Spreadsheet: f38f7889-1abb-42bd-aedf-da1bf438bb1c
Sheet: Sheet1

Table S12.  Comparative map contig list. | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 | Unnamed: 9
MGA  chrom | comp map contig | contig | GGA hit chrom | Start of contig | End of contig | Contig size | Other notes | Alternate matches including LLNL coord for GGA28 | Average contig size per chrom
1 | 1 | 1-1 | chr1 | 104450000 | 104459439 | 9439 | contig rearranged or mis-assembled, linkage map places at p telomere
1 | 2 | 1-2 | chr1 | 1 | 376597 | 376596
1 | 3.1 | 1-3.1 | chr1 | 407600 | 9650000
1 | 3.2 | 1-3.2 | chr1 | 10056710 | 74594001
1 | 3.3 | 1-3.3 | chr1 | 9713416 | 10050000 | 74116275 | this segment translocated to here
1 | 4.1 | 1-4.1 | chr1 | 74594873 | 75800000
1 | 4.2 | 1-4.2 | chr1 | 75800000 | 76000000 |  | this segment inverted rel to adjacent and to GGA seq
1 | 4.3 | 1-4.3 | chr1 | 76000000 | 76821378 | 2226505 | centromere between this and subsequent contig based on GGA seq
1 | 5 | 1-5 | chr1 | 78365202 | 79405892 | 1040690 | next gap site of [NAME] family, may be over-collapsed in chicken
1 | 6 | 1-6 | chr1 | 79464814 | 94393042 | 14928228
1 | 7.1 | 1-7.1 | chr1 | 94399974 | 104450000
1 | 7.2 | 1-7.2 | chr1 | 104597633 | 106883004 | 12335397
1 | 8 | 1-8 | chr1 | 106952406 | 112702151 | 5749745
1 | 9 | 1-9 | chr1 | 112746574 | 120415224 | 7668650
1 | 10.1 | 1-10.1 | chr1 | 120539199 | 125900000
1 | 10.2 | 1-10.2 | chr4 | 25500000 | 25550000
1 | 10.3 | 1-10.3 | chr1 | 126300000 | 134895815 | 14006616
1 | 12 | 1-12 | chr1 | 135073276 | 154278840 | 19205564
1 | 13 | 1-13 | chr1 | 154493589 | 155685995 | 1192406
1 | 14 | 1-14 | chr1 | 155835472 | 156017268 | 181796
1 | 15.1 | 1-15.1 | chr1 | 156303569 | 156600000
1 | 15.2 | 1-15.2 | chr4 | 73080000 | 73090000
1 | 15.3 | 1-15.3 | chr1 | 156601000 | 159235184 | 2940615
1 | 16 | 1-16 | chr1 | 159347319 | 161817320 | 2470001
1 | 17.1 | 1-17.1 | chr1 | 161829086 | 172800000
1 | 17.2 | 1-17.2 | chr1 | 172820000 | 172880000 |  | small inversion or mis-assembly of chick seq
1 | 17.3 | 1-17.3 | chr1 | 172900000 | 190221178 | 28352092
1 | 18 | 1-18 | chr1 | 190455285 | 199046530 | 8591245
1 | 19 | 1-19 | chr1 | 199277802 | 200792661 | 1514859 |  |  | 10939262.16666667
2 | 1.1 | 2-1.1 | chr3 | 6218 | 2344838 |  | inverted with 2.35 Mb adjacent to cen/telo and 0 Mb fused to ctg below
2 | 1.2 | 2-1.2 | chr3 | 2458156 | 5589642
2 | 1.3 | 2-1.3 | chr3 | 5605686 | 11605484 |  | inverted relative to GGA seq direction and fused above and below
2 | 1.4 | 2-1.4 | chr3 | 13160571 | 35801865 | 34111198
2 | 2 | 2-2 | chr3 | 36025641 | 47694214 | 11668573
2 | 3 | 2-3 | chr3 | 47813510 | 47852643 | 39133
2 | 4 | 2-4 | chr3 | 47852668 | 50277788 | 2425120
2 | 5 | 2-5 | chr3 | 50279004 | 52131621 | 1852617
2 | 6 | 2-6 | chr3 | 52264424 | 72089794 | 19825370
2 | 7 | 2-7 | chr3 | 72115676 | 92318912 | 20203236
2 | 8 | 2-8 | chr3 | 92325659 | 102233780 | 9908121
2 | 9 | 2-9 | chr3 | 102299219 | 109172251 | 6873032
2 | 10 | 2-10 | chr3 | 109296596 | 109977047 | 680451
2 | 11 | 2-11 | chr3 | 110081078 | 113517217 | 3436139 |  |  | 10092999.09090909
3 | 1.1 | 3-1.1 | chr2 | 54870224 | 56560442 |  | inverted and telomeric in turkey
3 | 1.2 | 3-1.2 | chr2 | 54398341 | 54413232 |  | inverted, relative to seq coordinates | possible misplacement of CNTNAP promoter in GGA
3 | 1.3 | 3-1.3 | chr2 | 54641337 | 54845268 |  | probably inverted, relative to seq coordinates
3 | 1.4 | 3-1.4 | chr2 | 54290000 | 54330000 |  | orientation uncertain | possible misplacement of Ctg254.6 in GGA
3 | 1.5 | 3-1.5 | chr2 | 54452395 | 54545188 |  | inverted, relative to seq coordinates
3 | 1.6 | 3-1.6 | chr2 | 53804240 | 54263147 |  | inverted, relative to seq coordinates
3 | 1.7 | 3-1.7 | chr2 | 56595850 | 108425113 | 54330003
3 | 2 | 3-2 | chr2 | 108425157 | 150393914 | 41968757
3 | 3 | 3-3 | chr2 | 150472902 | 153696086 | 3223184
3 | 4 | 3-4 | chr2 | 153791907 | 154597851 | 805944
3 | 5 | 3-5 | chr2 | 154786527 | 154860006 | 73479 |  |  | 20080273.4
4 | 1 | 4-1 | chr4 | 20886015 | 23274286 | 2388271
4 | 2 | 4-2 | chr4 | 23315675 | 23748706 | 433031
4 | 3 | 4-3 | chr4 | 23870041 | 24101425 | 231384
4 | 4 | 4-4 | chr4 | 24179216 | 25140728 | 961512
4 | 5 | 4-5 | chr4 | 25144461 | 25381360 | 236899
4 | 6 | 4-6 | chr4 | 25579574 | 25952787 | 373213 | small segment between this and above on MGA1
4 | 7 | 4-7 | chr4 | 26005009 | 32198861 | 6193852
4 | 8.1 | 4-8.1 | chr4 | 32232319 | 35828614
4 | 8.2 | 4-8.2 | chr4 | 35828614 | 38999936 | 6767617 | separated from contig above by small duplication of segment near 35.160 Mb
4 | 9 | 4-9 | chr4 | 39078972 | 40170453 | 1091481
4 | 10 | 4-10 | chr4 | 40211358 | 40601051 | 389693
4 | 11 | 4-11 | chr4 | 40887085 | 50312160 | 9425075
4 | 12 | 4-12 | chr4 | 50408834 | 54304177 | 3895343
4 | 13.1 | 4-13.1 | chr4 | 54507989 | 73089000
4 | 13.2 | 4-13.2 | chr4 | 73090000 | 82566701 | 28057712 | small segment between this and above on MGA1
4 | 14 | 4-14 | chr4 | 82613070 | 84527424 | 1914354
4 | 15 | 4-15 | chr4 | 84621596 | 90239565 | 5617969
4 | 16 | 4-16 | chr4 | 90247707 | 93124617 | 2876910
4 | 17 | 4-17 | chr4 | 93160879 | 93540193 | 379314
4 | 18 | 4-18 | chr4 | 93563631 | 93870557 | 306926 |  |  | 3974475.333333333
5 | 1 | 5-1 | chr5 | 1820689 | 6476995 | 4656306 |  | based on genetic map expect whole GGA p arm is inverted
5 | 2 | 5-2 | chr5 | 1722572 | 1783684 | 61112 |  | based on genetic map expect whole GGA p arm is inverted
5 | 3.1 | 5-3.1 | chr5 | 391460 | 1637658 |  |  | based on genetic map expect whole GGA p arm is inverted
5 | 3.2 | 5-3.2 | chr5 | 33112 | 270229 | 1483315 | inverted, relative to rest of GGA p arm | based on genetic map expect whole GGA p arm is inverted
5 | 4 | 5-4 | chr5 | 8023478 | 16580544 | 8557066
5 | 5 | 5-5 | chr5 | 16629934 | 20207952 | 3578018
5 | 6 | 5-6 | chr5 | 20281041 | 30708999 | 10427958
5 | 7 | 5-7 | chr5 | 30708999 | 35719626 | 5010627
5 | 8 | 5-8 | chr5 | 35766800 | 37586517 | 1819717
5 | 9 | 5-9 | chr5 | 37612962 | 42650970 | 5038008
5 | 10 | 5-10 | chr5 | 42650987 | 44803844 | 2152857
5 | 11 | 5-11 | chr5 | 44889480 | 56247122 | 11357642
5 | 12 | 5-12 | chr5 | 56264379 | 57874072 | 1609693
5 | 13 | 5-13 | chr5 | 57879954 | 61590855 | 3710901
5 | 14 | 5-14 | chr5 | 61803984 | 61958140 | 154156 |  |  | 4258384
6 | 1 | 6-1 | chr2 | 163499 | 52182155 | 52018656 |  |  | 52018656
7 | 1 | 7-1 | chr7 | 6895993 | 7248180 | 352187 | ctgs 1-4a (p arm) inverted as a block and fused 8.88 Mb
7 | 2 | 7-2 | chr7 | 1563650 | 6757478 | 5193828 | ctgs 1-4a (p arm) inverted as a block and fused 8.88 Mb
7 | 3.1 | 7-3.1 | chr7 | 33395 | 1560224 |  | ctgs 1-4a (p arm) inverted as a block and fused 8.88 Mb
7 | 3.2 | 7-3.2 | chr7 | 8876111 | 9073815 | 1724533 | fused to inverted p arm above
7 | 4 | 7-4 | chr7 | 9277483 | 10600791 | 1323308
7 | 5 | 7-5 | chr7 | 10740928 | 11321410 | 580482
7 | 6 | 7-6 | chr7 | 11459598 | 25901793 | 14442195
7 | 7 | 7-7 | chr7 | 26028569 | 37722951 | 11694382
7 | 8 | 7-8 | chr7 | 37731061 | 38362250 | 631189 |  |  | 4492763
8 | 1.1 | 8-1.1 | chr6 | 10430381 | 11438238 |  | linked to ctg below
8 | 1.2 | 8-1.2 | chr6 | 4318091 | 7654280 | 4344046 | inverted relative to GGA seq coord. and linked to ctg above
8 | 2.1 | 8-2.1 | chr6 | 4075907 | 4113451 |  | very small segment linked to below, orientation uncertain
8 | 2.2 | 8-2.2 | chr6 | 10348893 | 10369758 | 58409 | very small segment linked to below, orientation uncertain | may be another very small segment between this and that below
8 | 3 | 8-3 | chr6 | 3437262 | 3919764 | 482502 | inverted relative to GGA seq direction
8 | 4.1 | 8-4.1 | chr6 | 1576787 | 3333183 |  | inverted relative to GGA seq direction and fused to 10.3 Mb below
8 | 4.2 | 8-4.2 | chr6 | 7735050 | 10296511 |  | inverted relative to GGA seq direction and fused to 1.58 Mb above and to 11.53 Mb below
8 | 4.3 | 8-4.3 | chr6 | 11531176 | 12153164 |  | fused above and below
8 | 4.4 | 8-4.4 | chr6 | 12264632 | 13080207 |  | inverted and linked to ctgs above and below
8 | 4.5 | 8-4.5 | chr6 | 13140570 | 13662185 | 6277035
8 | 5 | 8-5 | chr6 | 13775918 | 37027732 | 23251814 |  |  | 6882761.2
9 | 1 | 9-1 | chr4 | 159831 | 18983379 | 18823548
9 | 2 | 9-2 | chr4 | 19099678 | 19248762 | 149084 |  |  | 9486316
10 | 1 | 10-1 | chr8_random | 64951 | 407592 | 342641 | (telomere adjacent, orientation unknown) | ctgs1-9a (entire p arm) inverted as a block and fused to 11.75 Mb
10 | 2 | 10-2 | chr8 | 9612808 | 10199791 | 586983 | inverted relative to GGA seq direction | ctgs1-9a (entire p arm) inverted as a block and fused to 11.75 Mb
10 | 3.1 | 10-3.1 | chr8 | 9250000 | 9580931 |  | inverted relative to GGA seq direction | ctgs1-9a (entire p arm) inverted as a block and fused to 11.75 Mb
10 | 3.2 | 10-3.2 | chr8 | 8992540 | 9250000 | 588391 | inverted and fused at 8.99 to segment above (same seq orientation as GGA seq) | ctgs1-9a (entire p arm) inverted as a block and fused to 11.75 Mb
10 | 4 | 10-4 | chr8 | 8427337 | 8972971 | 545634 | inverted relative to GGA seq direction | ctgs1-9a (entire p arm) inverted as a block and fused to 11.75 Mb
10 | 5 | 10-5 | chr8 | 7903951 | 8331245 | 427294 | inverted relative to GGA seq direction | ctgs1-9a (entire p arm) inverted as a block and fused to 11.75 Mb
10 | 6 | 10-6 | chr8 | 2752222 | 7894254 | 5142032 | inverted relative to GGA seq direction | ctgs1-9a (entire p arm) inverted as a block and fused to 11.75 Mb
10 | 7 | 10-7 | chr8 | 992884 | 2688360 | 1695476 | inverted relative to GGA seq direction | ctgs1-9a (entire p arm) inverted as a block and fused to 11.75 Mb
10 | 8.1 | 10-8.1 | chr8 | 44817 | 887186 |  | inverted relative to GGA seq direction and fused at 11.75 Mb to segment below | ctgs1-9a (entire p arm) inverted as a block and fused to 11.75 Mb
10 | 8.2 | 10-8.2 | chr8 | 11745890 | 26733208 | 15829687
10 | 9 | 10-9 | chr8 | 26743828 | 27430057 | 686229
10 | 10 | 10-10 | chr8 | 27432657 | 30091465 | 2658808
10 | 11 | 10-11 | chr8 | 30348298 | 30659823 | 311525 |  |  | 2619518.181818182
11 | 1.1 | 11-1.1 | chr9 | 1528027 | 4372460 |  | inverted rel to GGA seq direction and fused to below
11 | 1.2 | 11-1.2 | chr9 | 4521698 | 14950479 | 13273214
11 | 2 | 11-2 | chr9 | 14954975 | 25410652 | 10455677 |  |  | 11864445.5
12 | 1 | 12-1 | chr10 | 132022 | 22403335 | 22271313 | no internal centromere, likely distal at p end compared to chick seq |  | 22271313
13 | 1.1 | 13-1.1 | chr11 | 75337 | 2681245 |  | GGA11 p arm inverted to place centromere distal in MGA13
13 | 1.2 | 13-1.2 | chr11 | 3197512 | 21852426 | 21260822 |  |  | 21260822
14 | 1 | 14-1 | chr12 | 1050000 | 1100000 | 50000 | maybe telomeric, orientation uncertain
14 | 2 | 14-2 | chr12 | 95816 | 940546 | 844730 | may be inverted, orientation uncertain
14 | 3.1 | 14-3.1 | chr12 | 1164557 | 1399694 |  | inverted and fused to segment below
14 | 3.2 | 14-3.2 | chr12 | 1599552 | 2632117
14 | 3.3 | 14-3.3 | chr12 | 1128610 | 1134284 |  | translocated to between segment above and below
14 | 3.4 | 14-3.4 | chr12 | 2703753 | 20521125 | 19090748 |  |  | 6661826
15 | 1 | 15-1 | chr13 | 504597 | 1533291 | 1028694
15 | 2.1 | 15-2.1 | chr13 | 1583502 | 8120304
15 | 2.2 | 15-2.2 | chr13 | 8233861 | 8511782 |  | inverted, fused both above and below
15 | 2.3 | 15-2.3 | chr13 | 8613143 | 18771424 | 16973004 |  |  | 9000849
16 | 1.1 | 16-1.1 | chr14 | 42990 | 14370000
16 | 1.2 | 16-1.2 | chr14 | 14370000 | 15070000 |  | inverted, fused both above and below
16 | 1.3 | 16-1.3 | chr14 | 15070000 | 15937232 | 15894242 |  |  | 15894242
17 | 1 | 17-1 | chr15 | 35017 | 12963265 | 12928248 |  |  | 12928248
18 | 1 | 18-1 | chr16 | 110935 | 179003 | 68068 | coverage very poor in both turkey, chicken |  | 68068
19 | 1 | 19-1 | chr17 | 596337 | 10998633 | 10402296 |  |  | 10402296
20 | 1 | 20-1 | chr18 | 62050 | 591500 | 529450
20 | 2.1 | 20-2.1 | chr18 | 616751 | 5056017
20 | 2.2 | 20-2.2 | chr18 | 5062096 | 9882412 |  | inverted, fused both above and below
20 | 2.3 | 20-2.3 | chr18 | 9969749 | 10663287 | 9953120 |  |  | 5241285
21 | 1 | 21-1 | chr19 | 15185 | 9912622 | 9897437 |  |  | 9897437
22 | 1 | 22-1 | chr20 | 24785 | 1372029 | 1347244
22 | 2 | 22-2 | chr20 | 1546045 | 1913576 | 367531
22 | 3 | 22-3 | chr20 | 1935559 | 3421640 | 1486081
22 | 4 | 22-4 | chr20 | 3433668 | 13816927 | 10383259 |  |  | 3396028.75
23 | 1 | 23-1 | chr21 | 69272 | 6047126 | 5977854
23 | 2 | 23-2 | chr21 | 6148201 | 6324950 | 176749
23 | 3 | 23-3 | chr21 | 6549150 | 6923986 | 374836 |  |  | 2176479.666666667
24 | 1 | 24-1 | chr22 | 122932 | 1313782 | 1190850
24 | 2 | 24-2 | chr22 | 1488942 | 2793740 | 1304798
24 | 3 | 24-3 | chr22 | 3027592 | 3646605 | 619013
24 | 4 | 24-4 | chr22 | 3810461 | 3934148 | 123687 |  |  | 809587
25 | 1 | 25-1 | chr23 | 17639 | 1555409 | 1537770
25 | 2 | 25-2 | chr23 | 1591402 | 1877661 | 286259 | pericentromeric in GGA seq
25 | 3 | 25-3 | chr23 | 2553913 | 3032489 | 478576 | pericentromeric in GGA seq
25 | 4 | 25-4 | chr23 | 3169579 | 3422604 | 253025
25 | 5 | 25-5 | chr23 | 3495373 | 4956530 | 1461157
25 | 6 | 25-6 | chr23 | 5180217 | 5987585 | 807368 |  |  | 804025.8333333334
26 | 1 | 26-1 | chr24 | 97028 | 6527674 | 6430646 |  |  | 6430646
27 | 1 | 27-1 | chr25 | 68377 | 765902 | 697525
27 | 2 | 27-2 | chr25 | 904957 | 977918 | 72961
27 | 3 | 27-3 | chr25 | 1052313 | 1297471 | 245158
27 | 4 | 27-4 | chr25 | 1487201 | 1500001 | 12800
27 | 5 | 27-5 | chr25 | 1511488 | 1915197 | 403709 |  |  | 286430.6
28 | 1 | 28-1 | chr26 | 61649 | 220981 | 159332
28 | 2 | 28-2 | chr26 | 354262 | 998625 | 644363
28 | 3 | 28-3 | chr26 | 1166393 | 2692638 | 1526245
28 | 4 | 28-4 | chr26 | 2847756 | 3664877 | 817121
28 | 5 | 28-5 | chr26 | 3753587 | 4805234 | 1051647
28 | 6 | 28-6 | chr26 | 4823512 | 4909872 | 86360
28 | 7 | 28-7 | chr26 | 5087259 | 5096850 | 9591 |  |  | 613522.7142857143
29 | 1 | 29-1 | chr27 | 81436 | 496440 | 415004 | telomeric ~1 Mb repetitive and uncertain assembly, T cell receptor complex
29 | 2 | 29-2 | chr27 | 908385 | 1296301 | 387916
29 | 3 | 29-3 | chr27 | 1525354 | 2532444 | 1007090
29 | 4 | 29-4 | chr27 | 2590502 | 2776950 | 186448
29 | 5 | 29-5 | chr27 | 3004642 | 3653775 | 649133
29 | 6 | 29-6 | chr27 | 3815791 | 4020001 | 204210
29 | 7 | 29-7 | chr27 | 4165778 | 4830253 | 664475 |  |  | 502039.4285714286
30 | 1 | 30-1 | chr28 | 30242 | 1049001 | 1018759
30 | 2.1 | 30-2.1 | chr28 | 1550000 | 1620000 | 70000 | partial or complete duplication
30 | 2.2 | 30-2.2 | chr28 | 1057844 | 1620001 | 562157
30 | 3 | 30-3 | chr28 | 1702912 | 2464944 | 762032
30 | 4 | 30-4 | chr28 | 2485000 | 4500181 | 2015181 |  |  | 885625.8
Z |  |  |  |  |  |  | 131 contigs, not shown |  | 569465.6488549619
 |  |  |  |  | Average = | 6152256.333333333