Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,585,0580TC41.3% 71.3 / 10.9 46intergenic (+15/+23)yrhB/ggtstable heat shock chaperone/gamma‑glutamyltranspeptidase
Reads supporting (aligned to +/- strand):  ref base T (25/2);  new base C (0/19);  total (25/21)
Fisher's exact test for biased strand distribution p-value = 5.06e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCGCGCTTAGCTGGTAACGCACCTTTTATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGG‑AAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTGACCTTTT  >  NC_000913/3584908‑3585207
                                                                                                                                                       |                                                                                                                                                     
cgcgcgCTTAGCTGGTAACGCACCTTTTATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGG‑AAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCtt                                                                                                                                                       <  2:18465/151‑1 (MQ=255)
  cgcgcTTAGCTGGTAACGCACCTTTTATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGG‑AAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTcc                                                                                                                                                     >  2:142005/1‑151 (MQ=255)
         aGCTGGTAACGCACCTTTTATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGG‑AAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGa                                                                                                                                                >  2:526647/1‑149 (MQ=255)
                aaCGCACCTTTTATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGG‑AAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCg                                                                                                                                       >  1:339164/1‑151 (MQ=255)
                   gCACCTTTTATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGG‑AAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCt                                                                                                                                     >  2:432080/1‑150 (MQ=255)
                    cACCTTTTATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGG‑AAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTa                                                                                                                                    >  2:98664/1‑150 (MQ=255)
                    cACCTTTTATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGG‑AAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTa                                                                                                                                    >  2:15396/1‑150 (MQ=255)
                          ttattaTTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGG‑AAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCtt                                                                                                                               >  2:102690/1‑149 (MQ=255)
                           tattatTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGG‑AAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAg                                                                                                                             <  1:288183/150‑1 (MQ=255)
                                         aCAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGG‑AAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTaa                                                                                                               >  2:422892/1‑150 (MQ=255)
                                            gtggtgAAATTCATTCTCTGGGAACGGCAAAACCGCTGG‑AAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAatc                                                                                                            >  2:332476/1‑150 (MQ=255)
                                                   aaTTCATTCTCTGGGAACGGCAAAACCGCTGG‑AAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCg                                                                                                    >  1:41856/1‑151 (MQ=255)
                                                               ggaaacgaaaaacCCGCTGG‑AAAAATATCAACAGGATTACAAAAAAAAAAAGGCTCCCTTCGGCTTCCCCTGAAAAAATACCCCTCTCCCCCCGAAGGGGGCGGATACCCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCggg                                                                                            <  1:353314/138‑1 (MQ=255)
                                                                      ggaaaaCCGGCGGAAAGAATATCAACAGAATTAGAAAATAAAAAGGGCTACCTGCGTCTACCCCTAAAAAATAACCCCTTTCCCCAGGAGGAGCGCCCCTAACCTTATTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATgcg                                                                                   <  2:314542/148‑1 (MQ=255)
                                                                             cGCTGG‑AAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAAc                                                                          >  1:38195/1‑151 (MQ=255)
                                                                              gCTGG‑AAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACt                                                                         >  2:10515/1‑151 (MQ=255)
                                                                                  gaaaaataatCTACAGGATTACAAAAAAAAAAAGGCTCCTTTCGGTTTCCCCTAAAAAAATACCCCTCTCCCCAAGAGGGGGGCGGCTACCCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCa                                                                       <  1:518238/142‑1 (MQ=255)
                                                                                    aagaaTATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCAcc                                                                     >  2:208483/1‑150 (MQ=255)
                                                                                    aagaaTATCTACAGGATTACGAAATAAAAAAGGCTACCCTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCg                                                                    >  2:482811/1‑151 (MQ=255)
                                                                                          atCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGc                                                              >  1:390491/1‑151 (MQ=255)
                                                                                           tCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGcc                                                             >  1:358228/1‑151 (MQ=255)
                                                                                              aCAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCa                                                           >  2:65418/1‑150 (MQ=255)
                                                                                                   aTTACGAAAAAAAAAAGGCTCCCTTCGGCTGCCCCTGACAAAATAGCCCTCTCCCCACGAAGAGGCCCGCTACCCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCg                                                                <  2:565083/140‑1 (MQ=255)
                                                                                                      aCGAAAAAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTCCCCACAAAGAGGGCCGCTAACCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATaa                                                    <  1:554917/149‑1 (MQ=255)
                                                                                                         aaaaaaaaaaGGCTCCCTTCGGCTTGCCCTGAAAAAATAGCCCTCTCCCCACGAAGAGGCCCGCTAACCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCtt                                               <  2:639012/151‑1 (MQ=255)
                                                                                                         aaaaaaaaaaGGCTCCCTCCGGCTTGCCCTAAAAAAATACCCCTCTCCCCACAAAGAGGGCCGCTACCCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATg                                                  <  2:430870/148‑1 (MQ=255)
                                                                                                           aaaaaaaaGGCTCCCTTCGGCTTGCCCTGACAAAATCCCCCTCTCCCCACGAAGAGGGCCGCTACCCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTtg                                             <  2:353625/149‑1 (MQ=255)
                                                                                                                aaaGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTAc                                        >  1:506605/1‑151 (MQ=255)
                                                                                                                 aaGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACt                                       >  1:502361/1‑151 (MQ=255)
                                                                                                                 aaGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACt                                       >  2:644038/1‑151 (MQ=255)
                                                                                                                   ggCTCCCTTCGGTTTCCCCTAAAAAAATAGCCCTCTCCCCAGGAAGGGGGCCGCTACCCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTg                                      <  2:263710/150‑1 (MQ=255)
                                                                                                                   ggCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGc                                     >  2:63241/1‑151 (MQ=255)
                                                                                                                   ggCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGc                                     >  2:190166/1‑151 (MQ=255)
                                                                                                                   gcctcccTCCGGTTTCCCCTAACAAAATACCCCCCTCCCCCCGAGGGGGCCCGCTACCCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTg                                      <  1:278940/145‑1 (MQ=255)
                                                                                                                      tACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCAGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGccc                                   >  2:444944/1‑150 (MQ=255)
                                                                                                                       aCCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCAt                                 >  2:162853/1‑151 (MQ=255)
                                                                                                                         ctccgccTTCCCCTCACAAAATCGCCCCCTCCCCTGGATGGGGGCCGTTACCCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCa                                  <  1:141993/142‑1 (MQ=255)
                                                                                                                         cTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCg                               >  2:325662/1‑151 (MQ=255)
                                                                                                                          ttCGGCTTCCCCTAAAAAAATACCCCTCTCCCCACGAAGAGGGCCGCTACCCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATc                                <  2:65395/149‑1 (MQ=255)
                                                                                                                                   cccTGAAAAAATACCCCTCTCCCCACGAAGAGGCCCCCTAACCTTGGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCa                      <  1:566619/150‑1 (MQ=255)
                                                                                                                                   cccTAAAAAAATACCCCTCTCCCCCCGAGGAGGCCCGCTAACCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAg                     <  1:620641/151‑1 (MQ=255)
                                                                                                                                           aaatcccccTCCTCCCCCGAAGAGGGCCGCTACCCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACt              <  1:102682/144‑1 (MQ=255)
                                                                                                                                            aaTACCCCCCTCCCCCCGAAGAGGCCCGCAACCCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACttt            <  2:242779/151‑1 (MQ=255)
                                                                                                                                                 ccccCTCCCCACGAGGGGGGCCGCTACCTTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCt          <  1:651820/148‑1 (MQ=255)
                                                                                                                                                 cccTCTCCCCAGGAGGAGGCCCGCTACCCTTAGCCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCt          <  1:15392/148‑1 (MQ=255)
                                                                                                                                                 cccTCTCCCCACGAGGAGGGCCGCTACCCTTAGCCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTg         <  1:332439/149‑1 (MQ=255)
                                                                                                                                                  ccTCTCCCCACGAAGAGGCCCGCTACCCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTGAcc      <  2:425174/151‑1 (MQ=255)
                                                                                                                                                      ttCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTGACCtttt  >  2:5514/1‑151 (MQ=255)
                                                                                                                                                       |                                                                                                                                                     
CGCGCGCTTAGCTGGTAACGCACCTTTTATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGG‑AAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTGACCTTTT  >  NC_000913/3584908‑3585207

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑