Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913566,2770CT47.3% 9.9 / 72.5 55pseudogene (100/279 nt)exoDpseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
Reads supporting (aligned to +/- strand):  ref base C (12/17);  new base T (10/16);  total (22/33)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.59e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTA  >  NC_000913/566146‑566404
                                                                                                                                   |                                                                                                                               
gTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTcgc                                                                                                                          <  1:463087/139‑1 (MQ=255)
       ttttCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCAccc                                                                                                                   <  1:606330/139‑1 (MQ=255)
       ttttCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCAccc                                                                                                                   <  1:541172/139‑1 (MQ=255)
       ttttCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCAccc                                                                                                                   <  1:449329/139‑1 (MQ=255)
        tttCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCca                                                                                                                  <  1:572906/139‑1 (MQ=255)
          tCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTAATTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCcaca                                                                                                                >  1:380294/1‑139 (MQ=255)
            gATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATg                                                                                                              <  1:106441/139‑1 (MQ=255)
             aTGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGc                                                                                                             <  2:168639/139‑1 (MQ=255)
                   tCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACt                                                                                                       <  1:102670/139‑1 (MQ=255)
                      ggCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATg                                                                                                              <  1:283850/129‑1 (MQ=255)
                      ggCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATg                                                                                                              >  2:283850/1‑129 (MQ=255)
                       gCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCAc                                                                                                   <  2:569077/139‑1 (MQ=255)
                           gaTCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTgg                                                                                               <  2:599116/138‑1 (MQ=255)
                            aTCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTggg                                                                                              <  2:440968/139‑1 (MQ=255)
                             tctcGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTAGTGCACCTGGGc                                                                                             >  2:403099/1‑139 (MQ=255)
                                         tCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCAcc                                                                                                  >  2:236559/1‑122 (MQ=255)
                                         tCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCAcc                                                                                                  <  1:236559/122‑1 (MQ=255)
                                                             cGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAaccac                                                             <  1:172559/139‑1 (MQ=255)
                                                              gCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAaccacc                                                            >  2:319550/1‑139 (MQ=255)
                                                                             aaTGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCAt                                             <  1:319550/139‑1 (MQ=255)
                                                                              aTGCAGGCCTTCACGCTTCATGCTCGGGTCATAGTTGGCAAAGTACCAGGCATCGTTTCGCGTCACCCACATGCTGTACTGCACTTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATg                                            <  1:405803/139‑1 (MQ=255)
                                                                              aTGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATg                                            <  1:403099/139‑1 (MQ=255)
                                                                                    gCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTAc                                                                                                        >  2:411285/1‑73 (MQ=255)
                                                                                    gCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATcc                                      >  2:123855/1‑139 (MQ=255)
                                                                                    gCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTAACCCACATGCTGTAc                                                                                                        <  1:411285/73‑1 (MQ=255)
                                                                                    gCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCcaca                                                                                                                <  1:197319/65‑1 (MQ=255)
                                                                                    gCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCcaca                                                                                                                >  2:197319/1‑65 (MQ=255)
                                                                                    gCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATcc                                      >  1:602893/1‑139 (MQ=255)
                                                                                         cACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGc                                                                                    <  1:25710/88‑1 (MQ=255)
                                                                                         cACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGc                                                                                    >  2:25710/1‑88 (MQ=255)
                                                                                         cACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCg                                    <  1:586007/136‑1 (MQ=255)
                                                                                         cACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCg                                    >  2:586007/1‑136 (MQ=255)
                                                                                         cACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGa                                 <  2:510578/139‑1 (MQ=255)
                                                                                         cACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTcg                                                                                                                           <  2:205668/49‑1 (MQ=255)
                                                                                         cACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTcg                                                                                                                           >  1:205668/1‑49 (MQ=255)
                                                                                         cACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTAtg                                                                          <  1:424024/98‑2 (MQ=255)
                                                                                         cACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTAtg                                                                          >  2:424024/1‑97 (MQ=255)
                                                                                            gCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGt                              <  1:323315/139‑1 (MQ=255)
                                                                                              ttCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCt                                                                                                            >  1:539987/1‑59 (MQ=255)
                                                                                              ttCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCt                                                                                                            <  2:539987/59‑1 (MQ=255)
                                                                                                cATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGa                          <  2:24501/139‑1 (MQ=255)
                                                                                                        ggTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATCCCGGGAGGTaaacgggcattt                  >  1:546699/1‑128 (MQ=255)
                                                                                                        ggTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATCCCGGGAGGTaaacgggcattt                  <  2:546699/139‑12 (MQ=255)
                                                                                                        ggTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCAccc                                                                                                                   >  2:150936/1‑42 (MQ=255)
                                                                                                        ggTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCAccc                                                                                                                   <  1:150936/42‑1 (MQ=255)
                                                                                                        ggTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCg                                                      >  2:596648/1‑103 (MQ=255)
                                                                                                        ggTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCg                                                      <  1:596648/103‑1 (MQ=255)
                                                                                                        ggTCATAGTTGGCAAAGAACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGcc                  >  2:385811/1‑139 (MQ=255)
                                                                                                                   gCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTAc                                                                                                        <  1:599322/42‑1 (MQ=255)
                                                                                                                   gCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTAc                                                                                                        >  2:599322/1‑42 (MQ=255)
                                                                                                                   gCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCg                                                                    >  2:515493/1‑78 (MQ=255)
                                                                                                                   gCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCg                                                                    <  1:515493/78‑1 (MQ=255)
                                                                                                                   gCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGc       >  2:438608/1‑139 (MQ=255)
                                                                                                                        gTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGACGCGTGGCCTGTa  <  1:123855/139‑1 (MQ=255)
                                                                                                                        gTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTa  >  2:230771/1‑139 (MQ=255)
                                                                                                                                   |                                                                                                                               
GTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTA  >  NC_000913/566146‑566404

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑