Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913578,8090TC58.8% 17.5 / 29.2 34T29A (ACA→GCA) borDprophage lipoprotein BorD
Reads supporting (aligned to +/- strand):  ref base T (6/8);  new base C (10/10);  total (16/18)
Fisher's exact test for biased strand distribution p-value = 7.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.00e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGAGTTGAAATTTCATATTGTTAATATTTATTAATGTATGCCAGGTGCGATGAATCGTCATTGTATTCCCGGATTAACTATGTCCACAGCC  >  NC_000913/578593‑579054
                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                     
cATGCAATTATTGTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTCACAACATTTTCTGCGCCGCCACAAATTTTGGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGCCGGTTTGTTTTGAACAGTAAACGTCTGTTGAGc                                                                                                                                                                                                                      >  1:205718/1‑250 (MQ=255)
cATGCAATTATTGTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAAGAAAACCGAGCAATCCATTTACGAATGGTGGCTGGGTGTCTGTTTTAACAACATTTTCTGCGCAGCCACAAAGTTTGGCTGCATCGACAGTTTTCTTCTGTCCAATTCCAGAAACGAAGAAAGGATGGGTGATTGTGTCCTTTGGTGCTACTGCTGCCGGTTTGTTTTGAACAGTAAACGTCTGTTGAGc                                                                                                                                                                                                                      <  1:405053/250‑1 (MQ=255)
     aaTTATTGTGAGCAATACGCACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTGGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGGGATGGTTTCCTGTGGTGCTACTGCTGCCGGTTTGTTTTGAACAGTAAACGTCTGTTGAGCACATcc                                                                                                                                                                                                                <  1:202204/251‑1 (MQ=255)
                                                                  cGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAGCACATcc                                                                                                                                                                                                                >  1:199241/1‑190 (MQ=255)
                                                                     gCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAACAACATTTTATGCGCCGCCACAAATTTTAGCTACATAGACAGTTTTCTTCTGCCCAATTCCAGACACGAAGAAATGATGGGTGCTGGTTTCATTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGTTGTTATTCCCGATGCtt                                                                                                                                                >  1:309125/1‑251 (MQ=255)
                                                                                aCGAATGTTTGCTGGGTTTCTGTTTTAACAACAGTTTCTGCGCCGCCACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAAAGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTATCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCg                                                                                                                                     <  1:440367/251‑1 (MQ=255)
                                                                                 nnnnnnttnNNNNGGTNTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTGGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGCCGGTTTGTTTTGaa                                                                                                                                                                                                                                         <  2:265313/144‑1 (MQ=255)
                                                                                 ctaaTGTTTGCTGGGTTTCTGTTTTAACAACATTTTCTGCACCGCCACCCATTTTGGCCGCATCGAAAGTTTTATTCTGCCCAATTCCAGCAACGAACAACTGATGGGTGATGGATTACTTTGGTGATCCTGCTGCCGGTTTGTTTTGAACAGTAAACGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGAAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCg                                                                                                                                     >  1:424577/3‑250 (MQ=255)
                                                                                 cGAATGTTTGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTGGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGCCGGTTTGTTATGAACAGTAAACGTCTGTTGAGCACATCCTTTAATAAGCATGTCCAGCGCAGTAGCGAGTAGc                                                                                                                                                                              <  1:375991/209‑1 (MQ=255)
                                                                                      gTTTGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCAACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGACCAGCAAATGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGc                                                                                                                                                  >  1:437716/1‑232 (MQ=255)
                                                                                        ttGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGAGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAGCACATCCTGTAATAAGCAGGTCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATc                                                                                                                              <  1:448610/250‑1 (MQ=255)
                                                                                        ttGCTGGGTTTCTGGTTTAACAACATTTTCTGCGCCGCCACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGAGATGGTTTCCTTTGGTGCTACTGCTGTCGGTTTGTTTTGAACAGTAGATGTCTGTTGAGCACATCCTGTAATAAGCAGAGGCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATc                                                                                                                              <  1:448632/250‑1 (MQ=255)
                                                                                             gggTTTCTGTTTTAACACCATTTTCTGCGCCGCCTCAAATTTTGGCTGCATCGACAGTTTTCTTCTTCCCAATTCCAGAATCGAAGAAATGATTGGTGATGGTTTCCTTTGGTGCTACGGCTGCCGGTTTTTTTTGAACAGTAAACGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATATTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTAtn                                                                                                                         <  1:264548/250‑2 (MQ=255)
                                                                                              ggTTTCTGTTTTAACAACATTTTCTGCGCCGCCTCAAATTTTGGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAAGGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGCCGGTTTGTTTTGAACAGTAAACGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTAtgtg                                                                                                                       <  1:352350/251‑1 (MQ=255)
                                                                                                        taaacaacATTTTCTGCGCCGCCACAAATTTTGGCTGCATCGACAGTTTTCGTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGCCGGTTTGTTTTGAACAGTAAACGTc                                                                                                                                                                                                                              <  1:196305/136‑1 (MQ=255)
                                                                                                           acaacaTTTTCTGCGCCGCCACAAATTTTGGCTGCATCGACCGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCATTTGGTGATACTGCTGCCGGTTTGTTTTGAACCGTAAACGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGCGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTaaac                                                                                                          >  1:427006/1‑251 (MQ=255)
                                                                                                                aTTTTCTGCGCCGCCACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGtn                                                                                                                                       <  1:129697/217‑2 (MQ=255)
                                                                                                                          ccgccACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAgn                                                                                                                                                                                                                      <  1:79964/128‑2 (MQ=255)
                                                                                                                            gccACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAACTGATGGGGGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTaaa                                                                                                                                                                                                                                  >  1:195792/1‑114 (MQ=255)
                                                                                                                                         ncTGCATCGACAGTTTTCTTCTGCCCAATTCCAGACACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGCAGGTTTGTTTTGAACAGTAACCGTCTGTTGAGCCCATCCTGTAATAAGCAGGGCCAGCGCGGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAACATTAAACAAACCCTAAACAATGAGTTGAAATTTCat                                                                             >  1:48244/2‑250 (MQ=255)
                                                                                                                                         gCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGCCGGTTTGTTTTg                                                                                                                                                                                                                                           <  1:360982/92‑1 (MQ=255)
                                                                                                                                         gCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGAGTGATGGTTTCCTTTGGTGCTACTGCTGCCGGTTTGTTTTGAACAGTAAACGTCTGTTGATCACATCCTGTAAGAAGCAGGGcc                                                                                                                                                                                                <  1:161603/135‑1 (MQ=255)
                                                                                                                                           tGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGCCGGTTTGTTTTGAACAGTAAACGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGgt                                                                                                                                                                >  1:365798/1‑165 (MQ=255)
                                                                                                                                              aTCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGCTGGTTTCCTTTGGTGCTACTGCTGCCGGTTTGTTTTGAACAGTAAACGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCa                                                                                                                                                                                               >  1:439905/1‑131 (MQ=255)
                                                                                                                                                 gACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGCCGGTTTGTTTTGAACAGTAAACGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTa                                                                                                                                                                                       >  1:444149/1‑136 (MQ=255)
                                                                                                                                                   cAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGAGTTGAAATTTCATATTGTTAatat                                                                  >  1:222004/1‑251 (MQ=255)
                                                                                                                                                               gCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGCCGGTTTGTTTTGAACAGTAAACGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTg                                                                                                                                            >  1:11595/1‑165 (MQ=255)
                                                                                                                                                                       ccAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGCAGGTTTGTTTTGAACAGTAAACGTCTGTTGAGCACATCCTGTAATAAGAAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGAGTTGAAATTTCATATTGTTAATATTTATTAATGTATGTCAGGTg                                              >  1:401738/1‑251 (MQ=255)
                                                                                                                                                                         ngAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGCCGGTTTGTTTTGAACAGTAAACGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGAGTTGAAATTTCATATTGTTAATATTTATTAATGTATGTCAGGTGCg                                            >  1:266372/2‑251 (MQ=255)
                                                                                                                                                                           naaCGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGAGTTGAAATTTCa                                                                              >  1:271109/2‑215 (MQ=255)
                                                                                                                                                                                       gatgGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGGTTTGAACTGTAAATGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCAGTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGAGTTGAAATTTCATATTGTGAATATTTATTAATGTATGCCAGGTGCGATGAATCGTCATTg                              <  1:204364/251‑1 (MQ=255)
                                                                                                                                                                                                         ttGGTGCTACTTCTGCCGGTTTGTTTTGAACAGTAAACGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAATCCCTAAACAATGAGTTGAAATTTCATATTGTTAATATTTATTAATGTATGTCAGGTGCGATGAATCGTCATTGTATTCCCGGATTAACTa             <  1:393388/250‑1 (MQ=255)
                                                                                                                                                                                                               cTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAg                                                                                                                                         <  1:15823/120‑1 (MQ=255)
                                                                                                                                                                                                                    gctgTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGAGTTGAAATTTCATATTGTTAATATTTATTAATGTATGCCAGGTGCGATGAATCGTCATTGTATTCCCGGATTAACTATGTCCACAGcc  <  1:141702/250‑1 (MQ=255)
                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                     
CATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGAGTTGAAATTTCATATTGTTAATATTTATTAATGTATGCCAGGTGCGATGAATCGTCATTGTATTCCCGGATTAACTATGTCCACAGCC  >  NC_000913/578593‑579054

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑