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updated tests using Typed instead of real_allele
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26 changes: 13 additions & 13 deletions
26
lusSTR/tests/data/LUSPlus_stutter_test/LUSPlus_sequence_info.csv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,24 +1,24 @@ | ||
| SampleID,Locus,CE_Allele,LUS_Plus,Reads,allele_type,parent_allele1,parent_allele2,allele1_ref_reads,allele2_ref_reads,perc_noise,perc_stutter | ||
| Sample1,D4S2408,10.0,10_10_0,1022,real_allele,,,,,, | ||
| Sample1,D4S2408,10.0,10_10_0,1022,Typed,,,,,, | ||
| Sample1,D4S2408,9.0,9_9_0,116,-1_stutter/+1_stutter,10_10_0,8_8_0,1022.0,1050.0,, | ||
| Sample1,D4S2408,8.0,8_8_0,1050,real_allele,,,,,, | ||
| Sample1,D8S1179,14.0,14_12_1_0,869,real_allele,,,,,, | ||
| Sample1,D4S2408,8.0,8_8_0,1050,Typed,,,,,, | ||
| Sample1,D8S1179,14.0,14_12_1_0,869,Typed,,,,,, | ||
| Sample1,D8S1179,13.0,13_11_1_0,184,-1_stutter,14_12_1_0,,869.0,,,0.212 | ||
| Sample1,D8S1179,12.0,12_10_1_0,37,-2_stutter,14_12_1_0,,869.0,,,0.201 | ||
| Sample1,D9S1122,13.0,13_11,948,real_allele,,,,,, | ||
| Sample1,D9S1122,13.0,13_11,948,Typed,,,,,, | ||
| Sample1,D9S1122,12.0,12_10,108,-1_stutter,13_11,,948.0,,,0.114 | ||
| Sample1,D9S1122,11.0,11_11,991,real_allele,,,,,, | ||
| Sample1,D9S1122,11.0,11_11,991,Typed,,,,,, | ||
| Sample1,D9S1122,10.0,10_10,87,-1_stutter,11_11,,991.0,,,0.088 | ||
| Sample1,FGA,23.0,23_15_3_0,1436,real_allele,,,,,, | ||
| Sample1,FGA,23.0,23_15_3_0,1436,Typed,,,,,, | ||
| Sample1,FGA,22.0,22_14_3_0,262,-1_stutter,23_15_3_0,,1436.0,,,0.182 | ||
| Sample1,FGA,21.0,21_13_3_0,48,BelowAT,,,,,0.013, | ||
| Sample1,FGA,20.0,20_12_3_0,1750,real_allele,,,,,, | ||
| Sample1,FGA,18.0,18_10_3_0,181,real_allele,,,,,, | ||
| Sample1,FGA,20.0,20_12_3_0,1750,Typed,,,,,, | ||
| Sample1,FGA,18.0,18_10_3_0,181,Typed,,,,,, | ||
| Sample1,FGA,17.0,17_9_3_0,15,BelowAT,,,,,0.004, | ||
| Sample1,PENTA D,15.0,15_15,50,real_allele,,,,,, | ||
| Sample1,PENTA D,13.0,13_13,1000,real_allele,,,,,, | ||
| Sample1,PENTA E,7.0,7_7,505,real_allele,,,,,, | ||
| Sample1,TH01,7.0,7_7,2197,real_allele,,,,,, | ||
| Sample1,TH01,6.0,6_6,1632,real_allele,,,,,, | ||
| Sample1,PENTA D,15.0,15_15,50,Typed,,,,,, | ||
| Sample1,PENTA D,13.0,13_13,1000,Typed,,,,,, | ||
| Sample1,PENTA E,7.0,7_7,505,Typed,,,,,, | ||
| Sample1,TH01,7.0,7_7,2197,Typed,,,,,, | ||
| Sample1,TH01,6.0,6_6,1632,Typed,,,,,, | ||
| Sample1,TH01,5.0,5_5,66,BelowAT,,,,,0.017, | ||
| Sample1,TPOX,11.0,11_11,15,BelowAT,,,,,1.0, |
52 changes: 26 additions & 26 deletions
52
lusSTR/tests/data/LUSPlus_stutter_test/test_filtering_EFMoutput_sequence_info.csv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,26 +1,26 @@ | ||
| SampleID,Locus,LUS_Plus,Reads,allele_type,parent_allele1,parent_allele2,allele1_ref_reads,allele2_ref_reads,perc_noise,perc_stutter,CE_Allele | ||
| Sample1,D4S2408,10_10_0,900.0,real_allele,,,,,,, | ||
| Sample1,D4S2408,9_9_0,1357.0,real_allele,,,,,,, | ||
| Sample1,D4S2408,8_8_0,1000.0,real_allele,,,,,,, | ||
| Sample1,D8S1179,14_11_1_0,739.0,real_allele,,,,,,, | ||
| Sample1,D8S1179,13_11_1_0,95.0,real_allele,,,,,,, | ||
| Sample1,D8S1179,13_10_1_0,89.0,-1_stutter,14_11_1_0,,739.0,,,0.12, | ||
| Sample1,D8S1179,12_9_1_0,26.0,real_allele,,,,,,, | ||
| Sample1,D8S1179,12_10_1_0,11.0,BelowAT,,,,,0.01,, | ||
| Sample1,D9S1122,13_11,948.0,real_allele,,,,,,, | ||
| Sample1,D9S1122,12_10,108.0,-1_stutter,13_11,,948.0,,,0.114, | ||
| Sample1,D9S1122,11_11,991.0,real_allele,,,,,,, | ||
| Sample1,D9S1122,10_10,87.0,-1_stutter,11_11,,991.0,,,0.088, | ||
| Sample1,FGA,23_15_3_0,1436.0,real_allele,,,,,,, | ||
| Sample1,FGA,22_14_3_0,262.0,-1_stutter,23_15_3_0,,1436.0,,,0.182, | ||
| Sample1,FGA,21_13_3_0,48.0,BelowAT,,,,,0.013,, | ||
| Sample1,FGA,20_12_3_0,1750.0,real_allele,,,,,,, | ||
| Sample1,FGA,18_10_3_0,181.0,real_allele,,,,,,, | ||
| Sample1,FGA,17_9_3_0,15.0,BelowAT,,,,,0.004,, | ||
| Sample1,PENTA D,15_15,50.0,real_allele,,,,,,, | ||
| Sample1,PENTA D,13_13,1000.0,real_allele,,,,,,, | ||
| Sample1,PENTA E,7_7,505.0,real_allele,,,,,,,7.0 | ||
| Sample1,TH01,7_7,2197.0,real_allele,,,,,,, | ||
| Sample1,TH01,6_6,1632.0,real_allele,,,,,,, | ||
| Sample1,TH01,5_5,66.0,BelowAT,,,,,0.017,, | ||
| Sample1,TPOX,11_11,15.0,BelowAT,,,,,1.0,,11.0 | ||
| SampleID,Locus,LUS_Plus,Reads,allele_type,parent_allele1,parent_allele2,allele1_ref_reads,allele2_ref_reads,perc_noise,perc_stutter,CE_Allele | ||
| Sample1,D4S2408,10_10_0,900,Typed,,,,,,, | ||
| Sample1,D4S2408,9_9_0,1357,Typed,,,,,,, | ||
| Sample1,D4S2408,8_8_0,1000,Typed,,,,,,, | ||
| Sample1,D8S1179,14_11_1_0,739,Typed,,,,,,, | ||
| Sample1,D8S1179,13_11_1_0,95,Typed,,,,,,, | ||
| Sample1,D8S1179,13_10_1_0,89,-1_stutter,14_11_1_0,,739,,,0.12, | ||
| Sample1,D8S1179,12_9_1_0,26,Typed,,,,,,, | ||
| Sample1,D8S1179,12_10_1_0,11,BelowAT,,,,,0.01,, | ||
| Sample1,D9S1122,13_11,948,Typed,,,,,,, | ||
| Sample1,D9S1122,12_10,108,-1_stutter,13_11,,948,,,0.114, | ||
| Sample1,D9S1122,11_11,991,Typed,,,,,,, | ||
| Sample1,D9S1122,10_10,87,-1_stutter,11_11,,991,,,0.088, | ||
| Sample1,FGA,23_15_3_0,1436,Typed,,,,,,, | ||
| Sample1,FGA,22_14_3_0,262,-1_stutter,23_15_3_0,,1436,,,0.182, | ||
| Sample1,FGA,21_13_3_0,48,BelowAT,,,,,0.013,, | ||
| Sample1,FGA,20_12_3_0,1750,Typed,,,,,,, | ||
| Sample1,FGA,18_10_3_0,181,Typed,,,,,,, | ||
| Sample1,FGA,17_9_3_0,15,BelowAT,,,,,0.004,, | ||
| Sample1,PENTA D,15_15,50,Typed,,,,,,, | ||
| Sample1,PENTA D,13_13,1000,Typed,,,,,,, | ||
| Sample1,PENTA E,7_7,505,Typed,,,,,,,7 | ||
| Sample1,TH01,7_7,2197,Typed,,,,,,, | ||
| Sample1,TH01,6_6,1632,Typed,,,,,,, | ||
| Sample1,TH01,5_5,66,BelowAT,,,,,0.017,, | ||
| Sample1,TPOX,11_11,15,BelowAT,,,,,1,,11 |
52 changes: 26 additions & 26 deletions
52
lusSTR/tests/data/MPSproto_test/test_filtering_EFMoutput_sequence_info.csv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,26 +1,26 @@ | ||
| SampleID,Locus,UAS_Output_Sequence,CE_Allele,UAS_Output_Bracketed_Notation,Reads,allele_type,parent_allele1,parent_allele2,allele1_ref_reads,allele2_ref_reads,perc_noise,perc_stutter | ||
| Sample1,D4S2408,ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT,10.0,[ATCT]10,900,real_allele,,,,,, | ||
| Sample1,D4S2408,ATCTATCTATCTATCTATCTATCTATCTATCTATCT,9.0,[ATCT]9,1357,real_allele,,,,,, | ||
| Sample1,D4S2408,ATCTATCTATCTATCTATCTATCTATCTATCT,8.0,[ATCT]8,1000,real_allele,,,,,, | ||
| Sample1,D8S1179,TCTATCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,14.0,[TCTA]2 TCTG [TCTA]11,739,real_allele,,,,,, | ||
| Sample1,D8S1179,TCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,13.0,TCTA TCTG [TCTA]11,95,-1_stutter,[TCTA]2 TCTG [TCTA]11,,739.0,,,0.129 | ||
| Sample1,D8S1179,TCTATCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,13.0,[TCTA]2 TCTG [TCTA]10,89,-1_stutter,[TCTA]2 TCTG [TCTA]11,,739.0,,,0.12 | ||
| Sample1,D8S1179,TCTATCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTA,12.0,[TCTA]2 TCTG [TCTA]9,26,-2_stutter,[TCTA]2 TCTG [TCTA]11,,739.0,,,0.035 | ||
| Sample1,D8S1179,TCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,12.0,TCTA TCTG [TCTA]10,11,BelowAT,,,,,0.01, | ||
| Sample1,D9S1122,TAGATCGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,13.0,TAGA TCGA [TAGA]11,948,real_allele,,,,,, | ||
| Sample1,D9S1122,TAGATCGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,12.0,TAGA TCGA [TAGA]10,108,-1_stutter,TAGA TCGA [TAGA]11,,948.0,,,0.114 | ||
| Sample1,D9S1122,TAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,11.0,[TAGA]11,991,real_allele,,,,,, | ||
| Sample1,D9S1122,TAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,10.0,[TAGA]10,87,-1_stutter,[TAGA]11,,991.0,,,0.088 | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,23.0,[TTTC]3 TTTT TTCT [CTTT]15 CTCC [TTCC]2,1436,real_allele,,,,,, | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,22.0,[TTTC]3 TTTT TTCT [CTTT]14 CTCC [TTCC]2,262,-1_stutter,[TTTC]3 TTTT TTCT [CTTT]15 CTCC [TTCC]2,,1436.0,,,0.182 | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,21.0,[TTTC]3 TTTT TTCT [CTTT]13 CTCC [TTCC]2,48,BelowAT,,,,,0.013, | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,20.0,[TTTC]3 TTTT TTCT [CTTT]12 CTCC [TTCC]2,1750,real_allele,,,,,, | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,18.0,[TTTC]3 TTTT TTCT [CTTT]10 CTCC [TTCC]2,181,real_allele,,,,,, | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,17.0,[TTTC]3 TTTT TTCT [CTTT]9 CTCC [TTCC]2,15,BelowAT,,,,,0.004, | ||
| Sample1,PENTA D,AAAAGAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA,15.0,AAAAG [AAAGA]13,50,real_allele,,,,,, | ||
| Sample1,PENTA D,AAAAGAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA,13.0,AAAAG [AAAGA]13,1000,real_allele,,,,,, | ||
| Sample1,PENTA E,AAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA,7.0,[AAAGA]7,505,real_allele,,,,,, | ||
| Sample1,TH01,AATGAATGAATGAATGAATGAATGAATG,7.0,[AATG]7,2197,real_allele,,,,,, | ||
| Sample1,TH01,AATGAATGAATGAATGAATGAATG,6.0,[AATG]6,1632,real_allele,,,,,, | ||
| Sample1,TH01,AATGAATGAATGAATGAATG,5.0,[AATG]5,66,BelowAT,,,,,0.017, | ||
| Sample1,TPOX,AATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATG,11.0,[AATG]11,15,BelowAT,,,,,1.0, | ||
| SampleID,Locus,UAS_Output_Sequence,CE_Allele,UAS_Output_Bracketed_Notation,Reads,allele_type,parent_allele1,parent_allele2,allele1_ref_reads,allele2_ref_reads,perc_noise,perc_stutter | ||
| Sample1,D4S2408,ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT,10,[ATCT]10,900,Typed,,,,,, | ||
| Sample1,D4S2408,ATCTATCTATCTATCTATCTATCTATCTATCTATCT,9,[ATCT]9,1357,Typed,,,,,, | ||
| Sample1,D4S2408,ATCTATCTATCTATCTATCTATCTATCTATCT,8,[ATCT]8,1000,Typed,,,,,, | ||
| Sample1,D8S1179,TCTATCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,14,[TCTA]2 TCTG [TCTA]11,739,Typed,,,,,, | ||
| Sample1,D8S1179,TCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,13,TCTA TCTG [TCTA]11,95,-1_stutter,[TCTA]2 TCTG [TCTA]11,,739,,,0.129 | ||
| Sample1,D8S1179,TCTATCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,13,[TCTA]2 TCTG [TCTA]10,89,-1_stutter,[TCTA]2 TCTG [TCTA]11,,739,,,0.12 | ||
| Sample1,D8S1179,TCTATCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTA,12,[TCTA]2 TCTG [TCTA]9,26,-2_stutter,[TCTA]2 TCTG [TCTA]11,,739,,,0.035 | ||
| Sample1,D8S1179,TCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,12,TCTA TCTG [TCTA]10,11,BelowAT,,,,,0.01, | ||
| Sample1,D9S1122,TAGATCGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,13,TAGA TCGA [TAGA]11,948,Typed,,,,,, | ||
| Sample1,D9S1122,TAGATCGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,12,TAGA TCGA [TAGA]10,108,-1_stutter,TAGA TCGA [TAGA]11,,948,,,0.114 | ||
| Sample1,D9S1122,TAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,11,[TAGA]11,991,Typed,,,,,, | ||
| Sample1,D9S1122,TAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,10,[TAGA]10,87,-1_stutter,[TAGA]11,,991,,,0.088 | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,23,[TTTC]3 TTTT TTCT [CTTT]15 CTCC [TTCC]2,1436,Typed,,,,,, | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,22,[TTTC]3 TTTT TTCT [CTTT]14 CTCC [TTCC]2,262,-1_stutter,[TTTC]3 TTTT TTCT [CTTT]15 CTCC [TTCC]2,,1436,,,0.182 | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,21,[TTTC]3 TTTT TTCT [CTTT]13 CTCC [TTCC]2,48,BelowAT,,,,,0.013, | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,20,[TTTC]3 TTTT TTCT [CTTT]12 CTCC [TTCC]2,1750,Typed,,,,,, | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,18,[TTTC]3 TTTT TTCT [CTTT]10 CTCC [TTCC]2,181,Typed,,,,,, | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,17,[TTTC]3 TTTT TTCT [CTTT]9 CTCC [TTCC]2,15,BelowAT,,,,,0.004, | ||
| Sample1,PENTA D,AAAAGAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA,15,AAAAG [AAAGA]13,50,Typed,,,,,, | ||
| Sample1,PENTA D,AAAAGAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA,13,AAAAG [AAAGA]13,1000,Typed,,,,,, | ||
| Sample1,PENTA E,AAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA,7,[AAAGA]7,505,Typed,,,,,, | ||
| Sample1,TH01,AATGAATGAATGAATGAATGAATGAATG,7,[AATG]7,2197,Typed,,,,,, | ||
| Sample1,TH01,AATGAATGAATGAATGAATGAATG,6,[AATG]6,1632,Typed,,,,,, | ||
| Sample1,TH01,AATGAATGAATGAATGAATG,5,[AATG]5,66,BelowAT,,,,,0.017, | ||
| Sample1,TPOX,AATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATG,11,[AATG]11,15,BelowAT,,,,,1, |
28 changes: 14 additions & 14 deletions
28
lusSTR/tests/data/NGS_stutter_test/STRmix_Files_sequence_info.csv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,26 +1,26 @@ | ||
| SampleID,Locus,UAS_Output_Sequence,CE_Allele,UAS_Output_Bracketed_Notation,Reads,allele_type,parent_allele1,parent_allele2,allele1_ref_reads,allele2_ref_reads,perc_noise,perc_stutter | ||
| Sample1,D4S2408,ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT,10.0,[ATCT]10,900,real_allele,,,,,, | ||
| Sample1,D4S2408,ATCTATCTATCTATCTATCTATCTATCTATCTATCT,9.0,[ATCT]9,1357,real_allele,,,,,, | ||
| Sample1,D4S2408,ATCTATCTATCTATCTATCTATCTATCTATCT,8.0,[ATCT]8,1000,real_allele,,,,,, | ||
| Sample1,D8S1179,TCTATCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,14.0,[TCTA]2 TCTG [TCTA]11,739,real_allele,,,,,, | ||
| Sample1,D4S2408,ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT,10.0,[ATCT]10,900,Typed,,,,,, | ||
| Sample1,D4S2408,ATCTATCTATCTATCTATCTATCTATCTATCTATCT,9.0,[ATCT]9,1357,Typed,,,,,, | ||
| Sample1,D4S2408,ATCTATCTATCTATCTATCTATCTATCTATCT,8.0,[ATCT]8,1000,Typed,,,,,, | ||
| Sample1,D8S1179,TCTATCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,14.0,[TCTA]2 TCTG [TCTA]11,739,Typed,,,,,, | ||
| Sample1,D8S1179,TCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,13.0,TCTA TCTG [TCTA]11,95,-1_stutter,[TCTA]2 TCTG [TCTA]11,,739.0,,,0.129 | ||
| Sample1,D8S1179,TCTATCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,13.0,[TCTA]2 TCTG [TCTA]10,89,-1_stutter,[TCTA]2 TCTG [TCTA]11,,739.0,,,0.12 | ||
| Sample1,D8S1179,TCTATCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTA,12.0,[TCTA]2 TCTG [TCTA]9,26,-2_stutter,[TCTA]2 TCTG [TCTA]11,,739.0,,,0.035 | ||
| Sample1,D8S1179,TCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,12.0,TCTA TCTG [TCTA]10,11,BelowAT,,,,,0.01, | ||
| Sample1,D9S1122,TAGATCGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,13.0,TAGA TCGA [TAGA]11,948,real_allele,,,,,, | ||
| Sample1,D9S1122,TAGATCGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,13.0,TAGA TCGA [TAGA]11,948,Typed,,,,,, | ||
| Sample1,D9S1122,TAGATCGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,12.0,TAGA TCGA [TAGA]10,108,-1_stutter,TAGA TCGA [TAGA]11,,948.0,,,0.114 | ||
| Sample1,D9S1122,TAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,11.0,[TAGA]11,991,real_allele,,,,,, | ||
| Sample1,D9S1122,TAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,11.0,[TAGA]11,991,Typed,,,,,, | ||
| Sample1,D9S1122,TAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,10.0,[TAGA]10,87,-1_stutter,[TAGA]11,,991.0,,,0.088 | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,23.0,[TTTC]3 TTTT TTCT [CTTT]15 CTCC [TTCC]2,1436,real_allele,,,,,, | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,23.0,[TTTC]3 TTTT TTCT [CTTT]15 CTCC [TTCC]2,1436,Typed,,,,,, | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,22.0,[TTTC]3 TTTT TTCT [CTTT]14 CTCC [TTCC]2,262,-1_stutter,[TTTC]3 TTTT TTCT [CTTT]15 CTCC [TTCC]2,,1436.0,,,0.182 | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,21.0,[TTTC]3 TTTT TTCT [CTTT]13 CTCC [TTCC]2,48,BelowAT,,,,,0.013, | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,20.0,[TTTC]3 TTTT TTCT [CTTT]12 CTCC [TTCC]2,1750,real_allele,,,,,, | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,18.0,[TTTC]3 TTTT TTCT [CTTT]10 CTCC [TTCC]2,181,real_allele,,,,,, | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,20.0,[TTTC]3 TTTT TTCT [CTTT]12 CTCC [TTCC]2,1750,Typed,,,,,, | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,18.0,[TTTC]3 TTTT TTCT [CTTT]10 CTCC [TTCC]2,181,Typed,,,,,, | ||
| Sample1,FGA,TTTCTTTCTTTCTTTTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCCTTCC,17.0,[TTTC]3 TTTT TTCT [CTTT]9 CTCC [TTCC]2,15,BelowAT,,,,,0.004, | ||
| Sample1,PENTA D,AAAAGAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA,15.0,AAAAG [AAAGA]13,50,real_allele,,,,,, | ||
| Sample1,PENTA D,AAAAGAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA,13.0,AAAAG [AAAGA]13,1000,real_allele,,,,,, | ||
| Sample1,PENTA E,AAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA,7.0,[AAAGA]7,505,real_allele,,,,,, | ||
| Sample1,TH01,AATGAATGAATGAATGAATGAATGAATG,7.0,[AATG]7,2197,real_allele,,,,,, | ||
| Sample1,TH01,AATGAATGAATGAATGAATGAATG,6.0,[AATG]6,1632,real_allele,,,,,, | ||
| Sample1,PENTA D,AAAAGAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA,15.0,AAAAG [AAAGA]13,50,Typed,,,,,, | ||
| Sample1,PENTA D,AAAAGAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA,13.0,AAAAG [AAAGA]13,1000,Typed,,,,,, | ||
| Sample1,PENTA E,AAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA,7.0,[AAAGA]7,505,Typed,,,,,, | ||
| Sample1,TH01,AATGAATGAATGAATGAATGAATGAATG,7.0,[AATG]7,2197,Typed,,,,,, | ||
| Sample1,TH01,AATGAATGAATGAATGAATGAATG,6.0,[AATG]6,1632,Typed,,,,,, | ||
| Sample1,TH01,AATGAATGAATGAATGAATG,5.0,[AATG]5,66,BelowAT,,,,,0.017, | ||
| Sample1,TPOX,AATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATG,11.0,[AATG]11,15,BelowAT,,,,,1.0, |
16 changes: 8 additions & 8 deletions
16
lusSTR/tests/data/NGS_stutter_test/custom/test_stutter_sequence_info.csv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,19 +1,19 @@ | ||
| SampleID,Locus,Custom_Range_Sequence,CE_Allele,Custom_Bracketed_Notation,Reads,allele_type,parent_allele1,parent_allele2,allele1_ref_reads,allele2_ref_reads,perc_noise,perc_stutter | ||
| Sample1,D8S1179,TCTATCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,14.0,[TCTA]2 TCTG [TCTA]11,739,real_allele,,,,,, | ||
| Sample1,D8S1179,TCTATCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,14.0,[TCTA]2 TCTG [TCTA]11,739,Typed,,,,,, | ||
| Sample1,D8S1179,TCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,13.0,TCTA TCTG [TCTA]11,95,-1_stutter,[TCTA]2 TCTG [TCTA]11,,739.0,,,0.129 | ||
| Sample1,D8S1179,TCTATCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,13.0,[TCTA]2 TCTG [TCTA]10,89,-1_stutter,[TCTA]2 TCTG [TCTA]11,,739.0,,,0.12 | ||
| Sample1,D8S1179,TCTATCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTA,12.0,[TCTA]2 TCTG [TCTA]9,26,-2_stutter,[TCTA]2 TCTG [TCTA]11,,739.0,,,0.035 | ||
| Sample1,D8S1179,TCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,12.0,TCTA TCTG [TCTA]10,11,BelowAT,,,,,0.01, | ||
| Sample1,FGA,GGAAGGAAGGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAAAAAAGAAAGAAAGAAA,23.0,[GGAA]2 GGAG [AAAG]15 AGAA AAAA [GAAA]3,1436,real_allele,,,,,, | ||
| Sample1,FGA,GGAAGGAAGGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAAAAAAGAAAGAAAGAAA,23.0,[GGAA]2 GGAG [AAAG]15 AGAA AAAA [GAAA]3,1436,Typed,,,,,, | ||
| Sample1,FGA,GGAAGGAAGGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAAAAAAGAAAGAAAGAAA,22.0,[GGAA]2 GGAG [AAAG]14 AGAA AAAA [GAAA]3,262,-1_stutter,[GGAA]2 GGAG [AAAG]15 AGAA AAAA [GAAA]3,,1436.0,,,0.182 | ||
| Sample1,FGA,GGAAGGAAGGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAAAAAAGAAAGAAAGAAA,21.0,[GGAA]2 GGAG [AAAG]13 AGAA AAAA [GAAA]3,48,BelowAT,,,,,0.013, | ||
| Sample1,FGA,GGAAGGAAGGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAAAAAAGAAAGAAAGAAA,20.0,[GGAA]2 GGAG [AAAG]12 AGAA AAAA [GAAA]3,1750,real_allele,,,,,, | ||
| Sample1,FGA,GGAAGGAAGGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAAAAAAGAAAGAAAGAAA,18.0,[GGAA]2 GGAG [AAAG]10 AGAA AAAA [GAAA]3,181,real_allele,,,,,, | ||
| Sample1,FGA,GGAAGGAAGGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAAAAAAGAAAGAAAGAAA,20.0,[GGAA]2 GGAG [AAAG]12 AGAA AAAA [GAAA]3,1750,Typed,,,,,, | ||
| Sample1,FGA,GGAAGGAAGGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAAAAAAGAAAGAAAGAAA,18.0,[GGAA]2 GGAG [AAAG]10 AGAA AAAA [GAAA]3,181,Typed,,,,,, | ||
| Sample1,FGA,GGAAGGAAGGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAAAAAAGAAAGAAAGAAA,17.0,[GGAA]2 GGAG [AAAG]9 AGAA AAAA [GAAA]3,15,BelowAT,,,,,0.004, | ||
| Sample1,PENTA D,AAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA,14.0,[AAAGA]14,22,+1_stutter,[AAAGA]13,,1000.0,,,0.022 | ||
| Sample1,PENTA D,AAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA,13.0,[AAAGA]13,1000,real_allele,,,,,, | ||
| Sample1,PENTA E,TCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTT,7.0,[TCTTT]7,505,real_allele,,,,,, | ||
| Sample1,TH01,ATGGTGAATGAATGAATGAATGAATGAATGAATGAGGGA,7.0,ATGG TG [AATG]7 AGGG A,2197,real_allele,,,,,, | ||
| Sample1,TH01,ATGGTGAATGAATGAATGAATGAATGAATGAGGGA,6.0,ATGG TG [AATG]6 AGGG A,1632,real_allele,,,,,, | ||
| Sample1,PENTA D,AAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA,13.0,[AAAGA]13,1000,Typed,,,,,, | ||
| Sample1,PENTA E,TCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTT,7.0,[TCTTT]7,505,Typed,,,,,, | ||
| Sample1,TH01,ATGGTGAATGAATGAATGAATGAATGAATGAATGAGGGA,7.0,ATGG TG [AATG]7 AGGG A,2197,Typed,,,,,, | ||
| Sample1,TH01,ATGGTGAATGAATGAATGAATGAATGAATGAGGGA,6.0,ATGG TG [AATG]6 AGGG A,1632,Typed,,,,,, | ||
| Sample1,TH01,ATGGTGAATGAATGAATGAATGAATGAGGGA,5.0,ATGG TG [AATG]5 AGGG A,66,BelowAT,,,,,0.017, | ||
| Sample1,TPOX,AATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATG,11.0,[AATG]11,15,BelowAT,,,,,1.0, |
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