missing avg_distance_to_effective_3p_end

[stemangiola]

In analysis some BAM files I get these kind of results (one line shown)

chr17
748892
T
1
=:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00
A:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00
C:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 G:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 T:1:0.00:37.00:0.00:1:0:0.00:0.00:0.00:0:0.00:0.00:0.00 N:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00

Apparently none of the key info to use for example sinvict are present.

Is this a pathological result?

I aligned the reads with bwa

M04416:61:000000000-C2G5K:1:1101:20297:9269     77      *       0       0       *       *       0       0       GAGGGGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATG >1>A1>AAFFFFFAFFGAGGFFDFAGHGHHGCCEEEGGHFHGHHFA11F1GFFF0F?FEAFFAGHHHFHHGHBGFH0/GGEEGGEGEBHHH/FF@?EACHCC/B?FGHH2?GGB1FFB2FBGHHBGHHFHGGGGGHHGHFHHFGHBGGHHH AS:i:0  XS:i:0
M04416:61:000000000-C2G5K:1:1101:20297:9269     141     *       0       0       *       *       0       0       CAGCGGCAGACTTGCCACCAAGTCCAACCAAATCAAGCAACTTATCAGAAACGGCAGAAGTGCCAGCCTGCAACGTACCTTCAAGAAGTCCTTTACCAGCTTTAGCCATAGCACCAGAAACAAAACTAGGGACGGCCTCATCAGGGTTAGG A1>AA?@DDAFFGGGGGGG00BGFHH1BAFGGFD1AAF0FGFGFFGHHHHCGGECECGBGHDFHFEAEHHHHHG@CGEGDF@D1B1FHHHBGGHGHBGBE>FHBEGHHHH1>FGHHFFHHHGGHHHGHFHHGGGGGGGHHHHHHGHGHHHG AS:i:0  XS:i:0
M04416:61:000000000-C2G5K:1:1101:12893:9276     83      chr17   10123357        60      8S66M11S        =       10123357        -66     CCCCCTCCTCTGTTGCTGCTGGTCCAGGGACCACACTTTAAGAAGCCCTACCCTAGAATCTGAAGGTTGGAAAGCCATAGGATTC   GGGGFHGHHHHHHGHHHHHHHHHHHHHIHHGHHHGHHHHHHHHHHGGGHHGHHHHHHHHHHHHGGGGGGGGGGCFFFFFFCCBBB   NM:i:1  MD:Z:58C7       AS:i:61 XS:i:31
M04416:61:000000000-C2G5K:1:1101:12893:9276     163     chr17   10123357        60      8S66M11S        =       10123357        66      CCCCCTCCTCTGTTGCTGCTGGTCCAGGGACCACACTTTAAGAAGCCCTACCCTAGAATCTGAAGGTTGGAAAGCCATAGGATTC   ABCCCCCCFFFFGGGGGGGGGGGHHHGHGGGGHHHGHHHHHHHHHHHHHHHHHHHGHHHHHHHGHHHHHGHHHHGHHHHHHHHHH   NM:i:1  MD:Z:58C7       AS:i:61 XS:i:31

What is the best command to align the reads before using bam-readcount?

Thanks