Mercurial > repos > devteam > samtools_stats

comparison test-data/samtools_stats_out1.tab @ 8:e28839a4b932 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author iuc
date Tue, 28 Sep 2021 16:17:39 +0000
parents 95a7ddf617e7
children
comparison
equal deleted inserted replaced
7:145f6d74ff5e 8:e28839a4b932
1 # This file was produced by samtools stats (1.9+htslib-1.9) and can be plotted using plot-bamstats 1 # This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats
2 # This file contains statistics for all reads. 2 # This file contains statistics for all reads.
3 # The command line was: stats --ref-seq reference.fa infile 3 # The command line was: stats --ref-seq reference.fa -@ 0 infile
4 # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities 4 # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities
5 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) 5 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
6 CHK 1bd20fd8 58ad2167 29883386 6 CHK 1bd20fd8 58ad2167 29883386
7 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. 7 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
8 SN raw total sequences: 200 8 SN raw total sequences: 200 # excluding supplementary and secondary reads
9 SN filtered sequences: 0 9 SN filtered sequences: 0
10 SN sequences: 200 10 SN sequences: 200
11 SN is sorted: 1 11 SN is sorted: 1
12 SN 1st fragments: 100 12 SN 1st fragments: 100
13 SN last fragments: 100 13 SN last fragments: 100
18 SN reads paired: 200 # paired-end technology bit set 18 SN reads paired: 200 # paired-end technology bit set
19 SN reads duplicated: 0 # PCR or optical duplicate bit set 19 SN reads duplicated: 0 # PCR or optical duplicate bit set
20 SN reads MQ0: 6 # mapped and MQ=0 20 SN reads MQ0: 6 # mapped and MQ=0
21 SN reads QC failed: 0 21 SN reads QC failed: 0
22 SN non-primary alignments: 0 22 SN non-primary alignments: 0
23 SN supplementary alignments: 0
23 SN total length: 50200 # ignores clipping 24 SN total length: 50200 # ignores clipping
24 SN total first fragment length: 25100 # ignores clipping 25 SN total first fragment length: 25100 # ignores clipping
25 SN total last fragment length: 25100 # ignores clipping 26 SN total last fragment length: 25100 # ignores clipping
26 SN bases mapped: 6275 # ignores clipping 27 SN bases mapped: 6275 # ignores clipping
27 SN bases mapped (cigar): 6275 # more accurate 28 SN bases mapped (cigar): 6275 # more accurate
1092 GCC 247 32.00 14.00 13.00 41.00 0.00 0.00 1093 GCC 247 32.00 14.00 13.00 41.00 0.00 0.00
1093 GCC 248 18.00 18.00 25.00 39.00 0.00 0.00 1094 GCC 248 18.00 18.00 25.00 39.00 0.00 0.00
1094 GCC 249 25.00 23.00 21.00 31.00 0.00 0.00 1095 GCC 249 25.00 23.00 21.00 31.00 0.00 0.00
1095 GCC 250 27.50 22.50 17.50 32.50 0.00 0.00 1096 GCC 250 27.50 22.50 17.50 32.50 0.00 0.00
1096 GCC 251 13.50 20.50 36.50 29.50 0.00 0.00 1097 GCC 251 13.50 20.50 36.50 29.50 0.00 0.00
1098 # ACGT content per cycle, read oriented. Use `grep ^GCT | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]
1099 GCT 1 22.45 32.65 31.63 13.27
1100 GCT 2 26.00 17.00 10.00 47.00
1101 GCT 3 34.00 25.00 9.00 32.00
1102 GCT 4 13.00 32.00 10.00 45.00
1103 GCT 5 37.00 24.00 10.00 29.00
1104 GCT 6 44.00 26.00 17.00 13.00
1105 GCT 7 28.00 13.00 32.00 27.00
1106 GCT 8 49.00 16.00 18.00 17.00
1107 GCT 9 19.00 35.00 16.00 30.00
1108 GCT 10 35.00 13.00 22.00 30.00
1109 GCT 11 18.00 15.00 29.00 38.00
1110 GCT 12 28.00 24.00 22.00 26.00
1111 GCT 13 29.00 17.00 19.00 35.00
1112 GCT 14 21.21 24.24 24.24 30.30
1113 GCT 15 23.00 20.00 25.00 32.00
1114 GCT 16 35.00 15.00 20.00 30.00
1115 GCT 17 29.00 26.00 13.00 32.00
1116 GCT 18 31.00 30.00 18.00 21.00
1117 GCT 19 30.00 26.00 21.00 23.00
1118 GCT 20 23.00 21.00 20.00 36.00
1119 GCT 21 36.00 18.00 19.00 27.00
1120 GCT 22 39.00 31.00 13.00 17.00
1121 GCT 23 30.30 21.21 11.11 37.37
1122 GCT 24 36.00 14.00 20.00 30.00
1123 GCT 25 38.00 23.00 17.00 22.00
1124 GCT 26 36.00 21.00 13.00 30.00
1125 GCT 27 32.00 18.00 22.00 28.00
1126 GCT 28 30.00 13.00 25.00 32.00
1127 GCT 29 30.00 28.00 23.00 19.00
1128 GCT 30 34.00 21.00 13.00 32.00
1129 GCT 31 33.00 29.00 14.00 24.00
1130 GCT 32 38.00 20.00 20.00 22.00
1131 GCT 33 27.00 23.00 15.00 35.00
1132 GCT 34 43.00 17.00 20.00 20.00
1133 GCT 35 35.00 23.00 22.00 20.00
1134 GCT 36 41.00 25.00 16.00 18.00
1135 GCT 37 38.00 18.00 18.00 26.00
1136 GCT 38 23.00 26.00 25.00 26.00
1137 GCT 39 22.00 41.00 19.00 18.00
1138 GCT 40 29.00 14.00 23.00 34.00
1139 GCT 41 29.00 27.00 20.00 24.00
1140 GCT 42 29.00 27.00 18.00 26.00
1141 GCT 43 38.00 28.00 16.00 18.00
1142 GCT 44 21.00 26.00 23.00 30.00
1143 GCT 45 38.00 25.00 18.00 19.00
1144 GCT 46 27.00 21.00 22.00 30.00
1145 GCT 47 40.00 28.00 18.00 14.00
1146 GCT 48 25.00 22.00 20.00 33.00
1147 GCT 49 26.00 33.00 10.00 31.00
1148 GCT 50 49.00 20.00 10.00 21.00
1149 GCT 51 29.00 29.00 13.00 29.00
1150 GCT 52 43.00 22.00 22.00 13.00
1151 GCT 53 19.00 27.00 27.00 27.00
1152 GCT 54 25.00 18.00 25.00 32.00
1153 GCT 55 32.00 22.00 17.00 29.00
1154 GCT 56 36.00 20.00 16.00 28.00
1155 GCT 57 28.00 24.00 23.00 25.00
1156 GCT 58 23.00 39.00 17.00 21.00
1157 GCT 59 33.00 21.00 26.00 20.00
1158 GCT 60 30.00 26.00 19.00 25.00
1159 GCT 61 23.00 23.00 25.00 29.00
1160 GCT 62 35.00 19.00 20.00 26.00
1161 GCT 63 26.00 25.00 29.00 20.00
1162 GCT 64 30.00 20.00 27.00 23.00
1163 GCT 65 38.00 17.00 21.00 24.00
1164 GCT 66 33.00 26.00 14.00 27.00
1165 GCT 67 35.00 21.00 21.00 23.00
1166 GCT 68 39.00 28.00 15.00 18.00
1167 GCT 69 38.00 18.00 22.00 22.00
1168 GCT 70 40.00 13.00 22.00 25.00
1169 GCT 71 29.00 41.00 19.00 11.00
1170 GCT 72 33.00 26.00 28.00 13.00
1171 GCT 73 31.00 18.00 24.00 27.00
1172 GCT 74 31.00 32.00 13.00 24.00
1173 GCT 75 46.00 10.00 21.00 23.00
1174 GCT 76 23.00 28.00 25.00 24.00
1175 GCT 77 35.00 20.00 19.00 26.00
1176 GCT 78 29.00 30.00 26.00 15.00
1177 GCT 79 24.00 25.00 27.00 24.00
1178 GCT 80 40.00 18.00 29.00 13.00
1179 GCT 81 18.00 26.00 26.00 30.00
1180 GCT 82 30.00 25.00 28.00 17.00
1181 GCT 83 36.00 25.00 14.00 25.00
1182 GCT 84 22.00 39.00 23.00 16.00
1183 GCT 85 42.00 20.00 21.00 17.00
1184 GCT 86 12.00 47.00 16.00 25.00
1185 GCT 87 45.00 15.00 19.00 21.00
1186 GCT 88 26.00 24.00 31.00 19.00
1187 GCT 89 26.00 25.00 29.00 20.00
1188 GCT 90 24.00 22.00 26.00 28.00
1189 GCT 91 29.00 30.00 24.00 17.00
1190 GCT 92 22.00 13.00 32.00 33.00
1191 GCT 93 29.00 40.00 13.00 18.00
1192 GCT 94 30.00 16.00 25.00 29.00
1193 GCT 95 31.31 35.35 17.17 16.16
1194 GCT 96 34.00 27.00 15.00 24.00
1195 GCT 97 32.00 27.00 25.00 16.00
1196 GCT 98 21.21 31.31 24.24 23.23
1197 GCT 99 27.00 37.00 21.00 15.00
1198 GCT 100 29.00 15.00 26.00 30.00
1199 GCT 101 27.00 34.00 25.00 14.00
1200 GCT 102 20.00 14.00 36.00 30.00
1201 GCT 103 32.00 26.00 16.00 26.00
1202 GCT 104 30.00 28.00 22.00 20.00
1203 GCT 105 35.00 35.00 19.00 11.00
1204 GCT 106 22.00 32.00 25.00 21.00
1205 GCT 107 19.19 33.33 26.26 21.21
1206 GCT 108 27.27 33.33 21.21 18.18
1207 GCT 109 19.00 29.00 24.00 28.00
1208 GCT 110 20.20 31.31 28.28 20.20
1209 GCT 111 25.25 33.33 22.22 19.19
1210 GCT 112 39.39 28.28 16.16 16.16
1211 GCT 113 21.21 24.24 31.31 23.23
1212 GCT 114 19.00 31.00 35.00 15.00
1213 GCT 115 32.00 23.00 25.00 20.00
1214 GCT 116 20.00 29.00 35.00 16.00
1215 GCT 117 31.00 21.00 21.00 27.00
1216 GCT 118 25.00 14.00 35.00 26.00
1217 GCT 119 21.00 31.00 24.00 24.00
1218 GCT 120 19.00 24.00 27.00 30.00
1219 GCT 121 24.24 36.36 20.20 19.19
1220 GCT 122 18.00 25.00 23.00 34.00
1221 GCT 123 25.00 48.00 10.00 17.00
1222 GCT 124 10.00 31.00 35.00 24.00
1223 GCT 125 27.00 24.00 22.00 27.00
1224 GCT 126 24.00 19.00 26.00 31.00
1225 GCT 127 26.00 16.00 22.00 36.00
1226 GCT 128 16.00 35.00 30.00 19.00
1227 GCT 129 24.00 27.00 26.00 23.00
1228 GCT 130 25.00 19.00 23.00 33.00
1229 GCT 131 17.00 40.00 24.00 19.00
1230 GCT 132 20.00 27.00 24.00 29.00
1231 GCT 133 15.00 34.00 33.00 18.00
1232 GCT 134 22.00 19.00 31.00 28.00
1233 GCT 135 17.00 28.00 26.00 29.00
1234 GCT 136 25.00 33.00 14.00 28.00
1235 GCT 137 21.00 22.00 30.00 27.00
1236 GCT 138 15.00 30.00 29.00 26.00
1237 GCT 139 19.00 32.00 22.00 27.00
1238 GCT 140 19.00 24.00 29.00 28.00
1239 GCT 141 21.00 24.00 25.00 30.00
1240 GCT 142 17.00 32.00 35.00 16.00
1241 GCT 143 23.00 23.00 28.00 26.00
1242 GCT 144 20.00 33.00 24.00 23.00
1243 GCT 145 20.00 26.00 24.00 30.00
1244 GCT 146 26.00 15.00 40.00 19.00
1245 GCT 147 23.00 23.00 30.00 24.00
1246 GCT 148 12.00 32.00 33.00 23.00
1247 GCT 149 27.00 24.00 23.00 26.00
1248 GCT 150 12.00 32.00 21.00 35.00
1249 GCT 151 22.00 29.00 34.00 15.00
1250 GCT 152 16.00 21.00 26.00 37.00
1251 GCT 153 24.00 20.00 34.00 22.00
1252 GCT 154 25.00 22.00 28.00 25.00
1253 GCT 155 21.00 28.00 17.00 34.00
1254 GCT 156 16.00 23.00 36.00 25.00
1255 GCT 157 23.00 34.00 20.00 23.00
1256 GCT 158 21.00 33.00 21.00 25.00
1257 GCT 159 19.00 15.00 44.00 22.00
1258 GCT 160 24.00 31.00 22.00 23.00
1259 GCT 161 13.00 28.00 40.00 19.00
1260 GCT 162 33.00 19.00 20.00 28.00
1261 GCT 163 23.00 26.00 31.00 20.00
1262 GCT 164 33.00 19.00 20.00 28.00
1263 GCT 165 13.00 16.00 37.00 34.00
1264 GCT 166 20.00 36.00 30.00 14.00
1265 GCT 167 17.00 28.00 25.00 30.00
1266 GCT 168 16.00 24.00 31.00 29.00
1267 GCT 169 21.00 23.00 21.00 35.00
1268 GCT 170 22.00 24.00 27.00 27.00
1269 GCT 171 23.00 30.00 31.00 16.00
1270 GCT 172 24.00 22.00 30.00 24.00
1271 GCT 173 24.00 17.00 33.00 26.00
1272 GCT 174 21.00 24.00 33.00 22.00
1273 GCT 175 34.00 19.00 34.00 13.00
1274 GCT 176 17.00 37.00 24.00 22.00
1275 GCT 177 24.00 24.00 25.00 27.00
1276 GCT 178 19.00 26.00 30.00 25.00
1277 GCT 179 24.00 20.00 20.00 36.00
1278 GCT 180 22.00 25.00 31.00 22.00
1279 GCT 181 21.00 17.00 38.00 24.00
1280 GCT 182 35.00 21.00 20.00 24.00
1281 GCT 183 28.00 15.00 27.00 30.00
1282 GCT 184 17.00 30.00 29.00 24.00
1283 GCT 185 16.00 32.00 33.00 19.00
1284 GCT 186 21.00 22.00 36.00 21.00
1285 GCT 187 24.00 13.00 41.00 22.00
1286 GCT 188 29.00 19.00 30.00 22.00
1287 GCT 189 19.00 23.00 33.00 25.00
1288 GCT 190 24.00 28.00 25.00 23.00
1289 GCT 191 28.00 21.00 29.00 22.00
1290 GCT 192 37.00 25.00 13.00 25.00
1291 GCT 193 18.00 26.00 25.00 31.00
1292 GCT 194 21.00 34.00 24.00 21.00
1293 GCT 195 16.00 28.00 21.00 35.00
1294 GCT 196 23.00 23.00 27.00 27.00
1295 GCT 197 18.00 20.00 24.00 38.00
1296 GCT 198 15.00 19.00 39.00 27.00
1297 GCT 199 23.00 17.00 27.00 33.00
1298 GCT 200 25.00 27.00 23.00 25.00
1299 GCT 201 26.00 19.00 25.00 30.00
1300 GCT 202 23.00 23.00 21.00 33.00
1301 GCT 203 21.00 19.00 32.00 28.00
1302 GCT 204 26.00 29.00 24.00 21.00
1303 GCT 205 16.00 23.00 21.00 40.00
1304 GCT 206 28.00 25.00 21.00 26.00
1305 GCT 207 22.00 22.00 19.00 37.00
1306 GCT 208 12.00 32.00 32.00 24.00
1307 GCT 209 18.00 20.00 15.00 47.00
1308 GCT 210 18.00 15.00 45.00 22.00
1309 GCT 211 28.00 14.00 28.00 30.00
1310 GCT 212 23.00 27.00 22.00 28.00
1311 GCT 213 22.00 12.00 34.00 32.00
1312 GCT 214 16.00 24.00 26.00 34.00
1313 GCT 215 28.00 22.00 25.00 25.00
1314 GCT 216 18.00 17.00 26.00 39.00
1315 GCT 217 27.00 30.00 16.00 27.00
1316 GCT 218 18.00 24.00 24.00 34.00
1317 GCT 219 19.00 18.00 24.00 39.00
1318 GCT 220 28.00 23.00 24.00 25.00
1319 GCT 221 20.00 24.00 20.00 36.00
1320 GCT 222 22.00 21.00 19.00 38.00
1321 GCT 223 19.00 22.00 33.00 26.00
1322 GCT 224 19.00 20.00 27.00 34.00
1323 GCT 225 14.00 32.00 34.00 20.00
1324 GCT 226 20.00 20.00 29.00 31.00
1325 GCT 227 17.00 22.00 26.00 35.00
1326 GCT 228 34.00 20.00 25.00 21.00
1327 GCT 229 22.00 27.00 16.00 35.00
1328 GCT 230 23.00 33.00 15.00 29.00
1329 GCT 231 20.00 27.00 31.00 22.00
1330 GCT 232 25.00 23.00 11.00 41.00
1331 GCT 233 22.00 25.00 27.00 26.00
1332 GCT 234 14.00 27.00 23.00 36.00
1333 GCT 235 17.00 11.00 32.00 40.00
1334 GCT 236 29.00 20.00 24.00 27.00
1335 GCT 237 16.00 19.00 23.00 42.00
1336 GCT 238 22.00 25.00 29.00 24.00
1337 GCT 239 18.00 8.00 17.00 57.00
1338 GCT 240 27.00 26.00 14.00 33.00
1339 GCT 241 21.00 22.00 17.00 40.00
1340 GCT 242 26.00 28.00 10.00 36.00
1341 GCT 243 25.00 15.00 24.00 36.00
1342 GCT 244 15.00 24.00 16.00 45.00
1343 GCT 245 24.00 23.00 19.00 34.00
1344 GCT 246 18.00 25.00 29.00 28.00
1345 GCT 247 30.00 13.00 14.00 43.00
1346 GCT 248 22.00 17.00 26.00 35.00
1347 GCT 249 25.00 22.00 22.00 31.00
1348 GCT 250 25.00 20.00 20.00 35.00
1349 GCT 251 13.00 17.00 40.00 30.00
1097 # ACGT content per cycle for first fragments. Use `grep ^FBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] 1350 # ACGT content per cycle for first fragments. Use `grep ^FBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
1098 FBC 1 21.43 27.55 36.73 14.29 2.04 0.00 1351 FBC 1 21.43 27.55 36.73 14.29 2.04 0.00
1099 FBC 2 34.00 15.00 12.00 39.00 0.00 0.00 1352 FBC 2 34.00 15.00 12.00 39.00 0.00 0.00
1100 FBC 3 32.00 25.00 9.00 34.00 0.00 0.00 1353 FBC 3 32.00 25.00 9.00 34.00 0.00 0.00
1101 FBC 4 21.00 26.00 16.00 37.00 0.00 0.00 1354 FBC 4 21.00 26.00 16.00 37.00 0.00 0.00
1344 FBC 247 34.00 15.00 12.00 39.00 0.00 0.00 1597 FBC 247 34.00 15.00 12.00 39.00 0.00 0.00
1345 FBC 248 14.00 19.00 24.00 43.00 0.00 0.00 1598 FBC 248 14.00 19.00 24.00 43.00 0.00 0.00
1346 FBC 249 25.00 24.00 20.00 31.00 0.00 0.00 1599 FBC 249 25.00 24.00 20.00 31.00 0.00 0.00
1347 FBC 250 30.00 25.00 15.00 30.00 0.00 0.00 1600 FBC 250 30.00 25.00 15.00 30.00 0.00 0.00
1348 FBC 251 14.00 24.00 33.00 29.00 0.00 0.00 1601 FBC 251 14.00 24.00 33.00 29.00 0.00 0.00
1602 # ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
1603 FTC 6178 6247 5821 6841 13
1349 # ACGT content per cycle for last fragments. Use `grep ^LBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] 1604 # ACGT content per cycle for last fragments. Use `grep ^LBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
1350 LBC 1 22.45 32.65 31.63 13.27 2.04 0.00 1605 LBC 1 22.45 32.65 31.63 13.27 2.04 0.00
1351 LBC 2 26.00 17.00 10.00 47.00 0.00 0.00 1606 LBC 2 26.00 17.00 10.00 47.00 0.00 0.00
1352 LBC 3 34.00 25.00 9.00 32.00 0.00 0.00 1607 LBC 3 34.00 25.00 9.00 32.00 0.00 0.00
1353 LBC 4 13.00 32.00 10.00 45.00 0.00 0.00 1608 LBC 4 13.00 32.00 10.00 45.00 0.00 0.00
1596 LBC 247 30.00 13.00 14.00 43.00 0.00 0.00 1851 LBC 247 30.00 13.00 14.00 43.00 0.00 0.00
1597 LBC 248 22.00 17.00 26.00 35.00 0.00 0.00 1852 LBC 248 22.00 17.00 26.00 35.00 0.00 0.00
1598 LBC 249 25.00 22.00 22.00 31.00 0.00 0.00 1853 LBC 249 25.00 22.00 22.00 31.00 0.00 0.00
1599 LBC 250 25.00 20.00 20.00 35.00 0.00 0.00 1854 LBC 250 25.00 20.00 20.00 35.00 0.00 0.00
1600 LBC 251 13.00 17.00 40.00 30.00 0.00 0.00 1855 LBC 251 13.00 17.00 40.00 30.00 0.00 0.00
1856 # ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
1857 LTC 6413 6102 5966 6606 13
1601 # Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs 1858 # Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs
1602 # Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count 1859 # Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count
1603 RL 251 200 1860 RL 251 200
1604 # Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count 1861 # Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count
1605 FRL 251 100 1862 FRL 251 100