Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913753,1250TA42.5% 53.8 / 26.9 47intergenic (‑330/+60)ybgD/gltAputative fimbrial‑like adhesin protein/citrate synthase
Reads supporting (aligned to +/- strand):  ref base T (22/5);  new base A (0/20);  total (22/25)
Fisher's exact test for biased strand distribution p-value = 9.41e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTT‑AAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTC  >  NC_000913/752976‑753265
                                                                                                                                                      |                                                                                                                                            
cATTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTT‑AAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCatat                                                                                                                                              <  1:1175197/150‑1 (MQ=255)
 aTTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTT‑AAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATaa                                                                                                                                            <  1:302920/151‑1 (MQ=255)
   tttCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTT‑AAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATaaa                                                                                                                                           >  2:1181023/1‑150 (MQ=255)
   tttCATAAGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTT‑AAATATATATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCatat                                                                                                                                              >  2:176615/1‑147 (MQ=255)
           ggTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTT‑AAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAAcc                                                                                                                                   >  2:647540/1‑150 (MQ=255)
                  aaTGCGACTACCATGAATTTTTTAATTGAAAGTTTTGGTTTGCTGATAATTTGAGCTGTTCTTTTTTTTTT‑AAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCatat                                                                                                                           <  2:156863/151‑1 (MQ=255)
                              aTGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTT‑AAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGtt                                                                                                               >  2:976956/1‑151 (MQ=255)
                                    tttttAATTAAAAGTTTGGGGTTGCTGAAATTTTGGGTTTTTTTTTTTTTTTT‑AAATATTTATATGGTTTTTTTAATGATTTTTATTTTTAAAATTTTTGGTTTTTGGGAAAAAAAAAACCACCCCGCCATATGAACGGCGGGTTa                                                                                                              <  2:131006/146‑1 (MQ=255)
                                         aataaaaatttttGGTTTTCTGATATTTTGGGTTTTTCTTTTTTTTTT‑AAATATATATATAGTTTTTTAAATGGTTTTTATTTTTTCAATTTTTTGTTTTTAGGCATAAAAAAATAACCCCGCCATATGAACGGCGGGTTAAAATATTTAc                                                                                                    <  2:130693/140‑1 (MQ=255)
                                         aaTTAAAATTATGGGGTTGTTAATAATTTGGTCTTTTTTTTTTTTTTT‑AAATATAAATAGAGTTTTGTTATGGTTTTTTATTTTAAAAATTTTGTGTTTTAAGCTATAAAAAAAACACCCCGCCATATGAACGGCGGGTTAAAATATTTa                                                                                                     <  2:466012/150‑1 (MQ=255)
                                          aTTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTT‑AAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTAc                                                                                                    >  2:1129541/1‑150 (MQ=255)
                                           ttGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTT‑AAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACa                                                                                                   >  1:782055/1‑150 (MQ=255)
                                              aaatttttGGGTTGCTTATAATTTGAG‑TGTTTTTTTTTTTTTAAAATATTTATATAGTTCGTTAAAGGGATTTTATTTTAACATTTTTTGGTATTAAGTCATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACt                                                                                                <  2:975062/144‑1 (MQ=255)
                                              aaaGTATTGGTTTGCTAATATTTTGATCTTTTTTTTTTTTTTT‑AAATATATATATATTTCTTTAAATGGTTTTTTTTTTTACAATTTTTGGTTTTTAGGCAAAAAAAAAACAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACtt                                                                                               <  2:185869/151‑1 (MQ=255)
                                                  ttttGGTTTGTTTATATTTTGATCTTTTTTTTTTTTTTT‑AAATATTTATATAGTTTTTTAATTGTATTTTTTTTTTAAATTTTTTTTTTTTTAGAAAAAAAAAAACCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGc                                                                                            <  2:346958/148‑1 (MQ=255)
                                                   aTTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTT‑AAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTTAAATAATTACAATTTATCa                                                                                           >  1:64411/1‑150 (MQ=255)
                                                      ggtttGGTGATATTTTGAGTTTTTCTTTTTTTTTA‑AAATTTCTATATGGTTTTTTAAAGGGTTTTTTTTTTTCCATTTTTTTGTTTTTAGACATATAAAAATCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATc                                                                                        <  2:1187814/147‑1 (MQ=255)
                                                          ttcTGAAAGTTTGAGCTGTTCTATTCTTTTT‑AAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGCGTTTAGGCATATAAAAATCAATCCGCCATATGAACGGCGGTTTTTAATATTTATAACttcgtacttca                                                                                      >  2:506053/3‑139 (MQ=255)
                                                          tGCTGATAATTTGAGCTGTTCTATTCTTTTT‑AAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTTAAATATTTACAACTTAGCAATCAAcc                                                                                    >  2:1183975/1‑150 (MQ=255)
                                                                tAATTTGAGCTGTTCTATTCTTTTT‑AATTATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTTCAACTTAGCAATCAACCATTaa                                                                               >  1:1021057/1‑149 (MQ=255)
                                                                   tttGAGTTTTTTTATTCTTTTA‑AAATATCTATATGGGTTTTTTAATGGTTTTTATTTTTACAATTTTTTGTTTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAAc                                                                              <  1:931607/147‑1 (MQ=255)
                                                                   tttGAGCTGTTCTTTTCTTTTA‑AAATATCTATATAGTTCTGTAAATGTTTTTTTTTTTTACATTTTTTTGTGTTTAGGAATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTa                                                                                <  1:647571/145‑1 (MQ=255)
                                                                      gAGCTGTTCTATTCTTTTT‑AAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTTAAATATTTACAACTTAGCAATCAAACATTAACGCTTg                                                                         >  2:359322/1‑149 (MQ=255)
                                                                       aGCTGTTCTATTCTTTTT‑AAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTATCAATCAACCATTAACGCTTGa                                                                        >  2:23453/1‑149 (MQ=255)
                                                                          tGTTTTTTTTTTTTT‑AAATATTTATATGGGTTTGTTAATGTTTTTTTTTTTAACATTTTTTTGTGTTTAGCAAAAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGata                                                                      <  2:640611/148‑1 (MQ=255)
                                                                          tGTTCTATTCTTTTT‑AAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGGTTAAATATTTTCAACTTAGCAATCAACCATTAAAGCTTGatat                                                                     >  1:928372/1‑149 (MQ=255)
                                                                               tttttttttt‑AAATATTTATATAGGTTTTTTAATGTTTTTTTTTTTAAAATTTTTTTGTTTTTAGAAATAAAAAAAACAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCtt                                                                <  2:350863/144‑1 (MQ=255)
                                                                                 ttttttta‑AAATTTTTATATAGTTTTTTAAATGTTTTTTTTTTTTAAATTTTTTTGTTTTAAGAAATAAAAAAATCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCtttt                                                              <  2:863775/146‑1 (MQ=255)
                                                                                 ttCTTTTT‑AAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCtttt                                                              >  1:543006/1‑149 (MQ=255)
                                                                                 ttCTTTTT‑AAATATCTATATAGGTCTGTAAATGGTTTTTATTTTTACAATTTTTTGTGTTTAGGCATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCtttt                                                              <  1:1069910/149‑1 (MQ=255)
                                                                                     tttt‑AAATATTTATATAGGTTTTTTAATGGTTTTTTTTTTAACAATTTTTTGTGTTTAGGAATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTaaa                                                           <  1:886295/148‑1 (MQ=255)
                                                                                          aaaTATATATAAAGTTCTGTTAATGTATTTTATTTTTACATTTTTTTTTTTTAAGCTATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGt                                                    <  1:917740/151‑1 (MQ=255)
                                                                                              atCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTTAAATATTTACAAATTATCAAACAACCATTAACCCTTGATAACGCTTTTTAAGCCGCGttttt                                                >  2:284949/1‑151 (MQ=255)
                                                                                                             ttAATGAATTTTTTTTTTACATTTTTTTTTTTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGta                                     <  2:1127761/147‑1 (MQ=255)
                                                                                                               attGGTTTTTTTTTTTACATTTTTTTGTTTTTGGGAATAAAAAAACCAAGCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACa                                 <  1:1181099/147‑1 (MQ=255)
                                                                                                               aaggatttttttttttACATTTTTTTGTTTTTAGCCATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAg                                <  2:865855/144‑1 (MQ=255)
                                                                                                               aaTGGTTTTTATTTTTAAATTTTTTTGTTTTTAGGAATAAAAAAATCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACa                                 <  1:141883/149‑1 (MQ=255)
                                                                                                                aTGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGc                               >  1:141769/1‑150 (MQ=255)
                                                                                                                  ggATTTTTTTTTTCCATTTTTTTGTGTTTAGGCATAAAAAAACCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTg                             <  1:478055/150‑1 (MQ=255)
                                                                                                                  ggATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTTAAATATTTACAAAATAACAATCAACCATTAAAGCTTGATATCGCTTTTAAAGTCGCGGTTTTTATATCCTGTATACAGCTg                             >  2:818194/1‑150 (MQ=255)
                                                                                                                    attttattttTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTTTAAATTAGCAATCAACCATTAAACGTTGATATCGCTTTTAAAATCGCGCTTTTTATATCCTGTATAAACCTGa                            >  2:743091/1‑149 (MQ=255)
                                                                                                                     ttttattttTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTAAAACTTAGCAAACAAACATTAACGCTTGATATCGCTTTTTAAGTCGCGTTTTTCATATCCTGTATACAGCTGAcgc                         >  2:660130/1‑151 (MQ=255)
                                                                                                                       ttattttTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTTAAATATTTACAACTTAGCAATCAACCATTAAAGCTTGATATCGCTTTTAAAATCGCGTTTTTTATATCCTGTATACAGCTGACGCgg                       >  2:1069462/1‑151 (MQ=255)
                                                                                                                          tttttACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACg                    >  1:25618/1‑151 (MQ=255)
                                                                                                                             ttACAATTTTTTGTTTTTAGGCATAAAAAAACCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACgg                   <  1:870048/149‑1 (MQ=255)
                                                                                                                              tACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATTGCTTTTAAAGACGCGTTTTTTATATCCTGTATACAGCTGACGCgggcgggc                 >  2:895653/1‑150 (MQ=255)
                                                                                                                                      tttGTGTTTAGGAATAAAAAAATCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCa         <  1:833432/150‑1 (MQ=255)
                                                                                                                                      tttGTGATTAGGCATATAAAAATCAACCCGCCATATGACCGGCGGGTTAAAATATTTAAAACTTAGCAATCAACCATTAAAGCCTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCAGCATACATCCGGCGCGGGCGGTGAATCTTCAt        >  2:837221/1‑151 (MQ=255)
                                                                                                                                             ttAGGAATAAAAAAACCATCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTc  <  1:806077/150‑1 (MQ=255)
                                                                                                                                                      |                                                                                                                                            
CATTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTT‑AAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTC  >  NC_000913/752976‑753265

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑