PF0180-C strange sample, chromsome 14 only inferred 400 alt calls (1000 on average from the same population)

[shajoezhu]

From the Pf3k meta data, it seems pretty normal,

      sample       acc study
454 PF0180-C ERS017388  1017
                                                     study_title
454 Population genetics of natural populations in Northern Ghana
          contact_name        contact_email country     site collection_year
454 Lucas Amenga-Etego lucasmenga@gmail.com   Ghana Navrongo            2010
    sample_prep      bases bases_mapped bases_duplicated avg_read_length
454             4724041788   4631818296        855311135              75
    mean_base_quality bases_of_1X_coverage bases_of_5X_coverage
454              25.5             23156910             23082804
    bases_of_10X_coverage bases_of_50X_coverage mean_coverage
454              23005542              21841663        196.64
    mean_fragment_size sd_fragment_size X.callable IsFieldSample
454              323.1             45.2       89.9          True
    PreferredSample AllSamplesThisIndividual
454            True                 PF0180-C

DEploid result seems normal

           ID Population    Site  Depth Est_K P1 P2 P3 P4   group relatedness
1510 PF0180-C      Ghana Kassena 196.64     1  1  0  0  0 Africa2          NA
     N50_IBD_Length.kb Mean_IBD_goodness cluster year eff_k
1510                NA                NA    <NA> 2010     1