Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,498,2230AT20.7% 59.9 / 11.5 29intergenic (+283/‑49)intB/insC1pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase/IS2 repressor TnpA
Reads supporting (aligned to +/- strand):  ref base A (11/12);  new base T (3/3);  total (14/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TTATATACATTCAATAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAA  >  NC_000913/4498076‑4498322
                                                                                                                                                   |                                                                                                   
ttatATACATTCAATAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTaaa                                                                                                     >  6:75602/1‑148 (MQ=255)
   tataCATTCAATAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAg                                                                                                 <  6:165560/149‑1 (MQ=255)
      aCATTCAATAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCACGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTATTTAAGTGa                                                                                              >  3:55747/1‑149 (MQ=255)
       cATTCAATAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGa                                                                                              >  1:162694/1‑148 (MQ=255)
            aaTAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTATTTAAGTGATatt                                                                                          <  8:67561/147‑3 (MQ=255)
            aaTAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTATTTAAGTGATatt                                                                                          >  7:67561/1‑145 (MQ=255)
            aaTAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCt                                                                                        >  1:50792/1‑149 (MQ=255)
              tAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCtt                                                                                       >  6:97840/1‑148 (MQ=255)
                aaaaaGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTTCTGCATGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAAt                                                                                    <  7:157705/149‑1 (MQ=255)
                        aCCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGtt                                                                             <  3:47803/148‑1 (MQ=255)
                          cTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGtttt                                                                           >  4:148899/1‑148 (MQ=255)
                             aTAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACACCCAATATAACGTAAATAAGTTATAGTCTTAATACTAGTTTTTata                                                                       >  7:114878/1‑147 (MQ=255)
                              tAAAAAATCCTTTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGt                                                                              >  4:85523/1‑141 (MQ=255)
                              tAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGt                                                                              <  3:85523/141‑1 (MQ=255)
                                         gTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTg                                                             >  7:48059/1‑147 (MQ=255)
                                            cTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGaa                                                        <  2:162694/149‑1 (MQ=255)
                                             tCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTATTTAAGTGATatt                                                                                          <  3:121378/114‑3 (MQ=255)
                                             tCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTATTTAAGTGATatt                                                                                          >  4:121378/1‑112 (MQ=255)
                                                        tGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGAtgattgat                                            <  2:50792/149‑1 (MQ=255)
                                                              aTAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTa                                      <  8:48059/149‑1 (MQ=255)
                                                                  cTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGc                                  <  5:75602/149‑1 (MQ=255)
                                                                       gTAAGGAGTTCTTCATGGATTTTATGGTCCCTTTTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTATTTAAGTGATat                                                                                           <  3:148645/87‑2 (MQ=17)
                                                                          aGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGaaa                          <  3:148899/149‑1 (MQ=255)
                                                                                   gcAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACgg                 >  7:24530/1‑149 (MQ=255)
                                                                                               tGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTATTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGTCCGGAGAAACGCAGACGGCGTACcacaca      <  8:114878/148‑1 (MQ=255)
                                                                                                  tCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAg                                                                   <  5:158629/84‑1 (MQ=39)
                                                                                                  tCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAg                                                                   >  6:158629/1‑84 (MQ=39)
                                                                                                    ccTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGga                              <  3:138196/119‑1 (MQ=34)
                                                                                                    ccTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGga                              >  4:138196/1‑119 (MQ=34)
                                                                                                    ccTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGaa  >  3:63910/1‑147 (MQ=33)
                                                                                                                                                   |                                                                                                   
TTATATACATTCAATAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAA  >  NC_000913/4498076‑4498322

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑