SELDLA: Scaffold Extender with Low Depth Linkage Analysis
>scaffold_1 7245445
CCCCCTGCTAGCTTCCCCCTGCTCAGCCTCCCCCTGCTCAGCCTCCCCCC
TGCTCAGCCTCCCCCTTGTCCCCCCCCTTGTCCTCCTCTTGTCCTCCTCT
TGTCCCCCTCTCAGGTGATTTTATTCACCTCCGTTCCTCCAACCTCTCTG
GAACTCAAAGATGAACGATGACAGATGAACTTCAGCGCTGCTGCGAGGAA
ACAAAGCTTTCTCTCTTTTCGCTCCTTTTGTGATAAGTCAACTTTCTCCG
CTCTCACTCCACGAGGAGAAATCGGTGCACGTGTAGACGCGCTGACCCCC
GGGGCTGCTCACGCCCCCCTGGTAGGGTCAACGCCTCCCTGGTAGGGTCA
ACGCCCCCCTGGTAGGGTCAACGCCCCCCTGGTAGGGTCAACACCTCCCT
AGTAGGGTCAACACCTCCCAGGTAGGGTCAACGCTGCTTCTCCTCAGACT
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1 10 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 12 120 121 122 123 124 125 126 127 128 129 13 130 131 132 133 134 135 136 137 138 139 14 140 141 142 143 144 145 146 147 148 149 15 150 151 153 154 155 156 157 158 159 16 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 18 180 181 182 183 184 185 186 187 188 189 19 190 191 192 194 195 196 2 20 22 23 24 25 26 27 28 29 3 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 5 50 51 52 53 54 55 56 57 58 59 6 61 62 63 64 65 66 67 69 7 70 71 72 73 74 75 76 77 78 79 8 80 81 82 83 84 85 86 87 88 89 9 90 91 92 93 94 95 96 97 98 99 female male
scaffold_1 420 . A T 34.32 . AC=3;AF=0.100;AN=30;BaseQRankSum=-1.846;DP=171;Dels=0.00;FS=0.000;HaplotypeScore=0.0578;InbreedingCoeff=0.0003;MLEAC=3;MLEAF=0.100;MQ=10.39;MQ0=145;MQRankSum=-2.327;QD=1.63;ReadPosRankSum=0.241 GT:AD:DP:GQ:PL 0/0:2,0:2:6:0,6,63 ./. 0/0:3,0:3:3:0,3,32 ./. ./. ./. 0/0:1,0:1:3:0,3,32 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:5,0:5:3:0,3,32 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:3:0,3,32 ./. ./. 0/0:1,0:1:3:0,3,32 1/1:0,1:1:3:30,3,0 ./. 0/0:2,0:2:3:0,3,32 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:3:0,3,32 ./. ./. ./. 0/1:18,2:20:43:43,0,108 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:3:0,3,26 ./. ./. ./. 0/0:4,0:4:6:0,6,63 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:6:0,6,63 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:4,0:4:3:0,3,32 ./. ./. ./. ./. ./. ./. ./. 0/0:29,0:29:12:0,12,126
scaffold_1 1042 . T C 51.39 . AC=4;AF=1.00;AN=4;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=7.43;MQ0=41;QD=17.13 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3:41,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,2:2:3:30,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./.
scaffold_1 1297 . T C 1096.18 . AC=34;AF=1.00;AN=34;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=0.0489;InbreedingCoeff=male female 1 10 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 12 120 121 122 123 124 125 126 127 128 129 13 130 131 132 133 134 135 136 137 138 139 14 140 141 142 143 144 145 146 147 148 149 15 150 151 153 154 155 156 157 158 159 16 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 18 180 181 182 183 184 185 186 187 188 189 19 190 191 192 194 195 196 2 20 22 23 24 25 26 27 28 29 3 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 5 50 51 52 53 54 55 56 57 58 59 6 61 62 63 64 65 66 67 69 7 70 71 72 73 74 75 76 77 78 79 8 80 81 82 83 84 85 86 87 88 89 9 90 91 92 93 94 95 96 97 98 99-c "8" -m "64" -b "--mode=crossbreed --DP=1 -r 10000 --cs=2"
#1 26763950
1 scaffold_339 - 0 243467 0 10.1063829787234
1 scaffold_134 - 253467 1065365 10.1063829787234 25.531914893617
1 scaffold_2071 + 1075365 1106428 25.531914893617 26.063829787234
1 scaffold_235 - 1116428 1559930 26.063829787234 29.2553191489362
1 scaffold_130 - 1569930 2395664 29.2553191489362 37.2340425531915
1 scaffold_295 + 2405664 2720008 37.2340425531915 38.2978723404255
1 scaffold_2072 na 2730008 2760918 38.2978723404255 38.2978723404255
1 scaffold_581 na 2770918 2846777 38.2978723404255 38.2978723404255
1 scaffold_59 + 2856777 4275766 38.2978723404255 40.9574468085106
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1 10 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 12 120 121 122 123 124 125 126 127 128 129 13 130 131 132 133 134 135 136 137 138 139 14 140 141 142 143 144 145 146 147 148 149 15 150 151 153 154 155 156 157 158 159 16 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 18 180 181 182 183 184 185 186 187 188 189 19 190 191 192 194 195 196 2 20 22 23 24 25 26 27 28 29 3 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 5 50 51 52 53 54 55 56 57 58 59 6 61 62 63 64 65 66 67 69 7 70 71 72 73 74 75 76 77 78 79 8 80 81 82 83 84 85 86 87 88 89 9 90 91 92 93 94 95 96 97 98 99 female male
linkage_scaffold_4 6117318 . A T 34.32 . AC=3;AF=0.100;AN=30;BaseQRankSum=-1.846;DP=171;Dels=0.00;FS=0.000;HaplotypeScore=0.0578;InbreedingCoeff=0.0003;MLEAC=3;MLEAF=0.100;MQ=10.39;MQ0=145;MQRankSum=-2.327;QD=1.63;ReadPosRankSum=0.241 GT:AD:DP:GQ:PL 0/0:2,0:2:6:0,6,63 ./. 0/0:3,0:3:3:0,3,32 ./. ./. ./. 0/0:1,0:1:3:0,3,32 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:5,0:5:3:0,3,32 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:3:0,3,32 ./. ./. 0/0:1,0:1:3:0,3,32 1/1:0,1:1:3:30,3,0 ./. 0/0:2,0:2:3:0,3,32 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:3:0,3,32 ./. ./. ./. 0/1:18,2:20:43:43,0,108 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:3:0,3,26 ./. ./. ./. 0/0:4,0:4:6:0,6,63 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:6:0,6,63 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:4,0:4:3:0,3,32 ./. ./. ./. ./. ./. ./. ./. 0/0:29,0:29:12:0,12,126
linkage_scaffold_4 6117940 . T C 51.39 . AC=4;AF=1.00;AN=4;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=7.43;MQ0=41;QD=17.13 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3:41,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,2:2:3:30,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./.
linkage_scaffold_4 6118195 . T C 1096.18 . AC=34;AF=1.00;AN=34;DP=91;Dels=0.00;FS=0.000;Hapl