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Sheet1
FLAG flags pair proper? aligner?
73 1+8+64 73 1 map + unmap
133 1+4+128 133 2 unmap map +
89 1+8+16+64 89 1 map + unmap -
121 1+8+16+32+64 1 map - unmap -
165 1+4+32+128 165 2 unmap + map - ssaha
181 1+4+16+32+128 2 unmap - map - bwa
101 1+4+32+64 101 1 unmap + map - ssaha
117 1+4+16+32+64 1 unmap - map + bwa
153 1+8+16+128 153 2 map - unmap +
185 1+8+16+32+128 2 map - unmap -
69 1+4+64 69 1 unmap + map +
137 1+8+128 137 2 map + unmap +
77 1+4+8+64 77 1 unmap + unmap +
141 1+4+8+128 141 2 unmap + unmap +
99 1+2+32+64 99 1 map + map - y
147 0+1+2+16+128 147 2 map - map + y
83 1+2+16+64 83 1 map - map + y
163 1+2+32+128 163 2 map + map - y
67 1+2+64 67 1 map + map + y
131 1+2+128 131 2 map + map + y
115 1+2+16+32+64 115 1 map - map - y
179 1+2+16+32+128 179 2 map - map - y
81 1+16+64 81 1 map - map +
161 1+32+128 161 2 map + map -
97 1+32+64 97 1 map + map -
145 1+16+128 145 2 map - map +
65 1+64 65 1 map + map +
129 1+128 129 2 map + map +
113 1+16+32+64 113 1 map - map -
177 1+16+32+128 177 2 map - map -
Comment
are within the insert size…. , orientation do not seem to matter
mapped uniquely but wrong insert size, and could possibly reside in different contigs
itself mate
One of the mate is unmapped
Both unmapped
mapped within the insert size but wrong orientation (++ or - - )
mapped in correct orientation and within insert size
Page 1

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Sam output flag

  • 1. Sheet1 FLAG flags pair proper? aligner? 73 1+8+64 73 1 map + unmap 133 1+4+128 133 2 unmap map + 89 1+8+16+64 89 1 map + unmap - 121 1+8+16+32+64 1 map - unmap - 165 1+4+32+128 165 2 unmap + map - ssaha 181 1+4+16+32+128 2 unmap - map - bwa 101 1+4+32+64 101 1 unmap + map - ssaha 117 1+4+16+32+64 1 unmap - map + bwa 153 1+8+16+128 153 2 map - unmap + 185 1+8+16+32+128 2 map - unmap - 69 1+4+64 69 1 unmap + map + 137 1+8+128 137 2 map + unmap + 77 1+4+8+64 77 1 unmap + unmap + 141 1+4+8+128 141 2 unmap + unmap + 99 1+2+32+64 99 1 map + map - y 147 0+1+2+16+128 147 2 map - map + y 83 1+2+16+64 83 1 map - map + y 163 1+2+32+128 163 2 map + map - y 67 1+2+64 67 1 map + map + y 131 1+2+128 131 2 map + map + y 115 1+2+16+32+64 115 1 map - map - y 179 1+2+16+32+128 179 2 map - map - y 81 1+16+64 81 1 map - map + 161 1+32+128 161 2 map + map - 97 1+32+64 97 1 map + map - 145 1+16+128 145 2 map - map + 65 1+64 65 1 map + map + 129 1+128 129 2 map + map + 113 1+16+32+64 113 1 map - map - 177 1+16+32+128 177 2 map - map - Comment are within the insert size…. , orientation do not seem to matter mapped uniquely but wrong insert size, and could possibly reside in different contigs itself mate One of the mate is unmapped Both unmapped mapped within the insert size but wrong orientation (++ or - - ) mapped in correct orientation and within insert size Page 1