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Dear all,
Does anyone have an idea how the following is possible:
I have reads mapped in a proper pair (as indicated by the sam-flag) but they map to different contigs!!!???
Hope anyone can help on this!!
best ro
Does anyone have an idea how the following is possible:
I have reads mapped in a proper pair (as indicated by the sam-flag) but they map to different contigs!!!???
HWUSI-EAS300R:7:1:15:1404#0 147 FW_DM_LINE_Jockey 128 29 74M FW3_DM_LINE_Jockey 3131 0 TGCAAGATCGCTTAAATACATAGTGAATTGTTATCTTAAATAATAAAACTATGAGTCAGAATGACACTCGCGCC Y^S[]^\[]a_XSZ[_]]_`_`]```_^a^`^`[aa__`]V]```aa\a_`]aaaaaaaa`Ta\a`aaaba`aa XT:A:U NM:i:0 SM:i:29 AM:i:29 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:74
HWUSI-EAS300R:7:1:15:1495#0 147 Gypsy4_LTR_LTR_Gypsy 112 60 74M Gypsy4_I_LTR_Gypsy 6216 0 CATTCCACTGCCCGGAGCGTGTGAAGCGCAATGTCAGCATTCTGCCGTGAGCGCTGCTTCAAAAGACGGGCTAC XUPM^NHLSMW\SWSPM\MW]PW\TZ\aPMP^MS^S]]Z^M_^X]^Z^]Z^]`a]^Z_\aaS]Z`Sa]a`_a\a XT:A:U NM:i:3 XN:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:5T32C22G12
HWUSI-EAS300R:7:1:22:1504#0 147 FW_DM_LINE_Jockey 85 29 74M FW3_DM_LINE_Jockey 3125 0 AACTAAATAAAAAATCTGAAAGCGAAAGAGACGCTCTATGCGATGCAAGATCGCTTAAATACATAGTGAATTGT ]N^I_^WG[[[_YNFQP[XGM\_^^S\a__^``_Y[a^\_a_```aaa`a]a`a````ba_baa`a_bbaabaa XT:A:U NM:i:0 SM:i:29 AM:i:29 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:74
HWUSI-EAS300R:7:1:25:1975#0 83 BLOOD_I_LTR_Gypsy 145 29 13M3D61M BLASTOPIA_LTR_LTR_Gypsy 271 0
HWUSI-EAS300R:7:1:15:1495#0 147 Gypsy4_LTR_LTR_Gypsy 112 60 74M Gypsy4_I_LTR_Gypsy 6216 0 CATTCCACTGCCCGGAGCGTGTGAAGCGCAATGTCAGCATTCTGCCGTGAGCGCTGCTTCAAAAGACGGGCTAC XUPM^NHLSMW\SWSPM\MW]PW\TZ\aPMP^MS^S]]Z^M_^X]^Z^]Z^]`a]^Z_\aaS]Z`Sa]a`_a\a XT:A:U NM:i:3 XN:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:5T32C22G12
HWUSI-EAS300R:7:1:22:1504#0 147 FW_DM_LINE_Jockey 85 29 74M FW3_DM_LINE_Jockey 3125 0 AACTAAATAAAAAATCTGAAAGCGAAAGAGACGCTCTATGCGATGCAAGATCGCTTAAATACATAGTGAATTGT ]N^I_^WG[[[_YNFQP[XGM\_^^S\a__^``_Y[a^\_a_```aaa`a]a`a````ba_baa`a_bbaabaa XT:A:U NM:i:0 SM:i:29 AM:i:29 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:74
HWUSI-EAS300R:7:1:25:1975#0 83 BLOOD_I_LTR_Gypsy 145 29 13M3D61M BLASTOPIA_LTR_LTR_Gypsy 271 0
best ro
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