From dd12a5077539995f63057a81601380e468922e2d Mon Sep 17 00:00:00 2001 From: martinahansen Date: Thu, 28 Feb 2013 08:46:32 +0000 Subject: [PATCH] updated find_SNPs tests git-svn-id: http://biopieces.googlecode.com/svn/trunk@2104 74ccb610-7750-0410-82ae-013aeee3265d --- bp_test/in/find_SNPs.in | 141 ++++++++++++++------ bp_test/out/find_SNPs.out.1 | 252 ++++++++++++++++++++++++++++-------- bp_test/out/find_SNPs.out.2 | 245 +++++++++++++++++++++++++++++++++++ 3 files changed, 544 insertions(+), 94 deletions(-) create mode 100644 bp_test/out/find_SNPs.out.2 diff --git a/bp_test/in/find_SNPs.in b/bp_test/in/find_SNPs.in index 5f4ffc8..6402003 100644 --- a/bp_test/in/find_SNPs.in +++ b/bp_test/in/find_SNPs.in @@ -1,60 +1,117 @@ -MAPQ: 37 STRAND: - -Q_ID: ID00002249 -ALIGN: 63:->A -S_ID: gi|48994873|gb|U00096.2| +MAPQ: 42 +NM: 1 +Q_ID: M01168:19:000000000-A2YGD:1:1101:14450:1450 +ALIGN: 156:T>G REC_TYPE: SAM -S_BEG: 2937 -SEQ: TCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAAGTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGC -CIGAR: 63M1I36M +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 6486413 +SEQ: CTCGCCGGGCACTACCTGCGCTACGCCGGGCAGGCCGAATGGGAAAGCCTGCAGATCGAACCGGTGAAGGGCGGCTACCAGGCGAGCTTCGCCCTGATGCGCATCGGCAATCCGGAGAAACTGATGGAATATGGGCCCGCGGCGGTCGGCGAGTGGGCGGCTGGAGGGGCAAGGCGCCCTCTACCGACTGCGCAGCGAAGGCCTGGGCGCCGGCTGCAGCCTGCTGGTATGGCAGG +CIGAR: 236M +MD: 156T79 +S_END: 6486648 --- -MAPQ: 37 STRAND: - -Q_ID: ID00004198 -ALIGN: 8:G>C -S_ID: gi|48994873|gb|U00096.2| +MAPQ: 42 +NM: 1 +Q_ID: M01168:19:000000000-A2YGD:1:1101:14490:1470 +ALIGN: 103:C>A REC_TYPE: SAM -S_BEG: 993 -SEQ: CGCCGATTCTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAG -CIGAR: 100M +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 306977 +SEQ: GCAAGGGATGGTGACCCGGTAGGCTGGGCCGGCCAGATCCACGGCGGTCCAGATACCGGCTATCACCCAGCCGACCGGCCCGGCTAGCGCGGCGACGGCACGAACGCCAGCGAAGGTTCCCCCAGCAACCACCGCACTGCGCAGCCCGTGCCCAAGCAGCTGCTGAGCCATCGAGTTCACGATCACCGTCGAAGTGCGATAGAGGATTAGCCGTGCTACGGTCGGCACTACCA +CIGAR: 233M +MD: 103C129 +S_END: 307209 +--- +STRAND: + +MAPQ: 42 +NM: 1 +Q_ID: M01168:19:000000000-A2YGD:1:1101:16598:1488 +ALIGN: 6:T>A +REC_TYPE: SAM +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 6526264 +SEQ: GCCAGCACCAGATCACGAGCCGCGCGGTTGGCAGCGTCCAGGCCGTCAGCGATCTTCTTCTGACGCTCTTGCAGAGCCGCGATGACCGGAGGCCACACGAACTTCATGCAGAACAGCACAAAGATGAAGAACGCAACGGACTGGCCAATCAGGGTTGCATTAATGTTCAC +CIGAR: 170M +MD: 6T163 +S_END: 6526433 --- -MAPQ: 37 STRAND: - -Q_ID: ID00004198 -ALIGN: 8:G>C -S_ID: gi|48994873|gb|U00096.2| +MAPQ: 8 +NM: 10 +Q_ID: M01168:19:000000000-A2YGD:1:1101:15847:1490 +ALIGN: 54:C>G,62:C>G,88:C>G,92:T>G,97:G>C,123:T>A,128:C>G,143:T>G,144:G>T,148:T>G +REC_TYPE: SAM +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 1410225 +SEQ: GTCAGCGGCCGCCAGCGACGACAACGACGAGGAGCCCGCCGGGCAGGCGGGCGGGGAACAGGGCGAGGAGCGCCGCAGCCGGGTCCTGGGGGGCACCCCCGAGCGCCTGGACCGGCTGCTGGAAATCTGCAGCAAGTCGCTGGGTGAGGTCCAG +CIGAR: 154M +MD: 54C7C25C3T4G25T4C14T0G3T5 +S_END: 1410378 +--- +STRAND: - +MAPQ: 42 +NM: 3 +Q_ID: M01168:19:000000000-A2YGD:1:1101:16182:1497 +ALIGN: 201:C>G,220:T>G,222:C>A +REC_TYPE: SAM +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 2683318 +SEQ: TTGCAGCGCGCCTTGCGCTGACTGGCTCTTGCCGACCAGATCGGCCAGCACGCTTTCGTCTTCGCCCAGGTTCTGCGACACCTGCGCCTGCATCTGCATGGTGGTCTGCAAGCCGTTGAGCGTGTTCTTCCACCGCTCTTGGGCGTCGCGGTACATCTGGTCGCCGCTGACGGTGGCGGCGTACTGCTCCGGGTACAGGCGGGCGAACTCCCGATCCAGAGTAGTCACGTCGT +CIGAR: 233M +MD: 201C18T1C10 +S_END: 2683550 +--- +STRAND: + +MAPQ: 42 +NM: 1 +Q_ID: M01168:19:000000000-A2YGD:1:1101:16598:1488 +ALIGN: 6:T>A REC_TYPE: SAM -S_BEG: 993 -SEQ: CGCCGATTCTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAG -CIGAR: 100M +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 6526264 +SEQ: GCCAGCACCAGATCACGAGCCGCGCGGTTGGCAGCGTCCAGGCCGTCAGCGATCTTCTTCTGACGCTCTTGCAGAGCCGCGATGACCGGAGGCCACACGAACTTCATGCAGAACAGCACAAAGATGAAGAACGCAACGGACTGGCCAATCAGGGTTGCATTAATGTTCAC +CIGAR: 170M +MD: 6T163 +S_END: 6526433 --- -MAPQ: 37 STRAND: - -Q_ID: ID00009237 -ALIGN: 61:G>- -S_ID: gi|48994873|gb|U00096.2| +MAPQ: 8 +NM: 10 +Q_ID: M01168:19:000000000-A2YGD:1:1101:15847:1490 +ALIGN: 54:C>G,62:C>G,88:C>G,92:T>G,97:G>C,123:T>A,128:C>G,143:T>G,144:G>T,148:T>G REC_TYPE: SAM -S_BEG: 5440 -SEQ: CCTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGTCATGGTCCAGGCAAACATCACCGCTAAATGACAAATG -CIGAR: 61M1D39M +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 1410225 +SEQ: GTCAGCGGCCGCCAGCGACGACAACGACGAGGAGCCCGCCGGGCAGGCGGGCGGGGAACAGGGCGAGGAGCGCCGCAGCCGGGTCCTGGGGGGCACCCCCGAGCGCCTGGACCGGCTGCTGGAAATCTGCAGCAAGTCGCTGGGTGAGGTCCAG +CIGAR: 154M +MD: 54C7C25C3T4G25T4C14T0G3T5 +S_END: 1410378 --- -MAPQ: 37 STRAND: - -Q_ID: ID00009237 -ALIGN: 61:G>- -S_ID: gi|48994873|gb|U00096.2| +MAPQ: 42 +NM: 3 +Q_ID: M01168:19:000000000-A2YGD:1:1101:16182:1497 +ALIGN: 201:C>G,220:T>G,222:C>A REC_TYPE: SAM -S_BEG: 5440 -SEQ: CCTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGTCATGGTCCAGGCAAACATCACCGCTAAATGACAAATG -CIGAR: 61M1D39M +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 2683318 +SEQ: TTGCAGCGCGCCTTGCGCTGACTGGCTCTTGCCGACCAGATCGGCCAGCACGCTTTCGTCTTCGCCCAGGTTCTGCGACACCTGCGCCTGCATCTGCATGGTGGTCTGCAAGCCGTTGAGCGTGTTCTTCCACCGCTCTTGGGCGTCGCGGTACATCTGGTCGCCGCTGACGGTGGCGGCGTACTGCTCCGGGTACAGGCGGGCGAACTCCCGATCCAGAGTAGTCACGTCGT +CIGAR: 233M +MD: 201C18T1C10 +S_END: 2683550 --- -MAPQ: 37 STRAND: - -Q_ID: ID00009237 -ALIGN: 61:G>- -S_ID: gi|48994873|gb|U00096.2| +MAPQ: 42 +NM: 3 +Q_ID: M01168:19:000000000-A2YGD:1:1101:16182:1497 +ALIGN: 201:C>G,220:T>G,222:C>A REC_TYPE: SAM -S_BEG: 5440 -SEQ: CCTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGTCATGGTCCAGGCAAACATCACCGCTAAATGACAAATG -CIGAR: 61M1D39M +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 2683318 +SEQ: TTGCAGCGCGCCTTGCGCTGACTGGCTCTTGCCGACCAGATCGGCCAGCACGCTTTCGTCTTCGCCCAGGTTCTGCGACACCTGCGCCTGCATCTGCATGGTGGTCTGCAAGCCGTTGAGCGTGTTCTTCCACCGCTCTTGGGCGTCGCGGTACATCTGGTCGCCGCTGACGGTGGCGGCGTACTGCTCCGGGTACAGGCGGGCGAACTCCCGATCCAGAGTAGTCACGTCGT +CIGAR: 233M +MD: 201C18T1C10 +S_END: 2683550 --- diff --git a/bp_test/out/find_SNPs.out.1 b/bp_test/out/find_SNPs.out.1 index 2338ec0..654152f 100644 --- a/bp_test/out/find_SNPs.out.1 +++ b/bp_test/out/find_SNPs.out.1 @@ -1,81 +1,229 @@ -MAPQ: 37 STRAND: - -Q_ID: ID00002249 -ALIGN: 63:->A -S_ID: gi|48994873|gb|U00096.2| +MAPQ: 42 +NM: 1 +Q_ID: M01168:19:000000000-A2YGD:1:1101:14450:1450 +ALIGN: 156:T>G REC_TYPE: SAM -S_BEG: 2937 -SEQ: TCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAAGTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGC -CIGAR: 63M1I36M +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 6486413 +SEQ: CTCGCCGGGCACTACCTGCGCTACGCCGGGCAGGCCGAATGGGAAAGCCTGCAGATCGAACCGGTGAAGGGCGGCTACCAGGCGAGCTTCGCCCTGATGCGCATCGGCAATCCGGAGAAACTGATGGAATATGGGCCCGCGGCGGTCGGCGAGTGGGCGGCTGGAGGGGCAAGGCGCCCTCTACCGACTGCGCAGCGAAGGCCTGGGCGCCGGCTGCAGCCTGCTGGTATGGCAGG +CIGAR: 236M +MD: 156T79 +S_END: 6486648 --- -MAPQ: 37 STRAND: - -Q_ID: ID00004198 -ALIGN: 8:G>C -S_ID: gi|48994873|gb|U00096.2| +MAPQ: 42 +NM: 1 +Q_ID: M01168:19:000000000-A2YGD:1:1101:14490:1470 +ALIGN: 103:C>A REC_TYPE: SAM -S_BEG: 993 -SEQ: CGCCGATTCTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAG -CIGAR: 100M +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 306977 +SEQ: GCAAGGGATGGTGACCCGGTAGGCTGGGCCGGCCAGATCCACGGCGGTCCAGATACCGGCTATCACCCAGCCGACCGGCCCGGCTAGCGCGGCGACGGCACGAACGCCAGCGAAGGTTCCCCCAGCAACCACCGCACTGCGCAGCCCGTGCCCAAGCAGCTGCTGAGCCATCGAGTTCACGATCACCGTCGAAGTGCGATAGAGGATTAGCCGTGCTACGGTCGGCACTACCA +CIGAR: 233M +MD: 103C129 +S_END: 307209 +--- +STRAND: + +MAPQ: 42 +NM: 1 +Q_ID: M01168:19:000000000-A2YGD:1:1101:16598:1488 +ALIGN: 6:T>A +REC_TYPE: SAM +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 6526264 +SEQ: GCCAGCACCAGATCACGAGCCGCGCGGTTGGCAGCGTCCAGGCCGTCAGCGATCTTCTTCTGACGCTCTTGCAGAGCCGCGATGACCGGAGGCCACACGAACTTCATGCAGAACAGCACAAAGATGAAGAACGCAACGGACTGGCCAATCAGGGTTGCATTAATGTTCAC +CIGAR: 170M +MD: 6T163 +S_END: 6526433 +--- +STRAND: - +MAPQ: 8 +NM: 10 +Q_ID: M01168:19:000000000-A2YGD:1:1101:15847:1490 +ALIGN: 54:C>G,62:C>G,88:C>G,92:T>G,97:G>C,123:T>A,128:C>G,143:T>G,144:G>T,148:T>G +REC_TYPE: SAM +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 1410225 +SEQ: GTCAGCGGCCGCCAGCGACGACAACGACGAGGAGCCCGCCGGGCAGGCGGGCGGGGAACAGGGCGAGGAGCGCCGCAGCCGGGTCCTGGGGGGCACCCCCGAGCGCCTGGACCGGCTGCTGGAAATCTGCAGCAAGTCGCTGGGTGAGGTCCAG +CIGAR: 154M +MD: 54C7C25C3T4G25T4C14T0G3T5 +S_END: 1410378 --- -MAPQ: 37 STRAND: - -Q_ID: ID00004198 -ALIGN: 8:G>C -S_ID: gi|48994873|gb|U00096.2| +MAPQ: 42 +NM: 3 +Q_ID: M01168:19:000000000-A2YGD:1:1101:16182:1497 +ALIGN: 201:C>G,220:T>G,222:C>A +REC_TYPE: SAM +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 2683318 +SEQ: TTGCAGCGCGCCTTGCGCTGACTGGCTCTTGCCGACCAGATCGGCCAGCACGCTTTCGTCTTCGCCCAGGTTCTGCGACACCTGCGCCTGCATCTGCATGGTGGTCTGCAAGCCGTTGAGCGTGTTCTTCCACCGCTCTTGGGCGTCGCGGTACATCTGGTCGCCGCTGACGGTGGCGGCGTACTGCTCCGGGTACAGGCGGGCGAACTCCCGATCCAGAGTAGTCACGTCGT +CIGAR: 233M +MD: 201C18T1C10 +S_END: 2683550 +--- +STRAND: + +MAPQ: 42 +NM: 1 +Q_ID: M01168:19:000000000-A2YGD:1:1101:16598:1488 +ALIGN: 6:T>A REC_TYPE: SAM -S_BEG: 993 -SEQ: CGCCGATTCTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAG -CIGAR: 100M +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 6526264 +SEQ: GCCAGCACCAGATCACGAGCCGCGCGGTTGGCAGCGTCCAGGCCGTCAGCGATCTTCTTCTGACGCTCTTGCAGAGCCGCGATGACCGGAGGCCACACGAACTTCATGCAGAACAGCACAAAGATGAAGAACGCAACGGACTGGCCAATCAGGGTTGCATTAATGTTCAC +CIGAR: 170M +MD: 6T163 +S_END: 6526433 --- -MAPQ: 37 STRAND: - -Q_ID: ID00009237 -ALIGN: 61:G>- -S_ID: gi|48994873|gb|U00096.2| +MAPQ: 8 +NM: 10 +Q_ID: M01168:19:000000000-A2YGD:1:1101:15847:1490 +ALIGN: 54:C>G,62:C>G,88:C>G,92:T>G,97:G>C,123:T>A,128:C>G,143:T>G,144:G>T,148:T>G REC_TYPE: SAM -S_BEG: 5440 -SEQ: CCTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGTCATGGTCCAGGCAAACATCACCGCTAAATGACAAATG -CIGAR: 61M1D39M +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 1410225 +SEQ: GTCAGCGGCCGCCAGCGACGACAACGACGAGGAGCCCGCCGGGCAGGCGGGCGGGGAACAGGGCGAGGAGCGCCGCAGCCGGGTCCTGGGGGGCACCCCCGAGCGCCTGGACCGGCTGCTGGAAATCTGCAGCAAGTCGCTGGGTGAGGTCCAG +CIGAR: 154M +MD: 54C7C25C3T4G25T4C14T0G3T5 +S_END: 1410378 --- -MAPQ: 37 STRAND: - -Q_ID: ID00009237 -ALIGN: 61:G>- -S_ID: gi|48994873|gb|U00096.2| +MAPQ: 42 +NM: 3 +Q_ID: M01168:19:000000000-A2YGD:1:1101:16182:1497 +ALIGN: 201:C>G,220:T>G,222:C>A REC_TYPE: SAM -S_BEG: 5440 -SEQ: CCTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGTCATGGTCCAGGCAAACATCACCGCTAAATGACAAATG -CIGAR: 61M1D39M +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 2683318 +SEQ: TTGCAGCGCGCCTTGCGCTGACTGGCTCTTGCCGACCAGATCGGCCAGCACGCTTTCGTCTTCGCCCAGGTTCTGCGACACCTGCGCCTGCATCTGCATGGTGGTCTGCAAGCCGTTGAGCGTGTTCTTCCACCGCTCTTGGGCGTCGCGGTACATCTGGTCGCCGCTGACGGTGGCGGCGTACTGCTCCGGGTACAGGCGGGCGAACTCCCGATCCAGAGTAGTCACGTCGT +CIGAR: 233M +MD: 201C18T1C10 +S_END: 2683550 --- -MAPQ: 37 STRAND: - -Q_ID: ID00009237 -ALIGN: 61:G>- -S_ID: gi|48994873|gb|U00096.2| +MAPQ: 42 +NM: 3 +Q_ID: M01168:19:000000000-A2YGD:1:1101:16182:1497 +ALIGN: 201:C>G,220:T>G,222:C>A REC_TYPE: SAM -S_BEG: 5440 -SEQ: CCTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGTCATGGTCCAGGCAAACATCACCGCTAAATGACAAATG -CIGAR: 61M1D39M +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 2683318 +SEQ: TTGCAGCGCGCCTTGCGCTGACTGGCTCTTGCCGACCAGATCGGCCAGCACGCTTTCGTCTTCGCCCAGGTTCTGCGACACCTGCGCCTGCATCTGCATGGTGGTCTGCAAGCCGTTGAGCGTGTTCTTCCACCGCTCTTGGGCGTCGCGGTACATCTGGTCGCCGCTGACGGTGGCGGCGTACTGCTCCGGGTACAGGCGGGCGAACTCCCGATCCAGAGTAGTCACGTCGT +CIGAR: 233M +MD: 201C18T1C10 +S_END: 2683550 +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 6486569 +EVENT: T>G +SNP_COUNT: 1 +TYPE: MISMATCH --- REC_TYPE: SNP -S_ID: gi|48994873|gb|U00096.2| -POS: 3000 -EVENT: ->A +S_ID: gi|116048575|ref|NC_008463.1| +POS: 307080 +EVENT: C>A SNP_COUNT: 1 -TYPE: INSERTION +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 6526270 +EVENT: T>A +SNP_COUNT: 2 +TYPE: MISMATCH --- REC_TYPE: SNP -S_ID: gi|48994873|gb|U00096.2| -POS: 1001 +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410279 +EVENT: C>G +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410287 +EVENT: C>G +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410313 +EVENT: C>G +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410317 +EVENT: T>G +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410322 EVENT: G>C SNP_COUNT: 2 TYPE: MISMATCH --- REC_TYPE: SNP -S_ID: gi|48994873|gb|U00096.2| -POS: 5501 -EVENT: G>- +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410348 +EVENT: T>A +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410353 +EVENT: C>G +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410368 +EVENT: T>G +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410369 +EVENT: G>T +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410373 +EVENT: T>G +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 2683519 +EVENT: C>G SNP_COUNT: 3 -TYPE: DELETION +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 2683538 +EVENT: T>G +SNP_COUNT: 3 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 2683540 +EVENT: C>A +SNP_COUNT: 3 +TYPE: MISMATCH --- diff --git a/bp_test/out/find_SNPs.out.2 b/bp_test/out/find_SNPs.out.2 new file mode 100644 index 0000000..a98a084 --- /dev/null +++ b/bp_test/out/find_SNPs.out.2 @@ -0,0 +1,245 @@ +STRAND: - +MAPQ: 42 +NM: 1 +Q_ID: M01168:19:000000000-A2YGD:1:1101:14450:1450 +ALIGN: 156:T>G +REC_TYPE: SAM +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 6486413 +SEQ: CTCGCCGGGCACTACCTGCGCTACGCCGGGCAGGCCGAATGGGAAAGCCTGCAGATCGAACCGGTGAAGGGCGGCTACCAGGCGAGCTTCGCCCTGATGCGCATCGGCAATCCGGAGAAACTGATGGAATATGGGCCCGCGGCGGTCGGCGAGTGGGCGGCTGGAGGGGCAAGGCGCCCTCTACCGACTGCGCAGCGAAGGCCTGGGCGCCGGCTGCAGCCTGCTGGTATGGCAGG +CIGAR: 236M +MD: 156T79 +S_END: 6486648 +--- +STRAND: - +MAPQ: 42 +NM: 1 +Q_ID: M01168:19:000000000-A2YGD:1:1101:14490:1470 +ALIGN: 103:C>A +REC_TYPE: SAM +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 306977 +SEQ: GCAAGGGATGGTGACCCGGTAGGCTGGGCCGGCCAGATCCACGGCGGTCCAGATACCGGCTATCACCCAGCCGACCGGCCCGGCTAGCGCGGCGACGGCACGAACGCCAGCGAAGGTTCCCCCAGCAACCACCGCACTGCGCAGCCCGTGCCCAAGCAGCTGCTGAGCCATCGAGTTCACGATCACCGTCGAAGTGCGATAGAGGATTAGCCGTGCTACGGTCGGCACTACCA +CIGAR: 233M +MD: 103C129 +S_END: 307209 +--- +STRAND: + +MAPQ: 42 +NM: 1 +Q_ID: M01168:19:000000000-A2YGD:1:1101:16598:1488 +ALIGN: 6:T>A +REC_TYPE: SAM +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 6526264 +SEQ: GCCAGCACCAGATCACGAGCCGCGCGGTTGGCAGCGTCCAGGCCGTCAGCGATCTTCTTCTGACGCTCTTGCAGAGCCGCGATGACCGGAGGCCACACGAACTTCATGCAGAACAGCACAAAGATGAAGAACGCAACGGACTGGCCAATCAGGGTTGCATTAATGTTCAC +CIGAR: 170M +MD: 6T163 +S_END: 6526433 +--- +STRAND: - +MAPQ: 8 +NM: 10 +Q_ID: M01168:19:000000000-A2YGD:1:1101:15847:1490 +ALIGN: 54:C>G,62:C>G,88:C>G,92:T>G,97:G>C,123:T>A,128:C>G,143:T>G,144:G>T,148:T>G +REC_TYPE: SAM +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 1410225 +SEQ: GTCAGCGGCCGCCAGCGACGACAACGACGAGGAGCCCGCCGGGCAGGCGGGCGGGGAACAGGGCGAGGAGCGCCGCAGCCGGGTCCTGGGGGGCACCCCCGAGCGCCTGGACCGGCTGCTGGAAATCTGCAGCAAGTCGCTGGGTGAGGTCCAG +CIGAR: 154M +MD: 54C7C25C3T4G25T4C14T0G3T5 +S_END: 1410378 +--- +STRAND: - +MAPQ: 42 +NM: 3 +Q_ID: M01168:19:000000000-A2YGD:1:1101:16182:1497 +ALIGN: 201:C>G,220:T>G,222:C>A +REC_TYPE: SAM +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 2683318 +SEQ: TTGCAGCGCGCCTTGCGCTGACTGGCTCTTGCCGACCAGATCGGCCAGCACGCTTTCGTCTTCGCCCAGGTTCTGCGACACCTGCGCCTGCATCTGCATGGTGGTCTGCAAGCCGTTGAGCGTGTTCTTCCACCGCTCTTGGGCGTCGCGGTACATCTGGTCGCCGCTGACGGTGGCGGCGTACTGCTCCGGGTACAGGCGGGCGAACTCCCGATCCAGAGTAGTCACGTCGT +CIGAR: 233M +MD: 201C18T1C10 +S_END: 2683550 +--- +STRAND: + +MAPQ: 42 +NM: 1 +Q_ID: M01168:19:000000000-A2YGD:1:1101:16598:1488 +ALIGN: 6:T>A +REC_TYPE: SAM +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 6526264 +SEQ: GCCAGCACCAGATCACGAGCCGCGCGGTTGGCAGCGTCCAGGCCGTCAGCGATCTTCTTCTGACGCTCTTGCAGAGCCGCGATGACCGGAGGCCACACGAACTTCATGCAGAACAGCACAAAGATGAAGAACGCAACGGACTGGCCAATCAGGGTTGCATTAATGTTCAC +CIGAR: 170M +MD: 6T163 +S_END: 6526433 +--- +STRAND: - +MAPQ: 8 +NM: 10 +Q_ID: M01168:19:000000000-A2YGD:1:1101:15847:1490 +ALIGN: 54:C>G,62:C>G,88:C>G,92:T>G,97:G>C,123:T>A,128:C>G,143:T>G,144:G>T,148:T>G +REC_TYPE: SAM +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 1410225 +SEQ: GTCAGCGGCCGCCAGCGACGACAACGACGAGGAGCCCGCCGGGCAGGCGGGCGGGGAACAGGGCGAGGAGCGCCGCAGCCGGGTCCTGGGGGGCACCCCCGAGCGCCTGGACCGGCTGCTGGAAATCTGCAGCAAGTCGCTGGGTGAGGTCCAG +CIGAR: 154M +MD: 54C7C25C3T4G25T4C14T0G3T5 +S_END: 1410378 +--- +STRAND: - +MAPQ: 42 +NM: 3 +Q_ID: M01168:19:000000000-A2YGD:1:1101:16182:1497 +ALIGN: 201:C>G,220:T>G,222:C>A +REC_TYPE: SAM +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 2683318 +SEQ: TTGCAGCGCGCCTTGCGCTGACTGGCTCTTGCCGACCAGATCGGCCAGCACGCTTTCGTCTTCGCCCAGGTTCTGCGACACCTGCGCCTGCATCTGCATGGTGGTCTGCAAGCCGTTGAGCGTGTTCTTCCACCGCTCTTGGGCGTCGCGGTACATCTGGTCGCCGCTGACGGTGGCGGCGTACTGCTCCGGGTACAGGCGGGCGAACTCCCGATCCAGAGTAGTCACGTCGT +CIGAR: 233M +MD: 201C18T1C10 +S_END: 2683550 +--- +STRAND: - +MAPQ: 42 +NM: 3 +Q_ID: M01168:19:000000000-A2YGD:1:1101:16182:1497 +ALIGN: 201:C>G,220:T>G,222:C>A +REC_TYPE: SAM +S_ID: gi|116048575|ref|NC_008463.1| +S_BEG: 2683318 +SEQ: TTGCAGCGCGCCTTGCGCTGACTGGCTCTTGCCGACCAGATCGGCCAGCACGCTTTCGTCTTCGCCCAGGTTCTGCGACACCTGCGCCTGCATCTGCATGGTGGTCTGCAAGCCGTTGAGCGTGTTCTTCCACCGCTCTTGGGCGTCGCGGTACATCTGGTCGCCGCTGACGGTGGCGGCGTACTGCTCCGGGTACAGGCGGGCGAACTCCCGATCCAGAGTAGTCACGTCGT +CIGAR: 233M +MD: 201C18T1C10 +S_END: 2683550 +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 6486569 +COVERAGE: 1 +EVENT: T>G +SNP_COUNT: 1 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 307080 +COVERAGE: 1 +EVENT: C>A +SNP_COUNT: 1 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 6526270 +COVERAGE: 2 +EVENT: T>A +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410279 +COVERAGE: 2 +EVENT: C>G +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410287 +COVERAGE: 2 +EVENT: C>G +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410313 +COVERAGE: 2 +EVENT: C>G +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410317 +COVERAGE: 2 +EVENT: T>G +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410322 +COVERAGE: 2 +EVENT: G>C +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410348 +COVERAGE: 2 +EVENT: T>A +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410353 +COVERAGE: 2 +EVENT: C>G +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410368 +COVERAGE: 2 +EVENT: T>G +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410369 +COVERAGE: 2 +EVENT: G>T +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 1410373 +COVERAGE: 2 +EVENT: T>G +SNP_COUNT: 2 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 2683519 +COVERAGE: 3 +EVENT: C>G +SNP_COUNT: 3 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 2683538 +COVERAGE: 3 +EVENT: T>G +SNP_COUNT: 3 +TYPE: MISMATCH +--- +REC_TYPE: SNP +S_ID: gi|116048575|ref|NC_008463.1| +POS: 2683540 +COVERAGE: 3 +EVENT: C>A +SNP_COUNT: 3 +TYPE: MISMATCH +--- -- 2.39.2