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Thread: How many no calls and errors are normal?

  1. #1

    How many no calls and errors are normal?

    Hi,

    I have raw data from Ancestry (new V2.0 chip) and 23andme (V4). Since the new Ancestry chip is focused on medical related SNP's there are many SNP's that are tested on both platforms - 23andme and Ancestry.

    I compared both files and found around 500 mismatches. I was wondering if that's a lot or still within the normal range?

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     Little bit (06-18-2016)

  3. #2
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    That sounds like a lot to me. My Ancestry v1 and 23andMe v4 had only 14/299672 differences.

    One possibility is that there are strand differences. 23andMe aims to always report the plus strand. For instance, your genotype at 23andMe might be GA on the plus strand, which would be the same as CT on the minus strand. It's possible that AncestryDNA is using the minus strand if that's the way it's reported in dbSNP. If you run David Pike's utility, do any of the mismatches fit that scenario?

    http://www.math.mun.ca/~dapike/FF23utils/diffs.php

    You can look up individual SNPs at dbSNP

    http://www.ncbi.nlm.nih.gov/SNP/

    BTW, I am collecting mtDNA results (chromosome "26" in the raw data download). I've just seen a couple of examples, but I am concerned that there are some errors in the raw data. Would you (or anybody else) mind sending me those SNPs (195 of them)? My e-mail address is [email protected].

  4. #3
    Thank you. This is the result:

    298665 SNPs appear in both files

    2.523 % (7536) of these 298665 common SNPs are NoCalls (i.e. NoCall in at least one file)

    0.086 % (257) of the 298665 SNP results differ

    67 differing SNPs are both homozygous
    41 differing SNPs are homozygous in File1 but not in File2
    147 differing SNPs are homozygous in File2 but not in File1

    Obviously there are only 257 errors. I'm also getting Geno 2.0 NextGen and Genesforgood results soon. Let's see what they say and I might find out which file produce the most mistakes by comparing them to each other.

    I sent you an email.
    Last edited by aistea; 06-16-2016 at 05:59 PM.

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  6. #4
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    Thanks for the mtDNA dataset. There do appear to be a few SNPs that are consistently miscalled. I'd advise not using the mtDNA SNPs for the time being.

    The strand orientation issue wouldn't explain the SNPs that are homozygous in one file but not the other.

    How about the ones were both were homozygous? Are the results like CC in one file and GG in the other; or AA in one and TT in the other?

  7. #5
    Left: Ancestry
    Right: 23andme

    1 rs76667772 3150147 TT CC
    1 rs10158092 19537755 CC AC
    1 rs61752910 68903951 DD II
    1 rs63749059 68904948 II DD
    1 rs61750064 94508434 DD II
    1 rs61748531 94574247 DD II
    1 rs28365858 156083859 DD II
    1 rs1570805 156264648 CC CT
    1 rs4656525 167121665 GG AG
    1 rs4652554 181032155 CC CT
    1 rs12408910 181841744 GG AG
    1 rs80356649 193111146 DD II
    1 rs62635048 197297958 DD II
    1 rs62636272 197397067 DD II
    1 rs10920576 203129179 CC CT
    1 rs11240748 204453320 CC CT
    1 rs2217357 208520568 AG AA
    2 rs12713559 21229068 CC GG
    2 rs5742904 21229160 GG CC
    2 rs1718739 34083346 GG AG
    2 rs63750589 47630358 DD II
    2 rs63750614 47630362 DD II
    2 rs63751246 47630412 GG GT
    2 rs63751158 47635579 DD II
    2 rs63750786 47637456 DD II
    2 rs63750046 47641529 DD II
    2 rs63751219 47656930 DD II
    2 rs63750496 47656947 DD II
    2 rs63751169 47656995 DD II
    2 rs63751142 47657025 DD II
    2 rs63750104 47693879 DD II
    2 rs63750806 47702261 DD II
    2 rs63749878 47703568 DD II
    2 rs63751453 47703634 DD II
    2 rs63750722 47703660 II DD
    2 rs63750149 47705534 DD II
    2 rs63750803 47705559 DD II
    2 rs63750940 48027973 II DD
    2 rs3136351 48030632 CC GG
    2 rs63751427 48032091 DD II
    2 rs63751327 48032123 DD II
    2 rs63750731 48032834 DD II
    2 rs1568287 49909547 CC AC
    2 rs1483865 52853806 CC CT
    2 rs1364676 53379489 GG AG
    2 rs2540953 65272362 AA GG
    2 rs3755441 74569118 CC CT
    2 rs4366914 121135655 AG AA
    2 rs1427598 137548444 GG AG
    2 rs1519640 154540201 CC CT
    2 rs11884055 163509615 GG GT
    2 rs3812718 166909544 CC TT
    2 rs13012170 173396868 CC CT
    2 rs13028278 185242856 GG AG
    2 rs12620429 187489647 AC CC
    2 rs13006859 201135222 GG AG
    2 rs4673360 207508741 CC CT
    2 rs1346769 218637207 GG AG
    3 rs17043611 5849483 GG AG
    3 rs9855183 12618262 CC CT
    3 rs1881703 25578552 AC AA
    3 rs1449692 29051853 CC CT
    3 rs63751131 37035081 DD II
    3 rs63750658 37045936 DD II
    3 rs63750962 37061836 DD II
    3 rs63751015 37067299 II DD
    3 rs63751200 37090087 II DD
    3 rs63750282 37090404 DD II
    3 rs2320474 70327250 TT CT
    3 rs7613684 105234486 AG AA
    3 rs16852663 106324821 CC AC
    3 rs13098869 143283221 GG AG
    3 rs28933389 165548010 CC GG
    3 rs9882117 183076754 CC CT
    4 rs34311866 951947 CC TT
    4 rs17387271 16013048 CC CT
    4 rs10517102 44348032 CC CT
    4 rs1346839 65675052 CT CC
    4 rs17148188 70982011 GG AG
    4 rs1800759 100065509 TT GT
    4 rs1367066 126613855 CC CT
    4 rs6842514 190243940 AA AG
    5 rs13436220 2620072 GG GT
    5 rs16881512 8862669 GG AG
    5 rs1911856 19919301 CC CT
    5 rs1462417 99055048 GG AG
    5 rs1991012 104334555 GG AG
    5 rs1821908 110496071 CC AC
    5 rs3924161 123888562 CC AC
    5 rs647161 134499092 AC AA
    5 rs11949312 146126203 CC CT
    6 rs115074092 8511952 AG AA
    6 rs12199640 15598880 CC CT
    6 rs1142345 18130918 AA TT
    6 rs201311 21016532 GG GT
    6 rs9393387 23288843 GG GT
    6 rs2734979 29823161 AA AG
    6 rs356969 29977145 CG GG
    6 rs6905501 30015068 CC TT
    6 rs3815101 30514810 GG CC
    6 rs2853977 31379304 AA AT
    6 rs2071352 33044188 AA TT
    6 rs61755790 42689566 II DD
    6 rs61755786 42689611 II DD
    6 rs9454693 69808955 GT TT
    6 rs4839882 97360419 GG GT
    6 rs17052989 122980559 CT TT
    6 rs2243372 123101647 AA AG
    6 rs1853155 123970838 CT TT
    6 rs11154263 125096524 GG AG
    6 rs7767863 156476113 GT GG
    7 rs7797466 6046783 AG GG
    7 rs10281406 11298629 CC CT
    7 rs2222618 13599216 GG GT
    7 rs1551099 33712743 GG AG
    7 rs10255854 38959842 CT CC
    7 rs4470909 46489309 GG AG
    7 rs17799219 51137856 GG AG
    7 rs4236247 70911123 CC AA
    7 rs2032583 87160561 CT AG
    7 rs1357317 94312206 CC CT
    7 rs41303343 99250393 DD II
    7 rs6467148 127428382 AG GG
    7 rs2044455 129196616 CT TT
    7 rs2353348 138111275 CC CT
    7 rs1673223 138297714 CC AC
    7 rs430262 138432983 CT TT
    7 rs17170295 144320214 GG GT
    7 rs1358541 147198052 GG AG
    7 rs1689205 156019596 CT CC
    8 rs9774483 6883291 GG AG
    8 rs7011192 10535377 GG AG
    8 rs1729159 13211769 GG AG
    8 rs1550582 135542084 GG AG
    9 rs2034107 87580367 GG GT
    9 rs1880143 110503765 GG GT
    9 rs111033171 111662096 TT AA
    9 rs1324632 117150070 GG AG
    9 rs1889155 137144852 TT CT
    10 rs1009543 3319474 AG GG
    10 rs12415117 4526742 GG AG
    10 rs1544216 5651578 TT CT
    10 rs1934935 15777408 CC CT
    10 rs2244121 20414269 TT CC
    10 rs17154103 44166755 GG AG
    10 rs4987105 45869748 CT CC
    10 rs11006576 61322015 GG AG
    10 rs11000202 73933699 AG GG
    10 rs12360303 107886767 CC CT
    10 rs10787306 112863991 CT TT
    10 rs11200638 124220544 AG GG
    10 rs11146215 133966434 CC CT
    11 rs35477349 5248172 DD II
    11 rs63749918 5248174 II DD
    11 rs35699606 5248224 DD II
    11 rs151344623 17418602 GG CC
    11 rs2246192 20141839 GG AG
    11 rs2012543 20608950 CC CT
    11 rs294377 30626660 AC CC
    11 rs224632 32085420 GG AG
    11 rs10488736 34489252 CT TT
    11 rs36211723 47360071 CC CT
    11 rs3834458 61594921 ID DI
    11 rs1871042 67353844 CC CT
    11 rs506943 78919959 CC CT
    11 rs1522659 80841098 CC CT
    11 rs2226620 82235975 CC CT
    11 rs17151079 87674248 GG AG
    11 rs61753190 88911406 DD II
    11 rs2854116 116700169 CT CC
    11 rs2243935 117824960 GG AG
    11 rs4245096 130668732 CC CT
    12 rs10770645 20537935 CC CT
    12 rs1480043 26389769 CC CT
    12 rs17512639 32229817 GG AG
    12 rs12423751 44729627 GG AG
    12 rs2120296 54352645 CC AC
    12 rs1239919 70448434 AG GG
    12 rs2702775 87119057 GG GT
    12 rs12368906 94890011 GG AG
    12 rs62506951 103237523 DD II
    12 rs63749677 103288609 II DD
    12 rs1344542 110082154 AG AA
    12 rs10846630 124683205 CC CT
    12 rs1500106 125749565 CC CT
    13 rs4942312 44868790 CT CC
    13 rs1413137 71284358 GG AG
    13 rs12428146 74458852 GG GT
    13 rs2127125 81856417 GG AG
    13 rs9601955 83294195 GG AG
    13 rs160142 93646043 CC CT
    13 rs7324635 94828240 AA CC
    13 rs281083 103759750 AG GG
    13 rs4444189 108025668 GG AG
    14 rs61751270 21795829 DD II
    14 rs8013755 26904016 GG AG
    14 rs2383378 33282470 CC AC
    14 rs911009 37462757 CC CT
    14 rs4901617 56351774 CC CT
    14 rs7160912 71236728 CC AC
    14 rs63750762 73678573 DD II
    14 rs11621969 75814028 TT CT
    14 rs4344663 76851399 CT TT
    14 rs1420812 87488261 CC AC
    14 rs1034116 89955176 CC CT
    14 rs17128943 93687258 GG AG
    14 rs721909 101329803 AA AG
    15 rs12910496 25046976 CC CT
    15 rs16969959 33646961 CC CT
    15 rs1370154 35082225 CC CT
    15 rs7180947 53689742 GG GT
    15 rs12902903 54540592 GT GG
    15 rs7163680 61440507 GG GT
    15 rs1068705 62737452 TT CT
    15 rs12907251 71759406 GG AG
    15 rs121907954 72642859 GG CC
    15 rs121907970 72642925 CC GG
    15 rs1545470 85447220 CC CT
    16 rs2251984 10788106 GG AG
    16 rs79247025 24041856 GG AG
    16 rs4788683 72997747 GG GT
    16 rs1621902 86256231 AA GG
    17 rs6503236 9517923 GG AG
    17 rs34804195 9648230 GG AG
    17 rs57909628 39724442 DD II
    17 rs1076188 40219433 GT TT
    17 rs63751057 42426618 DD II
    17 rs63750405 42427626 II DD
    17 rs63751085 42428135 II DD
    17 rs63749988 42429079 II DD
    17 rs63749905 42429127 DD II
    18 rs17617822 2504483 CC AC
    18 rs1517610 2521466 CC AC
    18 rs1786224 33536145 TT CT
    18 rs2097055 47095487 CT TT
    18 rs2928953 49488572 AG GG
    18 rs12104016 67471466 GG AG
    18 rs1626732 73832730 CC CT
    18 rs9963578 74293754 CC CT
    19 rs8110742 3441385 AA AG
    19 rs164632 4139849 CC CT
    19 rs10424224 7240481 CT TT
    19 rs16020 13409710 AG GG
    19 rs2112464 13532476 GG GT
    19 rs75106035 17037080 CC AC
    19 rs61748444 48342767 DD II
    19 rs1820128 53270384 AG GG
    20 rs6084148 2712329 CC CT
    20 rs6124468 41128954 GG AG
    20 rs7273626 43485941 AG GG
    20 rs228838 50068701 CC CT
    20 rs6068699 52492074 GG AG
    20 rs2273505 61990878 CT CC
    21 rs17210156 17826778 GG AG
    21 rs2008980 34384588 GG AG
    22 rs362043 18596449 GG GT
    22 rs5759802 23779822 CC CT
    22 rs2000463 23803722 AA AG
    22 rs2073201 25294369 GG AG
    22 rs5757213 39053888 CC CT
    22 rs16947 42523943 AA AG
    22 rs2239400 45936264 CC CT
    23 rs5939319 2700157 GG G
    23 rs1419931 2703633 GG G
    24 rs11575897 2655180 GG G
    Last edited by aistea; 06-18-2016 at 08:11 AM.

  8. #6
    Errors are unexpected conditions that are not part of the normal operation of a ... Requiring that a function be called to check if the previous function failed.

  9. #7
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    Quote Originally Posted by Ann Turner View Post
    That sounds like a lot to me. My Ancestry v1 and 23andMe v4 had only 14/299672 differences.

    One possibility is that there are strand differences. 23andMe aims to always report the plus strand. For instance, your genotype at 23andMe might be GA on the plus strand, which would be the same as CT on the minus strand. It's possible that AncestryDNA is using the minus strand if that's the way it's reported in dbSNP.
    I don't have Ancestry v2, but I do have v1. In the header of my file, it says "The genotype is reported on the forward (+) strand with respect to the human reference." So unless they've changed their procedure for v2, this doesn't seem to explain the differences.

    When my Ancestry file is compared against my 23andMe file (v2 and v3), Pike's tool reports that

    669639 SNPs appear in both files

    0.238 % (1592) of these 669639 common SNPs are NoCalls (i.e. NoCall in at least one file)

    0.018 % (121) of the 669639 SNP results differ

    83 differing SNPs are both homozygous
    6 differing SNPs are homozygous in File1 but not in File2
    31 differing SNPs are homozygous in File2 but not in File1

    EDIT: As a general rule, I'd expect heterozygous results to be somewhat more likely to be accurate than homozygous results. Maybe it's coincidence, but Ancestry called a lot more SNPs as homozygous that were called as heterozygous by 23andMe, than the other way around.
    Last edited by geebee; 07-16-2016 at 04:01 PM.
    Besides British-German-Catalan, ancestry includes smaller amounts of French, Irish, Swiss, Choctaw & another NA tribe, possibly Catawba. Avatar picture is: my father, his father, & his father's father; baby is my eldest brother.

    GB

  10. #8
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    Files to be processed:
    File1: genome_Gary_v2_v3_Full_20160524202633.txt
    File2: AncestryDNA.txt

    Differently Reported SNPs:
    File1 File2
    1 rs4477212 82154 AA TT
    1 rs11573970 2489167 GG CC
    1 rs11580880 6275001 TT AA
    1 rs3845598 15189693 AA AG
    1 rs12096803 28892315 AA TT
    1 rs12724260 47882761 CC GG
    1 rs12060107 53352576 GG CC
    1 rs12137401 62677050 CT CC
    1 rs12135608 70621290 TT AA
    1 rs2297632 94517166 GG CC
    1 rs4147824 94560975 GG CC
    1 rs11102691 114421313 CT CC
    1 rs4656656 169138307 AC CC
    1 rs12133085 187135612 AC CC
    1 rs6693857 193788485 AG GG
    1 rs10754139 195346285 AG GG
    1 rs3024510 206941636 TT AA
    1 rs4846513 219013166 CT CC
    1 rs12023743 235334252 AA TT
    1 rs1691246 247112320 AG GG
    2 rs6729459 30208763 TT CC
    2 rs2579513 96691125 CC GG
    2 rs1201484 114227591 GG CC
    2 rs12615128 119025830 GG TT
    2 rs13392568 131991166 AA TT
    2 rs11568365 169851885 CC GG
    2 rs2287612 169852842 CC GG
    2 rs12999589 177132727 AA TT
    2 rs28626139 219246328 CC GG
    2 rs13020195 241508390 GG CC
    3 rs433032 13393384 CC GG
    3 rs7625419 40986300 AG GG
    3 rs13061999 48909446 GG CC
    3 rs2960546 49728927 CC GG
    3 rs28722064 171756932 AA TT
    4 rs10026884 47272392 AG GG
    4 rs12650894 47602599 GT GG
    4 rs17838982 74702263 CC GG
    4 rs1799883 120241902 GG CC
    4 rs13138416 163043362 CT CC
    5 rs16901165 31439859 GG AG
    5 rs662311 55494486 CC GG
    5 rs28591114 69175823 CC GG
    5 rs10054531 74801147 AA TT
    5 rs3909479 94787954 CT CC
    5 rs3749745 114462214 GG CC
    5 rs17876049 176827753 CC GG
    5 rs13360297 177239494 CC GG
    6 rs9505819 9200276 TT AA
    6 rs28549156 30299075 AA TT
    6 rs5030797 31759419 GG CC
    6 rs2734329 31937114 GG CC
    6 rs2746395 31939265 TT AA
    6 rs2746409 32015600 CC GG
    6 rs2855505 33146738 CC GG
    6 rs9501289 33231060 AA TT
    6 rs28385696 44233524 TT AA
    6 rs9294888 71933272 AG GG
    6 rs17780048 138179146 CT CC
    6 rs35656780 153332035 TT AA
    7 rs17172508 56149847 CC TT
    7 rs10239316 75006744 CC GG
    7 rs11763069 75979679 AG GG
    7 rs4646448 99268316 TT AA
    7 rs10267426 99994300 CC GG
    7 rs10251102 108861728 AG GG
    7 rs5054 134143772 TT AA
    7 rs17274 142224511 AG CT
    8 rs36029873 17737852 GG CC
    8 rs1511723 56803179 AG AA
    9 rs10758869 7513262 AG GG
    9 rs3750438 35792249 CC GG
    9 rs957692 83733322 AC CC
    9 rs7042161 113197263 CT CC
    9 rs1771221 116163118 AA TT
    10 rs2026628 6709658 AG GG
    10 rs543850 25630924 AG GG
    10 rs7393360 96594312 TT AA
    11 rs11024041 16817072 CC CT
    11 rs989570 32217782 AC AA
    11 rs11570112 47355475 GG CC
    11 rs4320922 105122451 GG AG
    12 rs28990684 2986266 CC GG
    12 rs2162470 40827479 CT CC
    12 rs12304591 56235363 TT AA
    12 rs11171817 56761845 AA TT
    12 rs7304073 101549254 CC GG
    12 rs35532624 101785983 AA TT
    12 rs17879774 102874421 TT AA
    13 rs17805016 39995662 CT CC
    13 rs1336488 40755278 CT TT
    13 rs17594917 67893311 AG AA
    13 rs7991842 111056745 AA GG
    13 rs7331967 114516254 GG CC
    14 rs1430477 82542483 CT CC
    15 rs2934067 28924405 GG CC
    15 rs28693826 75001949 TT AA
    16 rs2745101 1537839 GG AG
    16 rs9926129 23312779 AA TT
    16 rs12918181 23785404 AG GG
    16 rs4149407 28603889 CC GG
    16 rs17884850 31104402 CC GG
    16 rs1209760 46710000 AA TT
    16 rs1213198 67726943 AA TT
    16 rs12918064 68277790 AA TT
    16 rs35270463 81479272 CC GG
    16 rs458440 89623779 TT AA
    17 rs2323755 15504740 AA TT
    17 rs9906769 27717572 CC GG
    17 rs28588448 33335622 TT AA
    17 rs2246292 38507261 CC GG
    17 rs11657618 58227800 GG CC
    18 rs2123444 67664450 CT CC
    19 rs530411 39927540 CC CT
    19 rs28836244 42553198 AA TT
    19 rs12974700 42768288 AA TT
    19 rs34814003 50391762 CC GG
    19 rs3956158 51125485 GG CC
    20 rs13040250 49506700 AA TT
    21 rs28971224 10827533 AA TT
    21 rs2839208 47721036 TT AA

    At 23andMe, I have five brothers and sisters, my father, and my daughter to compare my results to. While I haven't been through more than a handful of these yet, so far my 23andMe results seem consistent with the results of other family members.
    Besides British-German-Catalan, ancestry includes smaller amounts of French, Irish, Swiss, Choctaw & another NA tribe, possibly Catawba. Avatar picture is: my father, his father, & his father's father; baby is my eldest brother.

    GB

  11. #9
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    Even though both companies claim to report on the forward (+) strand, I find it curious that where both result were homozygous but opposite, only three times could it not be explained as a flip.

    In fact, there was one SNP at which both companies called a heterozygous result, but opposite -- so a possible flip. This was at rs17274, where the calls were AG (23andMe) and CT (Ancestry).
    Besides British-German-Catalan, ancestry includes smaller amounts of French, Irish, Swiss, Choctaw & another NA tribe, possibly Catawba. Avatar picture is: my father, his father, & his father's father; baby is my eldest brother.

    GB

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