Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 761,379 C→T 8.4% intergenic (‑48/‑61) mngR ← / → mngA Transcriptional repressor for the mannosyl‑D‑glycerate catabolic operon/fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP009273761,3790CT 8.4% 129.9 / 3.2 51intergenic (‑48/‑61)mngR/mngATranscriptional repressor for the mannosyl‑D‑glycerate catabolic operon/fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component
Reads supporting (aligned to +/- strand):  ref base C (21/23);  new base T (2/2);  total (24/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.80e-01

AGTGGGTAACGCATCGCCAGGTTTAAGCTCGCCACGCGCAATTTGTTCACGAATGCGATCGGCAATCTGCCGGTATAAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTGGCGCGACTATAAAAACGATCAAGTGAGGATCATGATGAATCTGACGACTCTGACCCACCG  >  CP009273/761239‑761525
                                                                                                                                            |                                                                                                                                                  
aGTGGGTAACGCATCGCCAGGTTTAAGCTCGCCACGCGCAATTTGTTCACGAATGCGATCGGCAATCTGCCGGTATAAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTa                                                                                                                                            >  2:318405/1‑149 (MQ=255)
         cGCATCGCCAGGTTTAAGCTCGCCACGCGCAATTTGTTCACGAATGCGATCGGCAATCTGCCGGTATAAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATaataca                                                                                                                                   >  2:35557/1‑149 (MQ=255)
         cGCATCGCCAGGTTTAAGCTCGCCACGCGCAATTTGTTCACGAATGCGATCGGCAATCTGCCGGTATAAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATaataca                                                                                                                                   >  2:35587/1‑149 (MQ=255)
          gCATCGCCAGGTTTAAGCTCGCCACGCGCAATTTGTTCACGAATGCGATCGGCAATCTGCCGGTATAAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTTATCCTGTAAATaatacaa                                                                                                                                  >  2:758159/1‑149 (MQ=255)
          gCATCGCCAGGTTTAAGCTCGCCACGCGCAATTTGTTCACGAATGCGATCGGCAATCTGCCGGTATAAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTTATCCTGTAAATaatacaa                                                                                                                                  >  2:453680/1‑149 (MQ=255)
          gCATCGCCAGGTTTAAGCTCGCCACGCGCAATTTGTTCACGAATGCGATCGGCAATCTGCCGGTATAAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATaatacaa                                                                                                                                  >  1:679383/1‑149 (MQ=255)
               gCCAGGTTTAAGCTCGCCACGCGCAATTTGTTCACGAATGCGATCGGCAATCTGCCGGTATCGGAACTTGTGGCCCATTTTTAGTATCTCATTAATACGCATTTAATGGTTATGACCGATAAAGTACTCCTCTAAatgatatagctaca                                                                                                                             >  2:722281/1‑141 (MQ=255)
               gCCAGGTTTAAGCTCGCCACGCGCAATTTGTTCACGAATGCGATCGGCAATCTGCCGGTATAAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAACTTCATCCTGTGAATaatacaaataca                                                                                                                             >  2:58741/1‑149 (MQ=255)
                ccAGGTTTAAGCTCGCCACGCGCAATTTGTTCACGAATGCGATCGGCAATCTGCCGGTCTAAGGGATTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAatacaaatacaa                                                                                                                            >  2:244319/1‑149 (MQ=255)
                       tAAGCTCGCCACGCGCAATTTGTTCACGAATGCGATCGGCAATCTGCCGGTATAAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAaat                                                                                                                     >  2:626938/1‑149 (MQ=255)
                            tCGCCACGCGCAATTTGTTCACGAATGCGATCGGCAATCTGCCGGTATAAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATACttt                                                                                                                >  2:863338/1‑149 (MQ=255)
                               ccACGCGCAATTTGTTCACGAATGCGATCGGCAATCTGCCGGTATAAGGGCTTGTGTCCCCTTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTACATAATACAAATACCATACAAATAATTtcaa                                                                                                             >  1:82103/1‑149 (MQ=255)
                               ccACGCGCAATTTGTTCACGAATGCGATCGGCAATCTGCCGGTATAAGGGCTTGTGTCCCATTTTTTTTTTTTTTTTAATACGAATTTAACCATTATGCCCGATAAATGCATCCTGTAAGTAATACAAATACCCTCCAAATAACTtcaa                                                                                                             >  1:151838/1‑149 (MQ=255)
                               ccACGCGCAATTTGTTCACGAATGCGATCGGCAATCTGCCGGTATAAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTtcaa                                                                                                             >  1:445426/1‑149 (MQ=255)
                                   gcgcAATTTGTTCACGAATGCGATCGGCAATCTGCCGGTATCAGGGATTGCGACCCTGTTCTAGTTTCTCTTTAATACGAATTTCACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTtcaatcaa                                                                                                         <  2:165848/149‑1 (MQ=255)
                                   gcgcAATTTGTTCACGAATGCGATCGGCAATCTGCCGCTATAAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATCCAAATACAATACAAATAATTtcaatcaa                                                                                                         <  2:568066/149‑1 (MQ=255)
                                             ttCACGAATGCGATCGGCAATCTGCCGGTATAAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGa                                                                                               >  1:92939/1‑149 (MQ=255)
                                                gcGAATGCGATCGGCAATCTGCCGGTATAAGGGCTTGTGTCCCATTTTTAGTGTCTCATTAATACGAATTTAACCACTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATca                                                                                            <  1:479221/148‑1 (MQ=255)
                                                          tCGGCAATCTGCCGGTATAAGGGCTTGTGTTCCATTTTTAGTATCTCATTAATACGAATTTAACCATTAGGCCCTATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCGATCAAGTGAAATTGATCACATAATGGTa                                                                                  <  2:466263/149‑1 (MQ=255)
                                                               aaTCTGCCGGTATAAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGtt                                                                             <  1:787514/149‑1 (MQ=255)
                                                                   tGCCGGTATAAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGACTTTAACCATTATTCGCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTAt                                                                         >  1:832772/1‑149 (MQ=255)
                                                                    gCCGGTATAAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTTATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATc                                                                        <  1:758159/149‑1 (MQ=255)
                                                                    gCCGGTATAAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTTATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATc                                                                        <  1:453680/149‑1 (MQ=255)
                                                                     ccGGTATAAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATAACATCATGGTAATGTTTTCTCg                                                                       >  1:215021/1‑149 (MQ=255)
                                                                      cGGTATAAGGGCTTGTGTCCCATTTTTATTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCgg                                                                      <  2:231900/149‑1 (MQ=255)
                                                                         tataAGGGGTTGTGTCGTATTTTGAGTATGTCATTGATACGAATTTAACCATTATGGCCGATAAATTCATCCTGTAAATAATACAAATACAATACAGATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGca                                                                   <  1:382227/149‑1 (MQ=255)
                                                                         tataAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGca                                                                   <  1:471016/149‑1 (MQ=255)
                                                                           caaGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGcaca                                                                 <  2:843317/148‑1 (MQ=255)
                                                                              gggCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTg                                                              >  2:863422/1‑149 (MQ=255)
                                                                              gggCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTg                                                              <  1:35557/149‑1 (MQ=255)
                                                                              gggCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTg                                                              <  1:35587/149‑1 (MQ=255)
                                                                                  ttGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTGgcgc                                                          <  2:85354/149‑1 (MQ=255)
                                                                                  ttGTGTCCCATTTTTAGTATCTCAGTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTGgcgc                                                          <  2:85164/149‑1 (MQ=255)
                                                                                  ttGTGCCCCATTTTTAGCATCTCATTAAAACGAATTTAACCCTAATGCCGTAGAAATTCATCCTGGAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTGgcgc                                                          <  2:333697/149‑1 (MQ=255)
                                                                                    gtttCCCGTTTTTTGTACCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTACATAATACAAATACAATACAAATAATTTCAATCAAGCGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTGGCGCGa                                                        <  1:653782/146‑1 (MQ=255)
                                                                                    gtgtCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATCGTTTTATCGGGCACACTGGCGCGa                                                        <  2:648503/149‑1 (MQ=255)
                                                                                           aTTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTGGCGCGACTATaaa                                                 <  1:521549/149‑1 (MQ=255)
                                                                                            tttttACTATTTCATTAATACGAATTTAACCATTATGCCCGATAAATTAATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTGGCGCGACTATaaaa                                                <  1:244319/149‑1 (MQ=255)
                                                                                               ttAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTGGCGCGACTCTAAAAACg                                             >  1:207861/1‑149 (MQ=255)
                                                                                                tAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTGGCGCGACTATAAAAACGa                                            <  2:445426/149‑1 (MQ=255)
                                                                                                       tcATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTGGCGCGGCTATAAAAACGATCAAGTg                                     >  2:644073/1‑149 (MQ=255)
                                                                                                              tACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAGATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTGGCTCGACTATAAAAACGATCAAGTGAGGATCa                              >  1:639726/1‑149 (MQ=255)
                                                                                                                       aaCCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTGGCGCGACTATAAAAACGATCAAGTGAGGATCATGATGAATc                     >  2:303450/1‑149 (MQ=255)
                                                                                                                          cATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTGGCGCGACTATAAAAACGATCAAGTGAGGATCATGATGAATCTga                  <  2:679383/149‑1 (MQ=255)
                                                                                                                          cATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTGGCGCGACTATAAAAACGATCAAGTGAGGATCATGATGAATCTga                  <  2:492001/149‑1 (MQ=255)
                                                                                                                          aagtctGCCCCATAAATTGATCGTGTAAAGAATACAAATAAAATACACATAATTCCAACCAAGTGAAATTGATCACATAATGGTCTTGTTTTATCGGGCACACTTGCGCGACTATAAAAACGATCAAGTGAGGATCATGATGAATCTga                  <  2:611035/144‑1 (MQ=255)
                                                                                                                           aTTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTGGCGCGACTATAAAAACGATCAAGTGAGGATCATGATGAATCTgac                 <  2:555129/149‑1 (MQ=255)
                                                                                                                                       aaaTTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTGGCGCGACTATAAAAACGATCAAGTGAGGATCATGATGAATCTGACGACTCTGACCCa     <  2:832772/149‑1 (MQ=255)
                                                                                                                                        aaTTCATCTTGTAAATGATACAAATACAATAACAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTGGCGCGACTATAAAAACGATCAAGTGAGGATCATGATGAATCTGACGACTCTGACCCAc    <  1:238896/149‑1 (MQ=255)
                                                                                                                                          ttCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTTTTTTATCGGGCACACTGGCGCGACTATAAAAACGATCAAGTGAGGATCATGATGAATCTGACGACTCTGACCCACcg  >  1:359408/1‑149 (MQ=255)
                                                                                                                                          ttCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTGGCGCGACTATAAAAACGATCAAGTGAGGATCATGATGAATCTGACGACTCTGACCCACcg  >  2:22662/1‑149 (MQ=255)
                                                                                                                                            |                                                                                                                                                  
AGTGGGTAACGCATCGCCAGGTTTAAGCTCGCCACGCGCAATTTGTTCACGAATGCGATCGGCAATCTGCCGGTATAAGGGCTTGTGTCCCATTTTTAGTATCTCATTAATACGAATTTAACCATTATGCCCGATAAATTCATCCTGTAAATAATACAAATACAATACAAATAATTTCAATCAAGTGAAATTGATCACATAATGGTATTGTTTTATCGGGCACACTGGCGCGACTATAAAAACGATCAAGTGAGGATCATGATGAATCTGACGACTCTGACCCACCG  >  CP009273/761239‑761525

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: ‑