Table 4. The intravarietal SNPs found in coding region of date palm chloroplast genome.
| NO. | Gene name | Major(minor) SNP type | Major(minor) Codon | Major(minor) amino acid | Major(minor) Reads number | Major(minor) reads percentage | Strand | Position in CDS | Position in genome |
| 1 | psbAa | C(T) | acC(acT) | Thr(Thr) | 863(124) | 87.4(12.6) | − | 858 | 352 |
| 2 | psbAa | G(A) | gGa(gAa) | Gly(Glu) | 863(206) | 80.7(19.3) | − | 728 | 482 |
| 3 | psbAa | A(G) | gcA(gcG) | Ala(Ala) | 1167(296) | 79.8(20.2) | − | 564 | 646 |
| 4 | psbA | T(G) | cTa(cGa) | Leu(Arg) | 1117(250) | 81.7(18.3) | − | 350 | 860 |
| 5 | psbAa | C(T) | tcC(tcT) | Ser(Ser) | 1061(190) | 84.8(15.2) | − | 303 | 907 |
| 6 | atpFa | A(G) | gaA(gaG) | Glu(Glu) | 928(132) | 87.5(12.5) | − | 282 | 12699 |
| 7 | atpI | A(T) | Agt(Tgt) | Ser(Cys) | 774(93) | 89.3(10.7) | − | 559 | 15572 |
| 8 | rps2a | G(A) | Gcg(Acg) | Ala(Thr) | 558(62) | 90.0(10.0) | − | 475 | 16632 |
| 9 | rpoC2 | A(C) | aaA(aaC) | Lys(Asn) | 564(211) | 72.8(27.2) | − | 711 | 20742 |
| 10 | rpoC2 | C(A) | caC(caA) | His(Gln) | 988(202) | 83.0(17.0) | − | 636 | 20817 |
| 11 | rpoC2a | T(C) | caT(caC) | His(His) | 898(134) | 87.0(13.0) | − | 432 | 21021 |
| 12 | rpoC2 | A(C) | Aat(Cat) | Asn(His) | 828(101) | 89.1(10.9) | − | 352 | 21101 |
| 13 | rpoC2 | T(G) | tTa(tGa) | Leu(−) | 789(99) | 88.9(11.1) | − | 290 | 21163 |
| 14 | rpoC2 | T(C) | Ttt(GtC) | Phe(Val) | 398(94) | 80.9(19.1) | − | 240 | 21213 |
| 15 | rpoC2 | T(G) | 238 | 21215 | |||||
| 16 | rpoC1a | A(G) | aAt(aGt) | Asn(Ser) | 624(231) | 73.0(27.0) | − | 1931 | 21750 |
| 17 | rpoC1 | A(C) | ttA(ttC) | Leu(Phe) | 938(235) | 80.0(20.0) | − | 1503 | 22178 |
| 18 | rpoC1 | A(C) | ttA(ttC) | Leu(Phe) | 702(225) | 75.7(24.3) | − | 1230 | 22451 |
| 19 | rpoC1a | A(G) | ctA(ctG) | Leu(Leu) | 952(223) | 81.0(19.0) | − | 1113 | 22568 |
| 20 | rpoC1a | G(A) | gaG(gaA) | Glu(Glu) | 762(181) | 80.8(19.2) | − | 1092 | 22589 |
| 21 | rpoC1a | T(C) | ctT(ctC) | Leu(Leu) | 674(231) | 74.5(25.5) | − | 885 | 22796 |
| 22 | rpoC1 | T(G) | ttT(ttG) | Phe(Leu) | 256(53) | 82.8(17.2) | − | 537 | 23144 |
| 23 | rpoC1 | A(C) | Aga(Cga) | Arg(Arg) | 529(171) | 75.6(24.4) | − | 199 | 24221 |
| 24 | rpoB | T(G) | tTt(tGt) | Phe(Cys) | 661(165) | 80.0(20.0) | − | 2744 | 24909 |
| 25 | rpoBa | C(T) | tgC(tgT) | Cys(Cys) | 748(137) | 84.5(15.5) | − | 2601 | 25052 |
| 26 | rpoB | A(C) | tcA(tcC) | Ser(Ser) | 319(114) | 73.7(26.3) | − | 2487 | 25166 |
| 27 | rpoB | G(T) | Gat(Tat) | Asp(Tyr) | 963(132) | 87.9(12.1) | − | 2035 | 25618 |
| 28 | psaBa | T(C) | gaT(gaC) | Asp(Asp) | 789(106) | 88.2(11.8) | − | 1092 | 39000 |
| 29 | psaBa | G(T) | ggG(ggT) | Gly(Gly) | 874(100) | 89.7(10.3) | − | 864 | 39228 |
| 30 | psaB | G(T) | Gat(Tat) | Asp(Tyr) | 868(106) | 89.1(10.9) | − | 814 | 39278 |
| 31 | psaBa | A(G) | acA(acG) | Thr(Thr) | 647(87) | 88.1(11.9) | − | 795 | 39297 |
| 32 | psaBa | C(T) | agC(agT) | Ser(Ser) | 861(109) | 88.8(11.2) | − | 720 | 39372 |
| 33 | psaA | A(C) | ttA(ttC) | Leu(Phe) | 521(210) | 71.3(28.7) | − | 2118 | 40252 |
| 34 | psaA | A(C) | tcA(tcC) | Ser(Ser) | 858(145) | 85.5(14.5) | − | 1800 | 40570 |
| 35 | rps4a | A(C) | atA(atC) | Ile(Ile) | 836(132) | 86.4(15.6) | − | 282 | 46306 |
| 36 | ndhJa | T(C) | ttT(ttC) | Phe(Phe) | 407(113) | 78.3(21.7) | − | 456 | 49697 |
| 37 | atpB | A(C) | gtA(gtC) | Val(Val) | 1041(257) | 80.2(19.8) | − | 696 | 55445 |
| 38 | accD | G(A) | gaG(gaA) | Glu(Glu) | 708(88) | 88.9(11.1) | + | 48 | 59201 |
| 39 | accD | C(T) | tcC(tcT) | Ser(Ser) | 680(94) | 87.9(12.1) | + | 276 | 59429 |
| 40 | accD | C(A) | Cat(Aat) | His(Asn) | 863(108) | 88.9(11.1) | + | 403 | 59556 |
| 41 | accD | T(G) | Tac(Gac) | Tyr(Asp) | 852(106) | 88.9(11.1) | + | 406 | 59559 |
| 42 | accD | T(G) | ttT(ttG) | Phe(Leu) | 618(106) | 85.4(14.6) | + | 987 | 60140 |
| 43 | accD | G(A) | gGa(gAa) | Gly(Glu) | 877(114) | 88.5(11.5) | + | 1097 | 60250 |
| 44 | accD | C(T) | tcC(tcT) | Ser(Ser) | 848(102) | 89.3(10.7) | + | 1152 | 60305 |
| 45 | accD | A(C) | Aaa(Caa) | Lys(Gln) | 354(102) | 77.6(22.4) | + | 1177 | 60330 |
| 46 | cemA | G(C) | gtG(gtC) | Val(Val) | 1181(175) | 87.1(12.9) | + | 672 | 63407 |
| 47 | petA | A(G) | gcA(gcG) | Ala(Ala) | 844(113) | 88.2(11.8) | + | 828 | 64480 |
| 48 | psbEa | G(A) | ccG(ccA) | Pro(Pro) | 951(130) | 88.0(12.0) | − | 192 | 66208 |
| 49 | psbB | A(C) | ttA(ttC) | Leu(Phe) | 640(184) | 77.7(22.3) | + | 927 | 75429 |
| 50 | psbT | A(C) | atA(atC) | Ile(Ile) | 695(153) | 82.0(18.0) | + | 48 | 76250 |
| 51 | psbT | A(C) | Aaa(Caa) | Lys(Gln) | 233(151) | 60.7(39.3) | + | 100 | 76302 |
| 52 | psbH | A(G) | acA(acG) | Thr(Thr) | 782(115) | 87.2(12.8) | + | 120 | 76734 |
| 53 | psbH | G(A) | ttG(ttA) | Leu(Leu) | 651(89) | 88.0(12.0) | + | 174 | 76788 |
| 54 | psbH | T(G) | atT(atG) | Ile(Met) | 468(85) | 84.6(15.4) | + | 180 | 76794 |
| 55 | psbH | T(G) | Tat(Gat) | Tyr(Asp) | 469(85) | 84.7(15.3) | + | 181 | 76795 |
| 56 | petB | T(A) | aTa(aAa) | Ile(Lys) | 715(108) | 86.9(13.1) | + | 101 | 77843 |
| 57 | petB | T(G) | Tat(Gat) | Tyr(Asp) | 520(123) | 80.9(19.1) | + | 106 | 77848 |
| 58 | petB | T(G) | Tac(Gac) | Tyr(Asp) | 493(152) | 76.4(23.6) | + | 175 | 77917 |
| 59 | petB | A(C) | gtA(gtC) | Val(Val) | 576(219) | 72.5(27.5) | + | 450 | 78192 |
| 60 | rps11 | A(C) | Att(Ctt) | Ile(Leu) | 1007(120) | 89.4(10.6) | − | 118 | 81436 |
| 61 | ycf2 | T(G) | ttT(ttG) | Phe(Leu) | 917(121) | 88.3(11.7) | + | 3765 | 92696 |
| 62 | ndhA | T(G) | tTa(tGa) | Leu(−) | 793(100) | 88.8(11.2) | − | 1010 | 122904 |
a
the minor genotype in date palm is major genotype in oil palm, or vice versa.