Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913417,5330TG54.5% 3.5 / 17.7 22V131G (GTG→GGG) phoBresponse regulator in two‑component regulatory system with PhoR
Reads supporting (aligned to +/- strand):  ref base T (6/4);  new base G (12/0);  total (18/4)
Fisher's exact test for biased strand distribution p-value = 2.87e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.92e-04
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGAGGTGATTGAGATGCAGGGATTAAGTCTCGACCCGAC‑ATCTCACCGAGTGATGGC‑GGGCGAAGAGCCGCT‑GGAGATGGGGCCGACAGAATTTAAACTGCTG‑CACTTTTTTATGACGCATCCTGAGCGCGTGTACAGCCGCGAGCAG‑CTGTTAAACCACGTCTGGGGAACTAACGTGT  >  NC_000913/417304‑417706
                                                                                                                                                                                                                                     |                                                                                                                                                                                  
aTGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGCATTTCGCCACTGGCGGTGGGAGAGGGGCTTGAGAt                                                                                                                                                                           >  2:520164/1‑239 (MQ=255)
              cTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGAGGTGATTGAGATGCAGGGATTAAg                                                                                                                                                               >  1:565470/1‑237 (MQ=255)
                                     acCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGAGGGGATTGAGATGCAGGGATTAAGTCTCGACCCGAC‑ATCTCACCGAGTg                                                                                                                                     >  1:519144/1‑239 (MQ=255)
                                                 aGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGCAGAGGGGATTGAGATGCAGGGGTTAAGTACCCACCCGAC‑ATATCACCGCGTGATggt‑gggcgca                                                                                                                        >  2:633213/1‑237 (MQ=255)
                                                 aGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGAGGGGATTGGGATGCAGGGATTAAGTCTCGACCCGAC‑ATCTTACCGGGTGAAGGT‑GGGGGaa                                                                                                                        >  1:99399/1‑239 (MQ=255)
                                                 aGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGAGGGGATTGAGATGCAGGGATTAAGTCTCGACCCGAC‑ATCTCACCGAGTGATggc‑gggcgga                                                                                                                        >  1:293460/1‑237 (MQ=255)
                                                 aGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAAGGGGGGTTGGGCTGGCGGGGCTAAGTCTTCACCCGCCAATCACCCCGA‑TGATggg‑gggaggc                                                                                                                        >  2:782337/1‑235 (MQ=255)
                                                            cGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGGAGAGGGGATTGAGATGCAGGGGTTAAGTCTCGACCCGAC‑CACTCACCGAGGGATTGC‑GGGGGGAGAGACGCC‑ggc                                                                                                            >  2:724493/1‑238 (MQ=255)
                                                                     ccAGTGCTGCTGTTGCCCGCCAGTGGGGTTGAAGCAGGTCGCGCGGGCGTCCTCGAAACCGGCGCGATTCACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGACTCAAACTGGTAAACCTCCGTCGTTCGCCACTGGCGGTGGAGGAGGGGATTGGGAGGCGGGGGTTAAGTCTCGACCCCAC‑CACTCACCGCGGGATGGC‑TGACGAGAAGACGCG‑GCGGATgggagg                                                                                                   >  2:25804/1‑236 (MQ=255)
                                                                                                                                 ggCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGGAGAGGGGATTGAGATGCCGGGATTAAGTCTCGACCCGAC‑ATCTCACCGAGTGATGGG‑GGGGGGAGAGCCGCTGGGGGAGGGGGCGGCCAGAATTTAAAC‑GCTGCCACTTTTTTTTGTCCCATCTGGGGCGCGGGGACAGcgcca                                       >  2:39650/1‑235 (MQ=255)
                                                                                                                                                 tCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGGAGAGGGGATTGAGATGCAGGGATTAAGTCTCGACCCGAC‑ATCTCACCGAGTGATGTCGGGGGGAGGAGCGCCG‑GGGGAGGGGGCCCCCA‑AATTTTAAAAGCTG‑CACTTTTTTTTGACGCAGCCCGAGGGGGGGGAAAGCAGCCAGCAGCCGGTTAAAca                       >  2:611165/1‑237 (MQ=255)
                                                                                                                                                  cACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGAGGGGATTGAGATGCAGGGATTAAGTCTCGACCCGAC‑ATCTCACCGAGTGATGGC‑GGGCGAAAAACCGCT‑GGAGATGGGGCCGACAGAATTTAAACTGCTG‑CACTTTTTTATTACGCATCCTGAGCGCGTGTACAGCCGCGAGCAG‑CTGTTAAACCACg                    >  1:507915/1‑239 (MQ=255)
                                                                                                                                                         ccGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGAGGTGATTGAGATGCAGGGATTAAGTCTCGACCCGAC‑ATCTCACCGAGTGATGGC‑GGGCGAAGAGCCGCT‑GGGGATGGGGCCGACAGAATTTAAACTGCTG‑CACTTTTTTTTGACGCATCCTGAgc                                                      >  1:392/1‑199 (MQ=255)
                                                                                                                                                                     aagggtcgggtggCGCGAAACAAAGGGGTAATGCGTCGTATTTCGCACATGGCGGTGGAAGAGGTGGTTGGGATGAAGGGATTAGGTCTCGACCCGAC‑GTCTCGCCGAGTGATGGC‑GGGCGAAGGGCCGCT‑GGAGAGGGGGCCGACGGAATTTAAACGGCTG‑CAGTTTTTTATGACGCAGCCTGAGCGCGTGTACAGCCGCGAGCAG‑CTGTTAAACCACGTCTGGGGAACTAACgtgt  <  2:393925/230‑1 (MQ=255)
                                                                                                                                                                           cTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGAGGTGATTGAGATGCAGGGATTAAGTCCCGACCCGAC‑ATCTCACCGAGTGATGGC‑GGGCGGAGAGCCGCC‑GGGGAAGGGGGCGCCAAAATTTaaa                                                                                      >  2:102926/1‑150 (MQ=255)
                                                                                                                                                                                                      cgcCGTATTTCGCCAATGGCGGTGGAAGAGGTGATTGAGATGCAGGGATTAAGTCTCGACCCGAC‑ATCTCACCGAGTGATg                                                                                                                                  >  1:276687/1‑81 (MQ=255)
                                                                                                                                                                                                      cgcCGTATTTCGCCAATGGCGGTGGAAGAGGTGATTGAGATGCAGGGATTAAGTCTCGACCCGAC‑ATCTCACCGAGTGATGGC‑GGGTGAAGAGCCGCC‑GGAGATGGGGGCCACAGAATTTAAACTGCTG‑CCCTTTTTTATGACGCATCCTGAGGGCGGGTACAGCcgcg                                       >  1:284717/1‑169 (MQ=255)
                                                                                                                                                                                                      cgcCGTATTGCGCCAATGGCGGTGGAAGAGGTGATTGAGATGCGGGGATTAAGTCTCGACCCGAC‑ATCTCACCGAGTGATGGC‑GGGCGAAGAGCCGCT‑GGAGATGGGGCCGACAGAATTTAAACTGCTG‑CACTTTTTTATGACGCAGCCTGAGCGGGTGTACGGCCGCGGGCAG‑CTGTTAAACCACGTATGGGGAACTAACgtgt  <  1:343803/205‑1 (MQ=255)
                                                                                                                                                                                                           tATTTCGCCAATGGCGGTGGAAGAGGGGATTGAGATGCAGGGATTAAGTCTCGAc                                                                                                                                                        >  1:646111/1‑55 (MQ=255)
                                                                                                                                                                                                                      tGGCGGTGGAAGAGGTGATTGAGCTGCAGGGATTAAGTCTCGACCCGAC‑ATCTCACCGAGTGATGGC‑GGGCGAagat                                                                                                                     >  1:65451/1‑76 (MQ=255)
                                                                                                                                                                                                                          ggTGGAAGAGGTGATTGAGATGc                                                                                                                                                                         <  2:469808/23‑1 (MQ=255)
                                                                                                                                                                                                                                 gagGTGATTGAGATGCAGGTAtt                                                                                                                                                                  <  2:646111/23‑1 (MQ=255)
                                                                                                                                                                                                                                     |                                                                                                                                                                                  
ATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGAGGTGATTGAGATGCAGGGATTAAGTCTCGACCCGAC‑ATCTCACCGAGTGATGGC‑GGGCGAAGAGCCGCT‑GGAGATGGGGCCGACAGAATTTAAACTGCTG‑CACTTTTTTATGACGCATCCTGAGCGCGTGTACAGCCGCGAGCAG‑CTGTTAAACCACGTCTGGGGAACTAACGTGT  >  NC_000913/417304‑417706

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑