Mercurial > repos > devteam > samtools_stats
diff test-data/samtools_stats_out1.tab @ 0:0d71d9467847 draft
Uploaded
| author | devteam |
|---|---|
| date | Wed, 22 Apr 2015 10:29:35 -0400 |
| parents | |
| children | 24c5d43cb545 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out1.tab Wed Apr 22 10:29:35 2015 -0400 @@ -0,0 +1,1137 @@ +# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats +# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /Users/anton/galaxy-git/database/files/000/dataset_9.dat /Users/anton/galaxy-git/database/files/000/dataset_10.dat +# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities +# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) +CHK 1bd20fd8 58ad2167 29883386 +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 200 +SN filtered sequences: 0 +SN sequences: 200 +SN is sorted: 1 +SN 1st fragments: 100 +SN last fragments: 100 +SN reads mapped: 25 +SN reads mapped and paired: 0 # paired-end technology bit set + both mates mapped +SN reads unmapped: 175 +SN reads properly paired: 0 # proper-pair bit set +SN reads paired: 200 # paired-end technology bit set +SN reads duplicated: 0 # PCR or optical duplicate bit set +SN reads MQ0: 6 # mapped and MQ=0 +SN reads QC failed: 0 +SN non-primary alignments: 0 +SN total length: 50200 # ignores clipping +SN bases mapped: 6275 # ignores clipping +SN bases mapped (cigar): 6275 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 0 +SN mismatches: 591 # from NM fields +SN error rate: 9.418327e-02 # mismatches / bases mapped (cigar) +SN average length: 251 +SN maximum length: 251 +SN average quality: 34.7 +SN insert size average: 0.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 0 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 0 +# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. 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quality. Use `grep ^MPC | cut -f 2-` to extract this part. +# Columns correspond to qualities, rows to cycles. 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0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 2 0 0 0 3 0 0 0 +MPC 249 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 2 0 5 0 0 0 0 0 0 2 0 0 0 0 0 0 0 +MPC 250 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 2 0 0 0 2 0 0 0 +MPC 251 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 3 0 0 0 +MPC 252 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. +GCF 21.86 0 +GCF 44.22 2 +GCF 44.97 8 +GCF 45.48 4 +GCF 45.98 3 +GCF 46.48 5 +GCF 46.98 2 +GCF 47.49 3 +GCF 47.99 12 +GCF 48.49 13 +GCF 48.99 9 +GCF 49.50 2 +GCF 50.25 3 +GCF 51.01 6 +GCF 51.51 4 +GCF 52.01 1 +GCF 52.51 0 +GCF 53.02 1 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 21.86 0 +GCL 44.22 2 +GCL 44.97 8 +GCL 45.48 4 +GCL 45.98 3 +GCL 46.48 5 +GCL 46.98 2 +GCL 47.49 3 +GCL 47.99 12 +GCL 48.49 13 +GCL 48.99 9 +GCL 49.50 2 +GCL 50.25 3 +GCL 51.01 6 +GCL 51.51 4 +GCL 52.01 1 +GCL 52.51 0 +GCL 53.02 1 +# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle, and A,C,G,T counts [%] +GCC 1 21.50 29.50 33.50 15.50 +GCC 2 30.00 16.00 11.00 43.00 +GCC 3 33.00 25.00 9.00 33.00 +GCC 4 17.00 29.00 13.00 41.00 +GCC 5 37.00 22.00 12.00 29.00 +GCC 6 36.00 26.00 17.00 21.00 +GCC 7 29.50 13.50 31.50 25.50 +GCC 8 50.50 14.50 19.50 15.50 +GCC 9 17.00 33.00 18.00 32.00 +GCC 10 37.00 14.00 21.00 28.00 +GCC 11 20.50 14.50 29.50 35.50 +GCC 12 30.00 24.00 22.00 24.00 +GCC 13 27.00 15.00 21.00 37.00 +GCC 14 24.00 22.00 26.00 28.00 +GCC 15 25.50 20.50 24.50 29.50 +GCC 16 31.00 15.00 20.00 34.00 +GCC 17 28.00 25.00 14.00 33.00 +GCC 18 30.50 28.50 19.50 21.50 +GCC 19 29.00 26.00 21.00 24.00 +GCC 20 22.50 23.50 17.50 36.50 +GCC 21 35.50 17.50 19.50 27.50 +GCC 22 37.50 28.50 15.50 18.50 +GCC 23 31.00 19.00 13.00 37.00 +GCC 24 37.00 12.00 22.00 29.00 +GCC 25 35.50 22.50 17.50 24.50 +GCC 26 33.50 18.50 15.50 32.50 +GCC 27 34.50 14.50 25.50 25.50 +GCC 28 31.00 14.00 24.00 31.00 +GCC 29 30.00 27.00 24.00 19.00 +GCC 30 31.00 20.00 14.00 35.00 +GCC 31 33.50 29.50 13.50 23.50 +GCC 32 42.50 20.50 19.50 17.50 +GCC 33 25.50 23.50 14.50 36.50 +GCC 34 39.50 16.50 20.50 23.50 +GCC 35 32.50 23.50 21.50 22.50 +GCC 36 42.00 25.00 16.00 17.00 +GCC 37 38.00 17.00 19.00 26.00 +GCC 38 24.00 26.00 25.00 25.00 +GCC 39 22.50 41.50 18.50 17.50 +GCC 40 32.00 16.00 21.00 31.00 +GCC 41 33.00 28.00 19.00 20.00 +GCC 42 30.50 25.50 19.50 24.50 +GCC 43 35.00 29.00 15.00 21.00 +GCC 44 20.00 27.00 22.00 31.00 +GCC 45 40.50 21.50 21.50 16.50 +GCC 46 26.50 20.50 22.50 30.50 +GCC 47 38.50 29.50 16.50 15.50 +GCC 48 27.50 24.50 17.50 30.50 +GCC 49 28.50 32.50 10.50 28.50 +GCC 50 46.50 20.50 9.50 23.50 +GCC 51 34.50 28.50 13.50 23.50 +GCC 52 41.50 23.50 20.50 14.50 +GCC 53 20.00 28.00 26.00 26.00 +GCC 54 31.50 18.50 24.50 25.50 +GCC 55 30.50 22.50 16.50 30.50 +GCC 56 33.50 22.50 13.50 30.50 +GCC 57 23.00 24.00 23.00 30.00 +GCC 58 25.00 37.00 19.00 19.00 +GCC 59 34.00 23.00 24.00 19.00 +GCC 60 29.00 28.00 17.00 26.00 +GCC 61 25.50 23.50 24.50 26.50 +GCC 62 31.50 22.50 16.50 29.50 +GCC 63 27.50 28.50 25.50 18.50 +GCC 64 33.50 21.50 25.50 19.50 +GCC 65 35.50 19.50 18.50 26.50 +GCC 66 34.00 25.00 15.00 26.00 +GCC 67 37.00 23.00 19.00 21.00 +GCC 68 36.50 29.50 13.50 20.50 +GCC 69 38.50 19.50 20.50 21.50 +GCC 70 38.50 16.50 18.50 26.50 +GCC 71 25.50 38.50 21.50 14.50 +GCC 72 29.00 29.00 25.00 17.00 +GCC 73 32.50 20.50 21.50 25.50 +GCC 74 28.50 32.50 12.50 26.50 +GCC 75 41.50 12.50 18.50 27.50 +GCC 76 24.50 29.50 23.50 22.50 +GCC 77 36.00 21.00 18.00 25.00 +GCC 78 27.00 34.00 22.00 17.00 +GCC 79 21.50 26.50 25.50 26.50 +GCC 80 34.00 19.00 28.00 19.00 +GCC 81 17.00 26.00 26.00 31.00 +GCC 82 31.00 30.00 23.00 16.00 +GCC 83 31.50 26.50 12.50 29.50 +GCC 84 19.00 41.00 21.00 19.00 +GCC 85 37.50 24.50 16.50 21.50 +GCC 86 15.00 48.00 15.00 22.00 +GCC 87 41.00 16.00 18.00 25.00 +GCC 88 23.50 27.50 27.50 21.50 +GCC 89 26.50 27.50 26.50 19.50 +GCC 90 18.50 23.50 24.50 33.50 +GCC 91 27.00 32.00 22.00 19.00 +GCC 92 23.50 17.50 27.50 31.50 +GCC 93 25.50 37.50 15.50 21.50 +GCC 94 27.00 17.00 24.00 32.00 +GCC 95 26.50 37.50 14.50 21.50 +GCC 96 29.50 25.50 16.50 28.50 +GCC 97 29.00 31.00 21.00 19.00 +GCC 98 18.00 33.00 22.00 27.00 +GCC 99 24.50 33.50 24.50 17.50 +GCC 100 24.50 16.50 24.50 34.50 +GCC 101 25.00 40.00 19.00 16.00 +GCC 102 17.50 17.50 32.50 32.50 +GCC 103 31.00 26.00 16.00 27.00 +GCC 104 26.50 29.50 20.50 23.50 +GCC 105 34.00 33.00 21.00 12.00 +GCC 106 23.00 31.00 26.00 20.00 +GCC 107 17.50 35.50 23.50 23.50 +GCC 108 24.50 30.50 23.50 21.50 +GCC 109 17.00 31.00 22.00 30.00 +GCC 110 16.00 35.00 24.00 25.00 +GCC 111 24.00 32.00 23.00 21.00 +GCC 112 37.00 28.00 16.00 19.00 +GCC 113 19.50 22.50 32.50 25.50 +GCC 114 17.00 31.00 35.00 17.00 +GCC 115 29.50 24.50 23.50 22.50 +GCC 116 22.00 30.00 34.00 14.00 +GCC 117 27.00 23.00 19.00 31.00 +GCC 118 25.50 14.50 34.50 25.50 +GCC 119 22.50 34.50 20.50 22.50 +GCC 120 17.50 24.50 26.50 31.50 +GCC 121 27.50 33.50 22.50 16.50 +GCC 122 17.00 23.00 25.00 35.00 +GCC 123 23.50 46.50 11.50 18.50 +GCC 124 9.00 32.00 34.00 25.00 +GCC 125 24.00 27.00 19.00 30.00 +GCC 126 26.00 17.00 28.00 29.00 +GCC 127 26.50 16.50 21.50 35.50 +GCC 128 18.00 34.00 31.00 17.00 +GCC 129 25.50 25.50 27.50 21.50 +GCC 130 25.00 20.00 22.00 33.00 +GCC 131 17.50 39.50 24.50 18.50 +GCC 132 21.00 28.00 23.00 28.00 +GCC 133 13.50 31.50 35.50 19.50 +GCC 134 24.50 19.50 30.50 25.50 +GCC 135 16.50 23.50 30.50 29.50 +GCC 136 28.00 32.00 15.00 25.00 +GCC 137 22.50 21.50 30.50 25.50 +GCC 138 14.50 34.50 24.50 26.50 +GCC 139 20.50 29.50 24.50 25.50 +GCC 140 17.00 23.00 30.00 30.00 +GCC 141 20.50 23.50 25.50 30.50 +GCC 142 18.00 29.00 38.00 15.00 +GCC 143 22.00 24.00 27.00 27.00 +GCC 144 21.50 30.50 26.50 21.50 +GCC 145 22.00 21.00 29.00 28.00 +GCC 146 25.00 16.00 39.00 20.00 +GCC 147 26.50 22.50 30.50 20.50 +GCC 148 12.50 28.50 36.50 22.50 +GCC 149 26.50 23.50 23.50 26.50 +GCC 150 14.00 29.00 24.00 33.00 +GCC 151 19.50 30.50 32.50 17.50 +GCC 152 18.50 17.50 29.50 34.50 +GCC 153 22.50 22.50 31.50 23.50 +GCC 154 22.00 21.00 29.00 28.00 +GCC 155 21.00 26.00 19.00 34.00 +GCC 156 14.50 23.50 35.50 26.50 +GCC 157 22.00 31.00 23.00 24.00 +GCC 158 22.50 29.50 24.50 23.50 +GCC 159 17.50 12.50 46.50 23.50 +GCC 160 24.50 26.50 26.50 22.50 +GCC 161 13.00 23.00 45.00 19.00 +GCC 162 31.50 16.50 22.50 29.50 +GCC 163 19.50 21.50 35.50 23.50 +GCC 164 29.00 18.00 21.00 32.00 +GCC 165 14.50 17.50 35.50 32.50 +GCC 166 17.50 37.50 28.50 16.50 +GCC 167 16.50 21.50 31.50 30.50 +GCC 168 14.00 25.00 30.00 31.00 +GCC 169 18.50 20.50 23.50 37.50 +GCC 170 19.00 23.00 28.00 30.00 +GCC 171 20.00 28.00 33.00 19.00 +GCC 172 19.00 20.00 32.00 29.00 +GCC 173 24.50 16.50 33.50 25.50 +GCC 174 17.50 23.50 33.50 25.50 +GCC 175 33.50 17.50 35.50 13.50 +GCC 176 16.50 32.50 28.50 22.50 +GCC 177 19.00 22.00 27.00 32.00 +GCC 178 16.00 26.00 30.00 28.00 +GCC 179 18.00 18.00 22.00 42.00 +GCC 180 21.00 22.00 34.00 23.00 +GCC 181 20.50 19.50 35.50 24.50 +GCC 182 32.50 18.50 22.50 26.50 +GCC 183 24.50 13.50 28.50 33.50 +GCC 184 15.00 29.00 30.00 26.00 +GCC 185 15.00 32.00 33.00 20.00 +GCC 186 22.50 23.50 34.50 19.50 +GCC 187 19.00 14.00 40.00 27.00 +GCC 188 27.50 21.50 27.50 23.50 +GCC 189 17.00 22.00 34.00 27.00 +GCC 190 23.00 30.00 23.00 24.00 +GCC 191 25.00 22.00 28.00 25.00 +GCC 192 34.50 24.50 13.50 27.50 +GCC 193 18.50 25.50 25.50 30.50 +GCC 194 18.50 33.50 24.50 23.50 +GCC 195 16.00 26.00 23.00 35.00 +GCC 196 21.50 25.50 24.50 28.50 +GCC 197 20.00 21.00 23.00 36.00 +GCC 198 17.00 21.00 37.00 25.00 +GCC 199 20.50 18.50 25.50 35.50 +GCC 200 21.00 29.00 21.00 29.00 +GCC 201 27.00 21.00 23.00 29.00 +GCC 202 21.50 24.50 19.50 34.50 +GCC 203 21.50 24.50 26.50 27.50 +GCC 204 27.00 29.00 24.00 20.00 +GCC 205 19.50 21.50 22.50 36.50 +GCC 206 26.50 24.50 21.50 27.50 +GCC 207 22.50 21.50 19.50 36.50 +GCC 208 14.00 35.00 29.00 22.00 +GCC 209 16.00 23.00 12.00 49.00 +GCC 210 18.50 19.50 40.50 21.50 +GCC 211 26.00 20.00 22.00 32.00 +GCC 212 21.00 31.00 18.00 30.00 +GCC 213 24.00 15.00 31.00 30.00 +GCC 214 17.50 24.50 25.50 32.50 +GCC 215 26.00 24.00 23.00 27.00 +GCC 216 21.50 17.50 25.50 35.50 +GCC 217 26.00 29.00 17.00 28.00 +GCC 218 20.00 27.00 21.00 32.00 +GCC 219 17.00 21.00 21.00 41.00 +GCC 220 25.50 23.50 23.50 27.50 +GCC 221 21.50 23.50 20.50 34.50 +GCC 222 21.50 21.50 18.50 38.50 +GCC 223 20.00 27.00 28.00 25.00 +GCC 224 22.50 22.50 24.50 30.50 +GCC 225 14.50 35.50 30.50 19.50 +GCC 226 20.00 23.00 26.00 31.00 +GCC 227 20.50 24.50 23.50 31.50 +GCC 228 33.00 19.00 26.00 22.00 +GCC 229 22.50 24.50 18.50 34.50 +GCC 230 21.00 32.00 16.00 31.00 +GCC 231 23.00 28.00 30.00 19.00 +GCC 232 23.50 21.50 12.50 42.50 +GCC 233 21.00 27.00 25.00 27.00 +GCC 234 16.50 27.50 22.50 33.50 +GCC 235 20.00 15.00 28.00 37.00 +GCC 236 28.00 23.00 21.00 28.00 +GCC 237 20.50 19.50 22.50 37.50 +GCC 238 21.50 29.50 24.50 24.50 +GCC 239 20.00 8.00 17.00 55.00 +GCC 240 28.00 24.00 16.00 32.00 +GCC 241 22.50 22.50 16.50 38.50 +GCC 242 29.00 25.00 13.00 33.00 +GCC 243 22.50 15.50 23.50 38.50 +GCC 244 20.50 23.50 16.50 39.50 +GCC 245 28.00 23.00 19.00 30.00 +GCC 246 21.00 29.00 25.00 25.00 +GCC 247 32.00 14.00 13.00 41.00 +GCC 248 18.00 18.00 25.00 39.00 +GCC 249 25.00 23.00 21.00 31.00 +GCC 250 27.50 22.50 17.50 32.50 +GCC 251 13.50 20.50 36.50 29.50 +# 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 +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 251 200 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +ID 1 1 0 +ID 2 1 0 +ID 4 2 0 +ID 10 5 0 +ID 13 1 0 +ID 14 1 0 +ID 15 1 0 +ID 18 1 0 +ID 21 1 0 +ID 22 1 0 +ID 23 2 0 +ID 24 3 0 +ID 29 1 0 +ID 35 2 0 +ID 38 2 0 +# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev) +IC 2 1 0 0 0 +IC 4 2 0 0 0 +IC 5 3 0 0 0 +IC 210 2 0 0 0 +IC 219 1 0 0 0 +IC 220 1 0 0 0 +IC 224 2 0 0 0 +IC 225 2 0 0 0 +IC 226 1 0 0 0 +IC 228 1 0 0 0 +IC 230 1 0 0 0 +IC 233 1 0 0 0 +IC 234 1 0 0 0 +IC 235 1 0 0 0 +IC 236 1 0 0 0 +IC 239 1 0 0 0 +IC 240 1 0 0 0 +IC 241 1 0 0 0 +IC 247 1 0 0 0 +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 1 +COV [7-7] 7 1 +COV [18-18] 18 1 +COV [24-24] 24 1 +COV [25-25] 25 249 +# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile +GCD 0.0 100.000 0.000 0.000 0.000 0.000 0.000