how pd tag were defined in gaf file

Question

[chuanj8848]

Hi, VG team,

I have aligned some reads to reference using vg giraffe with -M 100 parameter . here is asample alignment for a read pair:

read8409/MER11C:309619:LEN::HG002#2#JAHKSD010000004.1:95278089-95279161 150     0       150     +       <37535814       193     4       154     150     150     60      AS:i:160        cs:Z::150       dv:f:0  fn:Z:read8409/MER11C:309619:LEN::HG002#2#JAHKSD010000004.1:95278089-95279161    pd:b:1
read8409/MER11C:309619:LEN::HG002#2#JAHKSD010000004.1:95278089-95279161 150     0       150     +       >37535823>37535821>37535820>37535818>37535817   610     316     466     149     150     60      AS:i:155        cs:Z::3*GT:146  dv:f:0.0067     fp:Z:read8409/MER11C:309619:LEN::HG002#2#JAHKSD010000004.1:95278089-95279161    pd:b:1

read8409/MER11C:309619:LEN::HG002#2#JAHKSD010000004.1:95278089-95279161 150     0       150     +       <76417106       262     81      236     141     155     0       AS:i:105        cs:Z::11*AG:4*TG:15*CA:63-CTTTA:12*TC*GA:5*TC:6*GA:3*AG:11*AG:11        dv:f:0.06       fn:Z:read8409/MER11C:309619:LEN::HG002#2#JAHKSD010000004.1:95278089-95279161
read8409/MER11C:309619:LEN::HG002#2#JAHKSD010000004.1:95278089-95279161 150     0       150     +       >76417103       408     101     251     132     150     0       AS:i:70 cs:Z::3*GT:7*CT:13*GT*GA:2*GT:6*AT:5*GT*GA:2*CG:3*AC:9*AG:2*AT:3*TC*GA:63*CT*AG:3*TC:10*CT:1    dv:f:0.12       fp:Z:read8409/MER11C:309619:LEN::HG002#2#JAHKSD010000004.1:95278089-95279161

Upon examining the reference graph, it seems that nodes 76417103 and 76417106 are within a reasonable distance, consistent with the expected sequencing fragment size.

So, my question is why the second alignment don't have pd tag? is it caused by its low alignment score?

there are more examples like these:

 read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697       150     0       150     +    >57299185<57299187>57299188>57299189>57299191<57299193>57299194<57299196>57299197       307     89      239     150     150 0       AS:i:160        cs:Z::150       dv:f:0  fn:Z:read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697  pd:b:1
 read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697       150     0       150     +       <57299206<57299204<57299203>57299202<57299200   233     58      208     150     150     0       AS:i:160        cs:Z::150 dv:f:0  fp:Z:read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697  pd:b:1
read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697       150     0       150     +       >60098202>60098203>60098205>60098206>60098208>60098209>60098211 438     144     294     150     150     0       AS:i:160 cs:Z::150       dv:f:0  fn:Z:read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697
read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697       150     0       150     +       <60098214<60098212<60098211     321     58      208     150     150     0       AS:i:160        cs:Z::150       dv:f:0  fp:Z:read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697
read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697       150     0       150     +       >60049037>60049035>60049034>60049032>60049031>60049029>60049028 438     144     294     150     150     0       AS:i:160 cs:Z::150       dv:f:0  fn:Z:read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697
read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697       150     0       150     +       <60049025<60049026<60049028     321     58      208     150     150     0       AS:i:160        cs:Z::150       dv:f:0  fp:Z:read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697
read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697       150     0       150     +       >60067486<60067488>60067489<60067491>60067492<60067494>60067495 438     144     294     150     150     0       AS:i:160  cs:Z::150       dv:f:0  fn:Z:read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697
read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697       150     0       150     +       <60067501<60067499<60067498>60067497<60067495   321     58      208     150     150     0       AS:i:160        cs:Z::150 dv:f:0  fp:Z:read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697
read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697       150     0       150     +       <60093907<60093905<60093904<60093902<60093901<60093899<60093898 375     115     265     150     150     0       AS:i:160 cs:Z::150       dv:f:0  fn:Z:read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697
read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697       150     0       150     +       >60093888>60093889>60093891>60093892>60093894>60093895>60093897>60093898        321     58      208     150     150     0 AS:i:160        cs:Z::150       dv:f:0  fp:Z:read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697
read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697       150     0       150     +       <55856031>55856030<55856028     412     93      243     148     150     0       AS:i:150        cs:Z::28*CG:64*CT:56    dv:f:0.0133     fn:Z:read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697  pd:b:1
read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697       150     0       150     +       >55856025>55856026>55856028     265     2       152     148     150     0       AS:i:150    cs:Z::8*TG:90*AG:50     dv:f:0.0133     fp:Z:read4312/HERVK3:168704:LEN::HG002#2#JAHKSD010000001.1:110498869-110500697  pd:b:1