Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913753,1250TA47.8% 39.8 / 29.7 46intergenic (‑330/+60)ybgD/gltAputative fimbrial‑like adhesin protein/citrate synthase
Reads supporting (aligned to +/- strand):  ref base T (17/7);  new base A (0/22);  total (17/29)
Fisher's exact test for biased strand distribution p-value = 2.13e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACT  >  NC_000913/752976‑753268
                                                                                                                                                     |                                                                                                                                               
cATTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCatat                                                                                                                                                 >  2:768689/1‑150 (MQ=255)
     tCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATaaaaa                                                                                                                                            <  2:662260/150‑1 (MQ=255)
     tCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAAt                                                                                                                                           >  1:222282/1‑151 (MQ=255)
      cATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATc                                                                                                                                          >  1:46964/1‑151 (MQ=255)
       aTAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCTTATAAAAATCa                                                                                                                                         <  2:711215/151‑1 (MQ=255)
            gTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCg                                                                                                                                    <  1:794977/151‑1 (MQ=255)
             ttATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGc                                                                                                                                   >  1:680323/1‑151 (MQ=255)
               ataAATGCGACTACCATGAAGTTTTTAATTGCAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGGTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGcc                                                                                                                                  >  2:853467/1‑150 (MQ=255)
                  aaTGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCatat                                                                                                                              >  1:82453/1‑151 (MQ=255)
                                  aGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTaaa                                                                                                               >  1:402626/1‑150 (MQ=255)
                                  aGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTaaa                                                                                                               >  1:66996/1‑150 (MQ=255)
                                    tttttAATTAAATGTTTTGGTTTGTTTATAATTTGAGATTTTGTATTCTTTTTAAATTTCTATAGGGGTTTTTAAATGGATTTTTTTTTAAAAATTTTTTGTGTTTAGCAATAAAAAAAACACCCCGCCATATGAACGGCGGGTTaa                                                                                                                <  2:521846/147‑1 (MQ=255)
                                    ttttaAATTAAAATTATGGGGTGGCTGATATTTTGAGCTTTTTTTTTTTTTTAAAATATTTTTACAGATTTTTTAATGTATTTTTTTTTTACATTTTTTGTTTTTTAGGAAAATAAAATCCACCCCGCCATATGAACGGCGGGTTaaaa                                                                                                              <  2:594147/149‑1 (MQ=255)
                                         aaTTAAAAGTATGGGGTTGCTAATAATTTGAGCTTTTTTTTTTTTTTAAAATATATATAAAGGTTTGTTAATGGATTTTATTTTAAAAATTTTTTGTTTTAAGGCATAAAAAAAACAACCCGCCATATGAACGGCGGGTTAAAATAttt                                                                                                         <  2:154785/149‑1 (MQ=255)
                                               aaGTATTGGGTTTCTGATATTTTGAGCTTTTCTTTTTTTTTAAAATATCTATATAGTTCTTTAAATGGATTTTATTTTTAAAATTTTTTGTTTTTAGGTAAAAAAAAACCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTa                                                                                                 <  2:121376/151‑1 (MQ=255)
                                                    ttGGTTTGCTGATATTTTGACTTTTTTTTTTTTTTTTAAATTTCTATATAGTTCTTTTAATGATTTTTTTTTTTACATTTTTTTGTTTTTAGGAATAAAAAAACCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCa                                                                                              <  1:497563/149‑1 (MQ=255)
                                                    ttGGGTTGCTGATAATTTGAGTTGTTTTATTTTTTTAAAATATTTATATAGGTGTTTTATTGGATTTTTTTTTTACAATTTTTTGTTTTTAGGCATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCaa                                                                                             <  1:469867/150‑1 (MQ=255)
                                                     tGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCaa                                                                                             >  2:563238/1‑149 (MQ=255)
                                                      ggtttGCTGATAATTGGGGCTTTTCTATTTTTTTTAAATATCTATATAGTTTTGTTAATGGTTTTTATTTTTAAATTTTTTTGTTTTTAGGCTTAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATc                                                                                           <  2:173087/147‑1 (MQ=255)
                                                            cTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTTAAATATTTTCAAATTAGCCATCAACCAtt                                                                                    >  2:337754/1‑151 (MQ=255)
                                                               aTAATTTGGGCTGTTTTATTTTTTTTAAATATATATATAGTTCTGTTATGGGATTTTTTTTTTAATATTTTTTGTGTTTAGGAAAAAAAAAACAACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCAtt                                                                                    <  1:580926/148‑1 (MQ=255)
                                                                   ttggAGCTGTTTTTTTCTTTTAAAATATATAAATGGTTTTGTAATTGGATTTTTTTTTTAAATTTTTTTTTGTTAAGGCTGAAAAAAACCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAAc                                                                                 <  2:292011/144‑1 (MQ=255)
                                                                           gTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTTAAATATTTACAACTTAGCAATCAACCATTAAAGCTTGATATCGc                                                                     >  2:844481/1‑151 (MQ=255)
                                                                                aTTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTTAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCtttt                                                                 >  2:402496/1‑150 (MQ=255)
                                                                                  tCTTTTTAAATTTCTTTATAGTTCTGTAAATGGATTTAATTTTAACAATTTTTTGTGTTAAGGCTTAAAAAAAACAAGCCGCCATATGAACGTCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCt                                                                    <  2:585552/145‑1 (MQ=255)
                                                                                         aaaTATTTATATAGGTCTTTAAATGAATTTTATTTTTAAAATTTTTTGTTTTTAGCCATAAAAAAACCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGt                                                       <  2:93909/151‑1 (MQ=255)
                                                                                         aaaTATCTATATAGGTCTTTTAAGGGTTTTTATTTTTACAATTTTTTTTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTcgcg                                                        <  1:686056/150‑1 (MQ=255)
                                                                                         aaaTATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATTGCTTTTTAAGTCGCGt                                                       >  1:108219/1‑151 (MQ=255)
                                                                                          aaTATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTATCAATAAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGtt                                                      >  2:52074/1‑151 (MQ=255)
                                                                                                 atataGGTTTTTTAATGGTTTTTTTTTTTAAAATTTTTTGTTTTTAGGAATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCa                                                 <  1:256628/149‑1 (MQ=255)
                                                                                                 atataGGTCTTTAAATGGATTTTATTTTTACATTTTTTTGTGTTTAGGAATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGttttt                                                   <  1:768749/147‑1 (MQ=255)
                                                                                                   ataGGTCTTTAAATGTTTTTTTTTTTTAAAATTTTTTGTGTTTAGGAATAAAAAAATAAACCCGCCATATGAACGGCGGGTTAAGATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCat                                                <  1:418219/148‑1 (MQ=255)
                                                                                                    taGGTCTGTAAATGTTTTTTATTTTTACATTTTTTTTTGTTTGGACATAAAAAAAACACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCata                                               <  2:619236/148‑1 (MQ=255)
                                                                                                      ggtttttaaaTGGATTTTATTTTTACAATTTTTTGTTTTTAGGCATATAAAAACCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTg                                          <  2:273772/143‑1 (MQ=255)
                                                                                                        ttttttAATGGTTTTTTTTTTTACATTTTTTTGTGTTTGGGAATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGt                                         <  1:347213/146‑1 (MQ=255)
                                                                                                          tGTTAATGTATTTTTTTTTTAAAATTTTTTGTTTTGAGGAATAAAAAAATAAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGtat                                       <  1:16134/150‑1 (MQ=255)
                                                                                                          tGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGtat                                       <  1:290909/150‑1 (MQ=255)
                                                                                                            ttAATGGATTTTTTTTTTACAATTTTTTTTGTTTAGGAAAAAAAAAATCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGtata                                      <  1:85052/149‑1 (MQ=255)
                                                                                                            ttAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTTAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATTGGTTTTAAAAACGCGTTTTTTATATCCTGTATAc                                     >  2:99982/1‑150 (MQ=255)
                                                                                                              aaTGGATTTTTTTTTTACATTTTTTTGTGTTTAGGCATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACa                                    <  1:624401/149‑1 (MQ=255)
                                                                                                              aaTGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATTTTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATAAAGc                                  >  2:805120/1‑151 (MQ=255)
                                                                                                                    tttttttttAAAATTTTTTTGTTTTTAGACATAAAAAAATCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGAc                              <  2:144574/149‑1 (MQ=255)
                                                                                                                     tttattttTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGAcgcg                           >  1:520443/1‑151 (MQ=255)
                                                                                                                         tttttAAATTTTTTTGTTTTTAGGAAAAAAAAAATCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTTATATCCTGTATACAGCTGACGCGGa                         <  1:167424/149‑1 (MQ=255)
                                                                                                                                     tttGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTTAAGTCGCGTTTTTTATATCCTTTATACAGCTGACGCGGACGGGCAATCTTCAt           >  2:32172/1‑151 (MQ=255)
                                                                                                                                           tttAGGAATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATAc         <  1:714097/147‑1 (MQ=255)
                                                                                                                                               ggCATAAAAAAACAAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACt  <  2:879875/150‑1 (MQ=255)
                                                                                                                                                     |                                                                                                                                               
CATTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACT  >  NC_000913/752976‑753268

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑