |  | MEI deletions
type | NA12878 | NA19240 | symdiff | corrected | uncert |  |  | type | NA12891 | NA12892 | symdiff | corrected | uncert |  | type | NA19238 | NA19239 | symdiff | corrected | uncert
Alu | 757 | 590 | 509 | 454 | 70 |  |  | Alu | 777 | 721 | 274 | 181 | 97 |  | Alu | 627 | 603 | 398 | 340 | 70
L1 | 90 | 63 | 63 | 57 | 20 |  |  | L1 | 90 | 84 | 28 | 17 | 25 |  | L1 | 68 | 66 | 52 | 47 | 19
SVA | 35 | 26 | 19 | 14 | 14 |  |  | SVA | 33 | 37 | 8 | 0 | 17 |  | SVA | 28 | 28 | 18 | 14 | 14
total | 882 | 679 | 591 | 525 | 74 |  |  | total | 900 | 842 | 310 | 197 | 102 |  | total | 723 | 697 | 468 | 401 | 74
combined MEI insertions+deletions |  |  |  |  |  |  |  | combined MEI insertions+deletions |  |  |  |  |  |  | combined MEI insertions+deletions
type | NA12878 | NA19240 | symdiff | corrected | uncert |  |  | type | NA12891 | NA12892 | symdiff | corrected | uncert |  | type | NA19238 | NA19239 | symdiff | corrected | uncert
Alu | 1544 | 1472 | 1594 | 1789 | 104 |  |  | Alu | 1294 | 1217 | 681 | 654 | 121 |  | Alu | 1337 | 1293 | 1174 | 1340 | 99
L1 | 184 | 175 | 193 | 219 | 55 |  |  | L1 | 161 | 165 | 86 | 7 | 62 |  | L1 | 163 | 150 | 155 | 91 | 54
SVA | 73 | 65 | 68 | 26 | 24 |  |  | SVA | 51 | 54 | 27 | 2 | 19 |  | SVA | 57 | 53 | 48 | 11 | 32
total | 2046 | 2004 | 2164 | 2034 | 120 |  |  | total | 1658 | 1590 | 912 | 663 | 137 |  | total | 1747 | 1703 | 1612 | 1442 | 117
Notes: | symbol | description
NA12878 | N1 | count of MEI detected in NA12878 relative to the reference |  |  |  |  |  | NA12891 | count of MEI detected in CEU father relative to the reference |  |  |  |  |  | NA19238 | count of MEI detected in YRI father relative to the reference
NA19240 | N2 | count of MEI detected in NA19240 relative to the reference |  |  |  |  |  | NA12892 | count of MEI detected in CEU mother relative to the reference |  |  |  |  |  | NA19239 | count of MEI detected in YRI mother relative to the reference
symdiff | N1 +N2 – N12 | count of MEI detected in one sample, but not both
corrected | DN | count of MEI variations between two samples corrected for [NAME] and detection sensivity
uncert | sDN | uncertainty in the count of MEI variations between two samples, including errors on [NAME] and detection sensivity
c) Search for de Novo insertions in trio children
CEU trio
. | p=NA12891 | m[NAME] | d=NA12878
. | p | m | d | p-only | m-only | d-only | p1m1d0 | p1m0d1 | p0m1d1 | p1m1d1 | denovo
ins | 755 | 744 | 834 | 100 | 94 | 27 | 48 | 205 | 200 | 402 | 1
del | 948 | 936 | 944 | 25 | 23 | 6 | 37 | 62 | 52 | 824 | 0
MEI | 1703 | 1680 | 1778 | 125 | 117 | 33 | 85 | 267 | 252 | 1226 | 1
1  candidate found in NA12892 (mother) by validation PCR experiment so it is not a de novo insertion
YRI trio
. | p=NA19238 | m=NA19239 | d=NA19240
. | p | m | d | p1 | m1 | d1 | pm | pd | md | pmd | denovo
ins | 1019 | 1000 | 1065 | 251 | 236 | 22 | 50 | 329 | 325 | 389 | 0
del | 903 | 895 | 906 | 33 | 30 | 15 | 53 | 79 | 74 | 738 | 0
MEI | 1922 | 1895 | 1971 | 284 | 266 | 37 | 103 | 408 | 399 | 1127 | 0
Notes:
p | trio father | total count
m | trio mother | total count
d | trio daughter | total count
p-only | trio father , not mother or daughter
m-only | trio mother, not faher or daughter
d-only | trio daughter, not mother or father (de novo candidate)
p1m1d0 | both father and mother, not daughter
p1m0d1 | both father and daughter, not mother
p0m1d1 | both mother and daughter, not father
p1m1d1 | found in all three trio samples
denovo | found in daughter, but no other sample (including parents)