Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,323,313 G→C 14.2% intergenic (‑83/+23) phnE ← / ← phnD defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily/phosphonate ABC transporter periplasmic binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,323,3130GC14.2% 171.7 / 16.9 56intergenic (‑83/+23)phnE/phnDdefective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily/phosphonate ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base G (24/24);  new base C (5/3);  total (29/27)
Fisher's exact test for biased strand distribution p-value = 7.07e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGTGGGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCAGGTCATCCAGCTGCGCCTGAATCTCGGTGGTTTTTGCCAGCTTGTCCTGCTCATTCAGTCCTTTAT  >  NC_000913/4323169‑4323460
                                                                                                                                                |                                                                                                                                                   
aCGGCCCAGCTCAGTAGCGAGAAGCAGCTCCGCTCGGGTGGGGCGATGGTGATGGTTTGCATGTTTGACTCCGTTCTGTAGGCCTGATGAGGTGCTTGCACCGCATCCGGCGTCAACGACTCGACATTGTCGGATGCGACGCCGGGGc                                                                                                                                                  >  4:706285/1‑148 (MQ=255)
      cAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGTGGGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGt                                                                                                                                                >  1:896050/1‑144 (MQ=255)
      cAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGTGGGGCGATGGTGATAGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGt                                                                                                                                                <  2:896050/144‑1 (MQ=255)
                          gCTGCGCTTGGGTGGGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCgggg                                                                                                                                                   <  2:528033/121‑1 (MQ=255)
                          gCTGCGCTTGGGTGGGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCgggg                                                                                                                                                   >  1:528033/1‑121 (MQ=255)
                           cTGCGCTTTGGTGGGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACTGCATCCGGCATCAACGCTTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCa                                                                                                                       <  3:706285/148‑1 (MQ=255)
                                         ggCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCTGGCATCAACGCCTGCACATTGTCGGATGAGACGCCCCGGCGt                                                                                                                                                <  4:752150/109‑1 (MQ=255)
                                         ggCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGAGACGCCCCGGCGt                                                                                                                                                >  3:752150/1‑109 (MQ=255)
                                                  gatggtTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCg                                                                                                                                        <  1:386085/108‑1 (MQ=255)
                                                  gatggtTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCg                                                                                                                                        >  2:386085/1‑108 (MQ=255)
                                                     ggtTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCgg                                                                                                                                                     >  4:26450/1‑92 (MQ=255)
                                                     ggtTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCgg                                                                                                                                                     <  3:26450/92‑1 (MQ=255)
                                                         tGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGt                                                                                                                                                <  4:666038/93‑1 (MQ=255)
                                                         tGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGt                                                                                                                                                >  3:666038/1‑93 (MQ=255)
                                                           cATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCAt                                                                                                 >  2:505503/1‑138 (MQ=255)
                                                           cATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCAt                                                                                                 <  1:505503/138‑1 (MQ=255)
                                                             tGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCt                                                                                                                  >  2:303835/1‑119 (MQ=255)
                                                             tGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCt                                                                                                                  <  1:303835/119‑1 (MQ=255)
                                                                      ccGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCg                                                                                                                                                 >  1:163349/1‑79 (MQ=255)
                                                                      ccGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCg                                                                                                                                                 <  2:163349/79‑1 (MQ=255)
                                                                          tCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACt                                                                                                             <  2:854090/111‑1 (MQ=255)
                                                                          tCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACt                                                                                                             >  1:854090/1‑111 (MQ=255)
                                                                           cTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCAt                                                                                                 <  1:121578/122‑1 (MQ=255)
                                                                           cTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCAt                                                                                                 >  2:121578/1‑122 (MQ=255)
                                                                                  ccGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCAt                                                                                                 <  3:1081765/115‑1 (MQ=255)
                                                                                  ccGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCAt                                                                                                 >  4:1081765/1‑115 (MQ=255)
                                                                                       tAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAAc                                                                                                     <  4:20898/106‑1 (MQ=255)
                                                                                       tAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAAc                                                                                                     >  3:20898/1‑106 (MQ=255)
                                                                                           gTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTc                                                                      >  2:666582/1‑133 (MQ=255)
                                                                                           gTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTc                                                                      <  1:666582/133‑1 (MQ=255)
                                                                                            tGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTc                                                                              >  3:47074/1‑124 (MQ=255)
                                                                                            tGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTc                                                                              <  4:47074/124‑1 (MQ=255)
                                                                                                tGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCgttg                                                                                 >  1:412095/1‑117 (MQ=255)
                                                                                                tGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCgttg                                                                                 <  2:412095/117‑1 (MQ=255)
                                                                                                    ccGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGa                                                                                                       <  2:109667/91‑1 (MQ=255)
                                                                                                    ccGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACCATTTACTGCACCGCTTTACTCACCGa                                                                                                       >  1:109667/1‑91 (MQ=255)
                                                                                                                    cGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATc                                                                                                <  2:852958/82‑1 (MQ=255)
                                                                                                                    cGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATc                                                                                                >  1:852958/1‑82 (MQ=255)
                                                                                                                        tGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCgt                                                                                   <  2:389578/91‑1 (MQ=255)
                                                                                                                        tGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCgt                                                                                   >  1:389578/1‑91 (MQ=255)
                                                                                                                               tGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCa                                                                    <  2:356801/99‑1 (MQ=255)
                                                                                                                               tGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCa                                                                    >  1:356801/1‑99 (MQ=255)
                                                                                                                                   ggATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCgt                                                                                   >  1:570333/1‑80 (MQ=255)
                                                                                                                                   ggATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCgt                                                                                   <  2:570333/80‑1 (MQ=255)
                                                                                                                                    gataagACGCCCCGGCGTCGCATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCAGGTCATCCAGCTGCGCCTGAAtctc                                           <  2:508179/114‑1 (MQ=255)
                                                                                                                                    gataagACGCCCCGGCGTCGCATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCAGGTCATCCAGCTGCGCCTGAAtctc                                           >  1:508179/6‑119 (MQ=255)
                                                                                                                                      taagACGCCCCGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCAGGTCATCCAGCTGCGCCTGAATCTCGGTGGTTTTTGCCAGCTTGTc                      >  1:328923/4‑138 (MQ=255)
                                                                                                                                      taagACGCCCCGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCAGGTCATCCAGCTGCGCCTGAATCTCGGTGGTTTTTGCCAGCTTGTc                      >  3:1138531/4‑138 (MQ=255)
                                                                                                                                      taagACGCCCCGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCAGGTCATCCAGCTGCGCCTGAATCTCGGTGGTTTTTGCCAGCTTGTc                      <  4:1138531/135‑1 (MQ=255)
                                                                                                                                      taagACGCCCCGGCGTCGCATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCAGGTCATCCAGCTGCGCCTGAATCTCGGTGGTTTTTGCCAGCTTGTCCTGCTCATTc            >  1:510982/4‑148 (MQ=255)
                                                                                                                                        cGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCAGGTCATc                                                             >  3:204776/1‑97 (MQ=255)
                                                                                                                                        cGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCAGGTCATc                                                             <  4:204776/97‑1 (MQ=255)
                                                                                                                                          aCGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCAGGTCa                                                               <  2:447676/93‑1 (MQ=255)
                                                                                                                                          aCGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCAGGTCa                                                               >  1:447676/1‑93 (MQ=255)
                                                                                                                                          aCGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCAGGTCATCCAGCTGCGCCTGAATCTCgg                                         >  1:1009401/1‑115 (MQ=255)
                                                                                                                                          aCGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCAGGTCATCCAGCTGCGCCTGAATCTCgg                                         <  2:1009401/115‑1 (MQ=255)
                                                                                                                                          aCGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCAGGTCATCCAGCTGCGCCTGAATCTCGGTGGTTTTTGcc                              <  3:479580/126‑1 (MQ=255)
                                                                                                                                          aCGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCAGGTCATCCAGCTGCGCCTGAATCTCGGTGGTTTTTGcc                              >  4:479580/1‑126 (MQ=255)
                                                                                                                                             ccGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCAGGTCATCCAGCTGCGCCTGAATCTCGGTGGTTTTTGCCAGCTTGTCCTGCTCATTCAGTCCtt     >  4:159189/1‑148 (MQ=255)
                                                                                                                                              cGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCAGGTCATCCAGCTGCGCCTGAATCTCGGTGGTTTTTGCCAGCTTGTCCTGCTCATTCAGTCCttt    <  3:159189/148‑1 (MQ=255)
                                                                                                                                                gggCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCAGGTCATCCAGCTGCGCCTGAATCTCGGTGGTTTTTGCCAGCTTGTCCTGCTCATTCAGTCCTTTAt  >  2:613797/1‑148 (MQ=255)
                                                                                                                                                |                                                                                                                                                   
ACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGTGGGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTACGATTTACTGCACCGCTTTACTCACCGAACTCATCGCGCTTAGCGCGTTGTTCAGGCGGTCCAGGTCATCCAGCTGCGCCTGAATCTCGGTGGTTTTTGCCAGCTTGTCCTGCTCATTCAGTCCTTTAT  >  NC_000913/4323169‑4323460

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: