Hi I was working on a Supplementary Table and happen to have very big values (order of tens of thousands) as well as very small values (third-fourth significant digit after zero) having to coexist in the same longtable environment.
As per this suggestion from Mico, I better go for two separate tables; however, I wanted to know whether a solution is available to have everything living in one environment.
Below the code (mostly from Mico) I slightly readapted it to fit the caption and avoid it to be repeated on the next page. If not possible to have one single table, would be feasible to remove the headers from the second table (see images) and has it as a continuation of the first? 
\documentclass[12pt]{report}
\usepackage[T1]{fontenc}
\usepackage[letterpaper,margin=1in]{geometry}
\usepackage{longtable,booktabs,siunitx}
\providecommand\tnd{{--}}
\providecommand\mc[1]{\multicolumn{1}{c}{#1}}
\newcommand{\bcaption}[2]{\caption[\textbf{#1}]{\textbf{#1} #2}}
\begin{document}
\begingroup
\footnotesize
\setlength\tabcolsep{0pt}
\setlength\LTleft{0pt}
\setlength\LTright{0pt}
\sisetup{group-minimum-digits=4}
\begin{longtable}{
@{\extracolsep{\fill}}
l
*{2}{S[table-format= 5.0]
S[table-format= 5.0]
S[table-format=-1.2, table-space-text-post=\%]<{\%}
S[table-format= 5.0]
S[table-format= 6.0]}
}
\bcaption{Short caption}{Long caption.}
\label{table:param_est-2} \\
\toprule
& \multicolumn{10}{c}{Approach} \\
\cmidrule{2-11}
& \multicolumn{5}{c}{Linear reference}
& \multicolumn{5}{c}{Pangenome graph} \\
\cmidrule{2-6} \cmidrule{7-11}
& {\textit{exp}} & {\textit{med}} & \mc{$R^2$} & {\textit{MinQ}} & {\textit{MaxQ}}
& {\textit{exp}} & {\textit{med}} & \mc{$R^2$} & {\textit{MinQ}} & {\textit{MaxQ}} \\
\cmidrule{2-11}
\endhead
\midrule
\multicolumn{11}{r}{(table continued on next page)}\\
\endfirsthead % prevent caption to be repeated
\bottomrule
\endlastfoot
nAR & 2555 & 2527 & 86.30 & 2335 & 2902 & 2495 & 2432 & 86.30 & 2304 & 2886 \\
nAFR & 29247 & 29321 & 59.50 & 9338 & 48364 & 30250 & 30836 & 59.50 & 10086 & 47949 \\
nG1 & 21615 & 20035 & 6.47 & 1407 & 45583 & 20695 & 19127 & 6.47 & 1046 & 45266 \\
nG2 & 21615 & 19569 & 13.88 & 997 & 47504 & 21391 & 19116 & 13.88 & 803 & 46953 \\
nBE & 25837 & 26073 & -1.28 & 2284 & 47676 & 25644 & 25645 & -1.28 & 2244 & 47876 \\
nEUR & 18824 & 12674 & 38.45 & 2117 & 45728 & 18574 & 12452 & 38.45 & 1789 & 44654 \\
nCEA & 30985 & 31087 & 49.41 & 11954 & 48772 & 28813 & 29113 & 49.41 & 9025 & 47363 \\
nPAP & 13278 & 10605 & 60.58 & 3712 & 35011 & 14031 & 10917 & 60.58 & 4121 & 35112 \\
nAFR-G1/BE/G2 & 27808 & 26002 & 93.57 & 17564 & 43458 & 25815 & 23931 & 93.57 & 16429 & 41473 \\
nN-NR & 2194 & 2151 & 94.50 & 1898 & 2706 & 2495 & 2429 & 94.50 & 2027 & 2901 \\
nD-D1/2 & 22918 & 19979 & 35.39 & 2513 & 48300 & 25192 & 24594 & 35.39 & 2731 & 48524 \\
nD-N & 17098 & 12169 & 43.85 & 2918 & 43354 & 16834 & 12423 & 43.85 & 2885 & 41932 \\
nAR-D-N & 19197 & 16445 & 22.00 & 1924 & 45600 & 18903 & 16445 & 22.00 & 1890 & 44981 \\
nAR-M & 23054 & 23128 & 99.80 & 19655 & 26341 & 19148 & 18975 & 99.80 & 16653 & 22435 \\
tdAFR-G1 & 97428 & 96736 & 50.95 & 56437 & 139325 & 94479 & 91173 & 50.95 & 55451 & 137513 \\
tdAFR-G2 & 94122 & 90719 & 50.93 & 55657 & 138184 & 95821 & 91886 & 50.93 & 56422 & 138758 \\
tdOA1 & 62685 & 57826 & 46.18 & 45729 & 96452 & 58110 & 54272 & 46.18 & 45663 & 90268 \\
tOAbot1 & 60630 & 54566 & 46.09 & 43497 & 93941 & 55656 & 51883 & 46.09 & 42971 & 85418 \\
tdOA2 & 49041 & 46917 & 24.25 & 40837 & 63729 & 47796 & 46030 & 24.25 & 40525 & 60121 \\
tOAbot2 & 46734 & 44773 & 24.22 & 37999 & 62973 & 45749 & 43668 & 24.22 & 37920 & 59744 \\
tdG2-BE & 73268 & 66597 & 22.40 & 50387 & 117577 & 72338 & 65073 & 22.40 & 50455 & 111864 \\
tdEUR-CEA & 38696 & 37550 & 11.25 & 30900 & 52793 & 37609 & 36408 & 11.25 & 30728 & 49491 \\
taD2-CEA & 30035 & 28725 & 1.79 & 20541 & 45124 & 29038 & 27876 & 1.79 & 20859 & 40769 \\
taBE-EUR & 24468 & 23277 & 0.87 & 11001 & 43495 & 24042 & 23406 & 0.87 & 11101 & 39080 \\
taD1-PAP & 44550 & 43098 & 17.72 & 31204 & 65179 & 43254 & 41473 & 17.72 & 31478 & 62175 \\
taAR-PAP & 52415 & 49013 & 33.25 & 37303 & 80960 & 49523 & 46828 & 33.25 & 36939 & 71169 \\
taN-EUR-CEA & 42778 & 40926 & 18.74 & 33088 & 56748 & 41427 & 39956 & 18.74 & 33298 & 55674 \\
taN-G2 & 52918 & 50734 & 30.19 & 43033 & 71761 & 51816 & 49771 & 30.19 & 42818 & 68086 \\
\end{longtable}
\sisetup{group-digits=none}
\begin{longtable}{
@{\extracolsep{\fill}}
l
*{2}{S[table-format= 1.4]
S[table-format= 1.4]
S[table-format=-1.2, table-space-text-post=\%]<{\%}
S[table-format= 1.4]
S[table-format= 1.4]}
}
\toprule
& \multicolumn{10}{c}{Approach} \\
\cmidrule{2-11}
& \multicolumn{5}{c}{Linear reference}
& \multicolumn{5}{c}{Pangenome graph} \\
\cmidrule{2-6} \cmidrule{7-11}
& {\textit{exp}} & {\textit{med}} & \mc{$R^2$} & {\textit{MinQ}} & {\textit{MaxQ}}
& {\textit{exp}} & {\textit{med}} & \mc{$R^2$} & {\textit{MinQ}} & {\textit{MaxQ}} \\
\cmidrule{2-11}
\endfirsthead
%keeps format consistent between the two tables
%\multicolumn{11}{l}{(table continued from preceding page)}\\
%\addlinespace
%\toprule
%\endhead
\midrule
\multicolumn{11}{r}{(table continued on next page)}\\
\endfoot
\bottomrule
\endlastfoot
rPAP & 0.0170 & 0.0132 & 10.55 & 0.0103 & 0.0327 & 0.0194 & 0.0132 & 10.55 & 0.0104 & 0.0346 \\
rEUR-CEA & 0.0194 & 0.0140 & 5.76 & 0.0103 & 0.0386 & 0.0183 & 0.0133 & 5.76 & 0.0103 & 0.0392 \\
paD2-CEA & 0.0510 & 0.0519 & -1.23 & 0.0075 & 0.0948 & 0.0515 & 0.0517 & -1.23 & 0.0073 & 0.0953 \\
paBE-EUR & 0.2775 & 0.2879 & -1.18 & 0.0756 & 0.4675 & 0.2768 & 0.2813 & -1.18 & 0.0694 & 0.4824 \\
paD1-PAP & 0.0539 & 0.0533 & -1.22 & 0.0071 & 0.0973 & 0.0521 & 0.0523 & -1.22 & 0.0089 & 0.0949 \\
paAR-PAP & 0.0528 & 0.0541 & -1.19 & 0.0055 & 0.0958 & 0.0522 & 0.0528 & -1.19 & 0.0066 & 0.0965 \\
paN-EUR-CEA & 0.0489 & 0.0473 & -1.23 & 0.0046 & 0.0943 & 0.0482 & 0.0452 & -1.23 & 0.0047 & 0.0953 \\
paN-G2 & 0.0510 & 0.0529 & -1.13 & 0.0057 & 0.0944 & 0.0526 & 0.0539 & -1.13 & 0.0057 & 0.0956 \\
m78 & 0.0005 & 0.0005 & 17.87 & 0.0000 & 0.0009 & 0.0005 & 0.0005 & 17.87 & 0.0001 & 0.0009 \\
m87 & 0.0005 & 0.0005 & -0.75 & 0.0000 & 0.0009 & 0.0005 & 0.0006 & -0.75 & 0.0001 & 0.0009 \\
m810 & 0.0005 & 0.0005 & 3.59 & 0.0001 & 0.0009 & 0.0005 & 0.0005 & 3.59 & 0.0001 & 0.0010 \\
m108 & 0.0004 & 0.0004 & 4.04 & 0.0000 & 0.0009 & 0.0005 & 0.0005 & 4.04 & 0.0000 & 0.0009 \\
m1011 & 0.0005 & 0.0006 & -0.19 & 0.0001 & 0.0010 & 0.0006 & 0.0006 & -0.19 & 0.0001 & 0.0010 \\
m1110 & 0.0003 & 0.0003 & 26.86 & 0.0000 & 0.0009 & 0.0003 & 0.0003 & 26.86 & 0.0000 & 0.0009 \\
m1112 & 0.0005 & 0.0005 & 18.87 & 0.0000 & 0.0010 & 0.0006 & 0.0006 & 18.87 & 0.0000 & 0.0010 \\
m1211 & 0.0006 & 0.0007 & 21.04 & 0.0001 & 0.0010 & 0.0007 & 0.0007 & 21.04 & 0.0001 & 0.0010 \\
m1213 & 0.0001 & 0.0001 & 36.13 & 0.0000 & 0.0004 & 0.0001 & 0.0001 & 36.13 & 0.0000 & 0.0005 \\
m1312 & 0.0003 & 0.0003 & 40.14 & 0.0000 & 0.0009 & 0.0004 & 0.0003 & 40.14 & 0.0000 & 0.0009 \\
m1\textunderscore1011 & 0.0005 & 0.0005 & -0.99 & 0.0001 & 0.0010 & 0.0006 & 0.0006 & -0.99 & 0.0001 & 0.0010 \\
m1\textunderscore1110 & 0.0005 & 0.0005 & 1.39 & 0.0001 & 0.0009 & 0.0005 & 0.0005 & 1.39 & 0.0000 & 0.0009 \\
m1\textunderscore1113 & 0.0005 & 0.0005 & 1.39 & 0.0001 & 0.0009 & 0.0005 & 0.0005 & 1.39 & 0.0001 & 0.0010 \\
m1\textunderscore1311 & 0.0005 & 0.0005 & 0.72 & 0.0000 & 0.0009 & 0.0005 & 0.0004 & 0.72 & 0.0000 & 0.0009 \\
\end{longtable}
\endgroup
\end{document}
29247would be displayed as 2.946E5, whereas0.0170would be displayed as1.7E-2, where "E" could be "10^". Please advise.29247with the conventionalS[table-format=5.0]while only decimal numbers are in scientific format (ideally 10^). Then, have the latter aligned with the first unit of the thousand range as in the previous solution. Thanks again!