Description of files containing discarded SVs
Each of the five SV filters generates a file in tab-delimited text format containing the discarded SVs. The first row of each file provides headers for the fields except the file generated by SNV filter. The meaning of each field in the file is described in detail below:
ratio filter
| field name | description | example value |
|---|
| left_window | chromosome/scaffold ID of the left anchoring window | Chr6 |
| start | start position of the left anchoring window | 10736 |
| end | end position of the left anchoring window | 10960 |
| strand | orientation of the abnormal reads mapped within the left window | F |
| right_window | chromosome/scaffold ID of the right anchoring window | Chr6 |
| start | start position of the right anchoring window | 11326 |
| end | end position of the right anchoring window | 11558 |
| strand | orientation of the abnormal reads mapped within the right window | R |
| SV_type | type of the SV | DELETION |
| #_abnorm_pairs | number of abnormal read pairs | 5 |
| LW_normal_pairs | number of normal read pairs in the left anchoring window | 1 |
| LW_ratio | ratio of normal pairs and abnormal pairs in the left anchoring window | 0.2 |
| RW_normal_pairs | number of normal read pairs in the right anchoring window | 11 |
| RW_ratio | ratio of normal pairs and abnormal pairs in the right anchoring window | 2.2 |
| max_ratio | higher ratio of normal pairs and abnormal pairs between the left and right anchoring windows | 2.2 |
SNV filter
The file containing discarded SVs by SNV filter has no header. For each removed SV, the file first lists the SV information, then provides the SNV information between normal and abnormal reads in the left and/or right anchoring windows of the SV.
Example SV information:
| Chr6 | 9618 | 9711 | F | Chr6 | 10721 | 10833 | R | 27 | DELETION |
Example SNV information:
| M | C->T; | Chr6 | 9670 | C | 3 | ,., | 27 | TTTTTTTTTTATTTTTTTTTTTTTTTT |
| M | T->C; | Chr6 | 9707 | T | 3 | ,., | 4 | CCCC |
| M | A->C; | Chr6 | 10773 | C | 6 | AAaaaa | 27 | ,,,,,,,,,,,,,,,,,,,,,,,,,,, |
For SV information, the fields correspond to "left_window", "start", "end", "strand", "right_window", "start", "end", "strand", "#_abnorm_pairs", "SV_type". Meanings of these fields are same as those described in "ratio filter".
For SNV information, the meaning of each field is described in the following table:
| field No. | example value | description |
|---|
| 1 | M | type of the SNV. "M" for single base change, "I" for insertion and "D" for deletion |
| 2 | C->T; | base difference between normal and abnormal reads |
| 3 | Chr6 | chromosome/scaffold ID |
| 4 | 9670 | chromosome/scaffold position |
| 5 | C | base of reference genome |
| 6 | 3 | sequencing depth at this position by normal reads |
| 7 | ,., | base of each normal read at this position |
| 8 | 27 | sequencing depth at this position by abnormal reads |
| 9 | TTTTTTTTTTATTTTTTTTTTTTTTTT | base of each abnormal read at this position | |
gap filter
| field name | description | example value |
|---|
| left_window | chromosome/scaffold ID of the left anchoring window | Chr6 |
| start | start position of the left anchoring window | 239732 |
| end | end position of the left anchoring window | 240078 |
| strand | orientation of the abnormal reads mapped within the left window | F |
| right_window | chromosome/scaffold ID of the right anchoring window | Chr6 |
| start | start position of the right anchoring window | 241639 |
| end | end position of the right anchoring window | 241982 |
| strand | orientation of the abnormal reads mapped within the right window | R |
| SV_type | type of the SV | DELETION |
| #_of_N | size of the gap (bp) in the SV region | 1111 |
| SV_size | size of the SV (bp) | 1560 |
| gap_perc | fraction of gaps in the SV region (gap size / SV size) | 0.7122 |
read coverage filter
| field name | description | example value |
|---|
| left_window | chromosome/scaffold ID of the left anchoring window | Chr6 |
| start | start position of the left anchoring window | 7841 |
| end | end position of the left anchoring window | 7976 |
| strand | orientation of the abnormal reads mapped within the left window | R |
| right_window | chromosome/scaffold ID of the right anchoring window | Chr6 |
| start | start position of the right anchoring window | 9617 |
| end | end position of the right anchoring window | 9712 |
| strand | orientation of the abnormal reads mapped within the right window | F |
| SV_type | type of the SV | DELETION |
| covered_pos | size of the SV region covered by normal reads (bp) | 1617 |
| #_of_N | size of the gap (bp) in the SV region | 0 |
| SV_size | size of the SV (bp) | 1640 |
| covered_ratio | fraction of the SV region covered by normal reads(covered_pos / (SV_size - #_of_N)) | 0.985976 |
sequencing depth filter
| field name | description | example value |
|---|
| left_window | chromosome/scaffold ID of the left anchoring window | Chr6 |
| start | start position of the left anchoring window | 199293 |
| end | end position of the left anchoring window | 199387 |
| strand | orientation of the abnormal reads mapped within the left window | R |
| right_window | chromosome/scaffold ID of the right anchoring window | Chr6 |
| start | start position of the right anchoring window | 816712 |
| end | end position of the right anchoring window | 816802 |
| strand | orientation of the abnormal reads mapped within the right window | F |
| SV_type | type of the SV | LARGE_DUPLI |
| genome_depth_median | median of the sequencing depth over the entire genome | 2 |
| genome_depth_avg | mean of the sequencing depth over the entire genome | 3.946 |
| genome_depth_std | standard deviation of the sequencing depth over the entire genome | 8.5 |
| genome_unmapped_ratio | fraction of the genome that is not covered by any reads | 0.2999 |
| dup_depth_median | median of the sequencing depth over the SV region | 2 |
| dup_depth_avg | mean of the sequencing depth over the SV region | 3.497 |
| dup_unmapped_ratio | fraction of the SV region that is not covered by any reads | 0.3004 |
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