Mercurial > repos > devteam > samtools_stats
diff test-data/11.stats.expected @ 3:95a7ddf617e7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
| author | iuc |
|---|---|
| date | Thu, 27 Sep 2018 09:05:10 -0400 |
| parents | |
| children | e28839a4b932 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/11.stats.expected Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,166 @@ +# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities +# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) +CHK cb2d2d82 bcd83869 62ec814e +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 26 +SN filtered sequences: 0 +SN sequences: 26 +SN is sorted: 1 +SN 1st fragments: 14 +SN last fragments: 12 +SN reads mapped: 26 +SN reads mapped and paired: 26 # paired-end technology bit set + both mates mapped +SN reads unmapped: 0 +SN reads properly paired: 24 # proper-pair bit set +SN reads paired: 26 # paired-end technology bit set +SN reads duplicated: 0 # PCR or optical duplicate bit set +SN reads MQ0: 1 # mapped and MQ=0 +SN reads QC failed: 0 +SN non-primary alignments: 0 +SN total length: 260 # ignores clipping +SN total first fragment length: 140 # ignores clipping +SN total last fragment length: 120 # ignores clipping +SN bases mapped: 260 # ignores clipping +SN bases mapped (cigar): 206 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 0 +SN mismatches: 0 # from NM fields +SN error rate: 0.000000e+00 # mismatches / bases mapped (cigar) +SN average length: 10 +SN average first fragment length: 10 +SN average last fragment length: 10 +SN maximum length: 10 +SN maximum first fragment length: 10 +SN maximum last fragment length: 10 +SN average quality: 13.1 +SN insert size average: 34.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 12 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 1 +SN percentage of properly paired reads (%): 92.3 +SN bases inside the target: 42 +SN percentage of target genome with coverage > 0 (%): 100.00 +# First Fragment Qualities. Use `grep ^FFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. First column is the cycle number. +FFQ 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 +FFQ 2 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 +FFQ 3 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 +FFQ 4 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 +FFQ 5 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 +FFQ 6 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 +FFQ 7 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 +FFQ 8 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 +FFQ 9 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 +FFQ 10 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 +# Last Fragment Qualities. Use `grep ^LFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. First column is the cycle number. +LFQ 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +LFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +LFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +LFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +LFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +LFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +LFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +LFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +LFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +LFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 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 19.85 0 +GCF 44.72 1 +GCF 54.77 4 +GCF 64.82 2 +GCF 74.87 4 +GCF 84.92 3 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 19.85 0 +GCL 44.72 2 +GCL 59.80 3 +GCL 74.87 4 +# ACGT content per cycle. Use `grep ^GCC | 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 [%] +GCC 1 19.23 42.31 15.38 23.08 0.00 0.00 +GCC 2 19.23 19.23 46.15 15.38 0.00 0.00 +GCC 3 23.08 38.46 19.23 19.23 0.00 0.00 +GCC 4 23.08 23.08 38.46 15.38 0.00 0.00 +GCC 5 11.54 38.46 26.92 23.08 0.00 0.00 +GCC 6 23.08 23.08 34.62 19.23 0.00 0.00 +GCC 7 15.38 34.62 26.92 23.08 0.00 0.00 +GCC 8 26.92 23.08 38.46 11.54 0.00 0.00 +GCC 9 23.08 26.92 26.92 23.08 0.00 0.00 +GCC 10 23.08 23.08 38.46 15.38 0.00 0.00 +# 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 [%] +FBC 1 21.43 42.86 21.43 14.29 0.00 0.00 +FBC 2 7.14 28.57 42.86 21.43 0.00 0.00 +FBC 3 28.57 35.71 21.43 14.29 0.00 0.00 +FBC 4 14.29 28.57 35.71 21.43 0.00 0.00 +FBC 5 14.29 35.71 35.71 14.29 0.00 0.00 +FBC 6 14.29 28.57 28.57 28.57 0.00 0.00 +FBC 7 14.29 28.57 35.71 21.43 0.00 0.00 +FBC 8 21.43 28.57 28.57 21.43 0.00 0.00 +FBC 9 21.43 21.43 35.71 21.43 0.00 0.00 +FBC 10 14.29 28.57 35.71 21.43 0.00 0.00 +# 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 [%] +LBC 1 16.67 41.67 8.33 33.33 0.00 0.00 +LBC 2 33.33 8.33 50.00 8.33 0.00 0.00 +LBC 3 16.67 41.67 16.67 25.00 0.00 0.00 +LBC 4 33.33 16.67 41.67 8.33 0.00 0.00 +LBC 5 8.33 41.67 16.67 33.33 0.00 0.00 +LBC 6 33.33 16.67 41.67 8.33 0.00 0.00 +LBC 7 16.67 41.67 16.67 25.00 0.00 0.00 +LBC 8 33.33 16.67 50.00 0.00 0.00 0.00 +LBC 9 25.00 33.33 16.67 25.00 0.00 0.00 +LBC 10 33.33 16.67 41.67 8.33 0.00 0.00 +# 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 +IS 0 0 0 0 0 +IS 1 0 0 0 0 +IS 2 0 0 0 0 +IS 3 0 0 0 0 +IS 4 0 0 0 0 +IS 5 0 0 0 0 +IS 6 0 0 0 0 +IS 7 0 0 0 0 +IS 8 0 0 0 0 +IS 9 0 0 0 0 +IS 10 0 0 0 0 +IS 11 0 0 0 0 +IS 12 0 0 0 0 +IS 13 0 0 0 0 +IS 14 0 0 0 0 +IS 15 0 0 0 0 +IS 16 0 0 0 0 +IS 17 0 0 0 0 +IS 18 0 0 0 0 +IS 19 0 0 0 0 +IS 20 0 0 0 0 +IS 21 0 0 0 0 +IS 22 0 0 0 0 +IS 23 0 0 0 0 +IS 24 0 0 0 0 +IS 25 0 0 0 0 +IS 26 0 0 0 0 +IS 27 0 0 0 0 +IS 28 0 0 0 0 +IS 29 0 0 0 0 +IS 30 0 0 0 0 +IS 31 0 0 0 0 +IS 32 0 0 0 0 +IS 33 0 0 0 0 +IS 34 12 12 0 0 +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 10 26 +# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count +FRL 10 14 +# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count +LRL 10 12 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +# 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) +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 1 +COV [2-2] 2 1 +COV [3-3] 3 2 +COV [4-4] 4 2 +COV [5-5] 5 23 +COV [6-6] 6 13 +# 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