What are the most common human indels?

Question

[Jeremy Leipzig]

What are the 100 insertion/deletion events with the highest minor allele frequency?

How did you find these?

Answer 1

[Pierre Lindenbaum]

using mysql+ucsc ?

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg38 -e 'select name,avHet,observed,class from snp141 where class in ("in-del","insertion","deletion") and avHet!=0 order by avHet desc limit 100'
+------------+----------+------------------------------+-----------+
| name       | avHet    | observed                     | class     |
+------------+----------+------------------------------+-----------+
| rs68155178 |    0.875 | lengthTooLong                | in-del    |
| rs66718999 | 0.857143 | lengthTooLong                | in-del    |
| rs66904857 | 0.833333 | AGGC/AGGT/CA/CAGC/GG/GGGT    | in-del    |
| rs17244502 | 0.788194 | -/GTGTGTGTGTGT               | deletion  |
| rs70962736 | 0.777778 | lengthTooLong                | in-del    |
| rs67228163 |     0.75 | lengthTooLong                | in-del    |
| rs68040605 |     0.75 | lengthTooLong                | in-del    |
| rs66616493 |     0.75 | GTTTTT/TTTTG                 | in-del    |
| rs71472203 |     0.75 | AC/T                         | in-del    |
| rs71487491 |     0.75 | lengthTooLong                | in-del    |
| rs71229282 |     0.75 | -/CTTTTTCT/T/TTTTTC          | in-del    |
| rs66821783 |     0.75 | -/ATATATG/G/GGTGT            | insertion |
| rs11352206 |     0.75 | -/GTGGTGGT/T/TTGGTGG         | in-del    |
| rs71311216 |     0.75 | -/AGGAAGGAAGGAG/G/GAGAA      | in-del    |
| rs67326935 |     0.75 | -/A/ATCT/GCC                 | in-del    |
| rs66480816 |     0.75 | C/GGTT                       | in-del    |
| rs67186389 |     0.75 | AT/C                         | in-del    |
| rs71485248 |     0.75 | -/AA/T/TAT                   | in-del    |
| rs67088535 |     0.75 | -/C                          | deletion  |
| rs71291864 |     0.75 | CGT/GGC/GGCT/TGTC            | in-del    |
| rs71301364 |     0.75 | lengthTooLong                | in-del    |
| rs66520943 |     0.75 | -/ATATATAC/TT/TTATATATAT     | insertion |
| rs71587750 |     0.75 | CCCCCC/GCCCCCT               | in-del    |
| rs71230868 |     0.75 | -/G/T/TT                     | in-del    |
| rs71326385 |     0.75 | -/T                          | deletion  |
| rs67181300 |     0.75 | lengthTooLong                | in-del    |
| rs66531628 |     0.75 | lengthTooLong                | in-del    |
| rs71291864 |     0.75 | CGT/GGC/GGCT/TGTC            | in-del    |
| rs71587033 |     0.75 | -/ATCT/TATC/TATCTATC         | in-del    |
| rs71636742 |     0.75 | -/A/AA/T                     | in-del    |
| rs74180031 |     0.75 | C/TT                         | in-del    |
| rs71285081 |     0.75 | lengthTooLong                | in-del    |
| rs71383516 |     0.75 | A/TTT                        | in-del    |
| rs67880442 |     0.75 | -/A                          | deletion  |
| rs74174551 |     0.75 | CGTGTGTGT/TGC                | in-del    |
| rs66770246 |     0.75 | -/C/CTTT/CTTTCTTT/TCTT/TTCTT | insertion |
| rs71455104 |     0.75 | -/A/ATCTCA/GTCTC             | in-del    |
| rs34744319 |     0.75 | -/A                          | deletion  |
| rs66507035 |     0.75 | -/AT/CGTACAT/GGTAC           | insertion |
| rs66908101 |     0.75 | -/ACAT                       | deletion  |
| rs74189605 |     0.75 | lengthTooLong                | in-del    |
| rs71607540 |     0.75 | A/TTT                        | in-del    |
| rs10659532 |     0.75 | -/AAAAACC/CC/CCTTAT/T/TTAT   | insertion |
| rs67100457 |     0.75 | AGGT/CA/GG/GGGC              | in-del    |
| rs67066375 |     0.75 | CAC/CAGAG/GAG/GAGCC          | in-del    |
| rs75936347 |     0.75 | G/TATGTATGT                  | in-del    |
| rs59109777 |     0.75 | -/AAAA/C/CAAAT               | in-del    |
| rs71369082 |     0.75 | AA/TTT                       | in-del    |
| rs71494030 |     0.75 | AG/T                         | in-del    |
| rs56231608 |     0.75 | -/G                          | deletion  |
| rs71291864 |     0.75 | CGT/GGC/GGCT/TGTC            | in-del    |
| rs71291864 |     0.75 | CGT/GGC/GGCT/TGTC            | in-del    |
| rs74211456 |     0.75 | AC/CG/CGAAA/TGAAT            | in-del    |
| rs67074009 |     0.75 | lengthTooLong                | in-del    |
| rs71112789 |     0.75 | lengthTooLong                | in-del    |
| rs71229282 |     0.75 | -/CTTTTTCT/T/TTTTTC          | in-del    |
| rs68040605 |     0.75 | lengthTooLong                | in-del    |
| rs71291864 |     0.75 | CGT/GGC/GGCT/TGTC            | in-del    |
| rs61029624 |     0.75 | -/AA/AAA/G                   | in-del    |
| rs71339237 |     0.75 | CGTCTCA/TGTCTC               | in-del    |
| rs74206639 |     0.75 | -/CA/CGTGTA/TA/TATACGTG      | in-del    |
| rs58027030 |     0.75 | -/A                          | deletion  |
| rs67550478 |     0.75 | CTTTTT/TTTA                  | in-del    |
| rs56187504 |     0.75 | -/A/C/CT                     | in-del    |
| rs71291864 |     0.75 | CGT/GGC/GGCT/TGTC            | in-del    |
| rs5833935  |     0.75 | -/ACT/G/GACTACAC             | in-del    |
| rs71291864 |     0.75 | CGT/GGC/GGCT/TGTC            | in-del    |
| rs71276311 |     0.75 | -/C/CT/TCTC                  | insertion |
| rs71244404 |     0.75 | -/A/AAGAAGA/G                | in-del    |
| rs71441888 |     0.75 | -/CC/CCCC/T                  | insertion |
| rs71402875 |     0.75 | A/TT                         | in-del    |
| rs68079386 |     0.75 | ACAAACAGAG/GA/TCAAACAGAC/TT  | in-del    |
| rs71301316 |     0.75 | lengthTooLong                | in-del    |
| rs71291864 |     0.75 | CGT/GGC/GGCT/TGTC            | in-del    |
| rs66484140 |     0.75 | G/TTTTTT                     | in-del    |
| rs35232684 |     0.75 | lengthTooLong                | in-del    |
| rs71224979 |     0.75 | -/AAAAG/G/TAT                | in-del    |
| rs67613384 |     0.75 | AAAAAT/CAAAAAA               | in-del    |
| rs67488005 |     0.75 | lengthTooLong                | in-del    |
| rs11301828 |     0.75 | -/A                          | deletion  |
| rs10633864 | 0.722222 | lengthTooLong                | in-del    |
| rs71194811 | 0.722222 | -/AC/CA/CACA                 | insertion |
| rs66493022 | 0.722222 | lengthTooLong                | in-del    |
| rs59850965 | 0.722222 | -/A/G/GA                     | insertion |
| rs5819239  | 0.722222 | lengthTooLong                | in-del    |
| rs59539536 | 0.722222 | -/AAA/AAAA/G                 | insertion |
| rs67447711 | 0.722222 | -/G/GT/T                     | insertion |
| rs3044705  | 0.722222 | -/TA/TATA/TATATA             | insertion |
| rs60595588 | 0.722222 | lengthTooLong                | in-del    |
| rs3075240  | 0.722222 | -/A/GA/GAA                   | insertion |
| rs68150973 | 0.722222 | -/CT/GCCCCCCCC/T             | in-del    |
| rs56694006 | 0.722222 | lengthTooLong                | in-del    |
| rs11478422 | 0.722222 | -/A                          | deletion  |
| rs60206546 | 0.722222 | -/AG/CA/CACA/CACACACA        | in-del    |
| rs67537228 | 0.722222 | -/TA/TATA/TATATA             | insertion |
| rs55842865 | 0.722222 | -/AT/TA/TATATA/TATATATA      | insertion |
| rs3075240  | 0.722222 | -/A/GA/GAA                   | insertion |
| rs3034426  | 0.722222 | -/C/TC/TTC                   | insertion |
| rs57202860 | 0.722222 | lengthTooLong                | in-del    |
| rs11286411 | 0.722222 | -/G/GTG/T                    | in-del    |
+------------+----------+------------------------------+-----------+