Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,173,361 Δ2 bp 100% pseudogene (1‑2/442 nt) gatC ← pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,173,3610C.75.0% 22.0 / 4.4 12pseudogene (2/442 nt)gatCpseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
Reads supporting (aligned to +/- strand):  ref base C (1/2);  new base . (8/1);  total (9/3)
Fisher's exact test for biased strand distribution p-value = 1.27e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.
*NC_0009132,173,3620C.75.1% 22.1 / 3.3 12pseudogene (1/442 nt)gatCpseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base . (8/1);  total (9/3)
Fisher's exact test for biased strand distribution p-value = 3.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

TAGTTTGCGTCGCGATCCACAGGGTGATGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGA‑CCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCA‑GCTGCAATACACCTTTGACATCGTAACCCGCGAGGATGCCG  >  NC_000913/2173154‑2173574
                                                                                                                                                                                                                ||                                                                                                                                                                                                                     
tAGTTTGCGTCGCGATCCACAGGGTGATGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGA‑CCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATAAGGCTTGCCGGAACCACCC‑‑CCGTATGTCCcagcagaa                                                                                                                                                                                                  >  1:559969/1‑226 (MQ=255)
                         gATGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGA‑CCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGCAACCA‑‑CAGCCGTATGTCCCAGCAGAAACGCCGGAACAAAGCCaacccgac                                                                                                                                                                          >  1:312322/1‑221 (MQ=255)
                           tGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGA‑CCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGGGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATAAAGGCCAATCAGGAACt                                                                                                                                                                       >  1:380797/1‑228 (MQ=255)
                                                                 ataTTTCCCCGAAGCCCCGGGACCCGCCAACCCCCAGAAAAGGCAGAGGGGGGAAAAATCACAAAAGGGAAGCACATAAATCCCCGGCACACAAAAAGAAATAAAAATGGTGAGGGGAATAAAAATCGGGCTGCCCGATCCCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGc                                                                                                                                  <  2:548018/226‑1 (MQ=255)
                                                                               cACGGCGA‑CCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAAATCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGACTGCTTAGCGATgg                                                                                                                    >  1:162870/1‑227 (MQ=255)
                                                                                                                                                        cacacaACGCGCAATAAAAATGGTGAGTGGGATAAAAATCA‑GCCTGGCGGTACC‑CCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGACCTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCA‑g                                          <  1:223575/228‑1 (MQ=255)
                                                                                                                                                        cacacaAA‑AACAATTAAAAGGGGTAGGGGGAAAAAAACCCCGCATGGCCACACC‑CACCCCCGTAGCCCCCAGCAGACCCCCCGAAAAAAGGCCAACCAGGACCCCCTGACCGCCGAACTTCCCCTGTAAACGACTACGAGCCTGCTGAGCGATGGGCGTTAAACCATCCATGATGGTTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCA‑g                                          <  2:384834/228‑1 (MQ=255)
                                                                                                                                                          cacaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCA‑GCt                                        >  1:384834/1‑228 (MQ=255)
                                                                                                                                                                  gCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGCCTACGAGCCTGCTTAGCGATGGGCGTTAAACACTCCATGATGGGTTTAATCACCCTGGGCATTAGCAGCATCACTGCCGCCGTTTTTTCCGCCA‑CCTGCAATac                                 >  2:186896/1‑227 (MQ=255)
                                                                                                                                                                                 aGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCAGGGCATTAGCAGCAACACTGCCGCCGTTTTTACAGCCA‑CCGGCAAAACACCTTTGACACCGaaa                 >  2:45319/1‑228 (MQ=255)
                                                                                                                                                                                      gATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTACCGATGGGCGTTAAACCATCCATAAGGGGTTTAATCACCCGTGACATTAGGCCATTCACTGCCACC‑TCTTTTTCGCCACCCTGGAATACCCCTTTGCCATccacaccccc            >  2:98517/1‑219 (MQ=255)
                                                                                                                                                                                                aGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGATTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCA‑CCCGCAATCCACCTTTGACATCGTAACCCCCGTGGactccc  >  2:110162/1‑223 (MQ=255)
                                                                                                                                                                                                                ||                                                                                                                                                                                                                     
TAGTTTGCGTCGCGATCCACAGGGTGATGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGA‑CCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCA‑GCTGCAATACACCTTTGACATCGTAACCCGCGAGGATGCCG  >  NC_000913/2173154‑2173574

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑