Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 17,135 T→C 13.9% intergenic (+129/‑354) sokC → / → nhaA sRNA antisense regulator blocking mokC, and hence hokC, translation/sodium‑proton antiporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_00091317,1350TC13.9% 100.1 / 6.2 43intergenic (+129/‑354)sokC/nhaAsRNA antisense regulator blocking mokC, and hence hokC, translation/sodium‑proton antiporter
Reads supporting (aligned to +/- strand):  ref base T (15/22);  new base C (3/3);  total (18/25)
Fisher's exact test for biased strand distribution p-value = 6.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01

TATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAAATTAATTATTACTTTTCCTAATTAATCCCTCAG  >  NC_000913/16988‑17280
                                                                                                                                                    |                                                                                                                                                 
tatCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAAtt                                                                                                                                                  <  1:712275/149‑1 (MQ=255)
   cccccGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAAttttt                                                                                                                                               <  1:40925/145‑1 (MQ=255)
   cccTCGGGGCTTTTCTCTACCTGCCGTTCAGCTAATGCCTGAGACAGTCAGCTTCAAGCACCCTCCGCTATTATATCTCTCTCTTTAACCCATTTTGTTTTATCTATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAAttttt                                                                                                                                               <  2:652294/147‑1 (MQ=255)
   cACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAGTGCCTGAGACAGACAGCCTCAAACACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTGTTATCTATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAAttttt                                                                                                                                               <  2:652545/149‑1 (MQ=255)
     cTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTa                                                                                                                                             >  2:287126/1‑149 (MQ=255)
              tttCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTaa                                                                                                                                    <  1:330434/149‑1 (MQ=255)
                      tCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGTGTAATTTTTTAATGATTTAATTATTTaa                                                                                                                            <  1:418370/149‑1 (MQ=255)
                            gTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTaa                                                                                                                      >  2:181107/1‑149 (MQ=255)
                               cAGCTAATGCCTGAGACAGGCAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACG‑AACACTTTCCATGTGGCGTAACTTCTTAATGATTTAATTATTTAACTTTAAttt                                                                                                                   >  1:179552/1‑149 (MQ=255)
                               cAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTCTTAATGATTTAATTATTTAACTTTAAttt                                                                                                                   <  2:432043/149‑1 (MQ=255)
                               cAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAACTTTTTAATGATTTAATTATTTAACTTTAAttt                                                                                                                   >  2:784098/1‑149 (MQ=255)
                               cAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAACTTTTTAATGATTTAATTATTTAACTTTAAttt                                                                                                                   >  1:272813/1‑149 (MQ=255)
                                        gcTGGGACAGACAACCTCAAGCATCCGCCGCTATTCTCTCGCCATCTTTAACCGGTTTTTTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACGTTAATTTATCTCTTCa                                                                                                          <  2:552236/148‑1 (MQ=255)
                                        ccTGAGCCAGCCAGCCTCAAGGTCCGTCCCCTATTATCTCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCa                                                                                                          <  2:587244/149‑1 (MQ=255)
                                                  acagCCTCAAGCACCCGCCGCTACTATAACGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGTGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAattat                                                                                                >  1:511821/1‑149 (MQ=255)
                                                   cagCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAattatt                                                                                               <  2:631010/149‑1 (MQ=255)
                                                       cTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTGTCTCTTAATCTCAATTATTcact                                                                                           >  1:100741/1‑148 (MQ=255)
                                                       cTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTgacg                                                                                           >  2:675887/1‑149 (MQ=255)
                                                       cTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTgacg                                                                                           >  2:438331/1‑149 (MQ=255)
                                                             cACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGc                                                                                     <  1:361728/149‑1 (MQ=255)
                                                               cccGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCCTCGCAATTATTGACGACAACCTg                                                                                   >  2:122031/1‑149 (MQ=255)
                                                                     gcTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGattat                                                                             >  2:729127/1‑149 (MQ=255)
                                                                             atCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGaaa                                                                     <  2:709927/149‑1 (MQ=255)
                                                                                   ctctTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTgg                                                               <  2:219841/149‑1 (MQ=255)
                                                                                      tttAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCt                                                            >  2:729712/1‑149 (MQ=255)
                                                                                         accccATGTTCTTTTCTCGATTCTAATCCTGAAGACGGCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCCTCGCACTTTTTTATCTTTTGCTGGATTATTCTTGAAATATTGGCCTAAc                                                         <  1:576396/147‑1 (MQ=255)
                                                                                         aaCCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCCTT‑TTTGTTGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAAc                                                         <  2:365870/149‑1 (MQ=255)
                                                                                          aCCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACa                                                        <  2:524248/149‑1 (MQ=255)
                                                                                          aCCCATTTTGTTTTATCGATTCTAATCCTGAAGAAGAATTGCATT‑TTTGTGGCGTAATTTTTTAATGATTTACTTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGGCAAGCTGGATTATTTTTGAAATATTGGCCTAACa                                                        >  1:381343/1‑149 (MQ=255)
                                                                                               ttttGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTAGCCTAACAAGCAt                                                   >  2:762264/1‑149 (MQ=255)
                                                                                                      ttATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTGTTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCgcc                                            >  1:346324/1‑147 (MQ=255)
                                                                                                      ttATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGAc                                            >  2:173144/1‑149 (MQ=255)
                                                                                                      ttATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGAc                                            <  2:736101/149‑1 (MQ=255)
                                                                                                          cGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGAGTTGATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGac                                        <  1:733047/149‑1 (MQ=255)
                                                                                                              tCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGacaaca                                    <  1:110140/149‑1 (MQ=255)
                                                                                                              tCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGacaaca                                    <  2:772191/149‑1 (MQ=255)
                                                                                                                     cTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAaattaat                             >  2:518488/1‑149 (MQ=255)
                                                                                                                          gccGCCTCGCATT‑TTTGTTGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGTCGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAAATTAAttatta                        <  1:344792/147‑1 (MQ=255)
                                                                                                                                    aTT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAAATTAATTATTACTTTTCCtaa              <  1:287126/149‑1 (MQ=255)
                                                                                                                                          tgtgGCGTAACTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAAATTAATTATTACTTTTCCtaattaat         <  2:272813/149‑1 (MQ=255)
                                                                                                                                          tgtgGCGTAACTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAAATTAATTATTACTTTTCCtaattaat         <  2:179552/149‑1 (MQ=255)
                                                                                                                                          tgtgGCGTAACTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAAATTAATTATTACTTTTCCtaattaat         <  1:784098/149‑1 (MQ=255)
                                                                                                                                           gtgGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAAATTAATTATTACTTTTCCTAATTAATc        <  1:35149/149‑1 (MQ=255)
                                                                                                                                           gtgGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAAATTAATTATTACTTTTCCTAATTAATc        <  2:495655/149‑1 (MQ=255)
                                                                                                                                                gTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAAATTAATTATTACTTTTCCTAATTAATCCCTCa   <  1:729127/149‑1 (MQ=255)
                                                                                                                                                gTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATGATGAACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACACCAAATTAAGAATTACTTTTCCTAATTACTCCCTCa   >  2:394983/1‑149 (MQ=255)
                                                                                                                                                 tAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAAATTAATTATTACTTTTCCTAATTAATCCCTCAg  <  1:657225/149‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                                 
TATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATT‑TTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAAATTAATTATTACTTTTCCTAATTAATCCCTCAG  >  NC_000913/16988‑17280

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑