Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 2,729,033 T→A 8.6% L254Q (CTG→CAG)  PP_2390 → LysR family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029472,729,0330TA 8.6% 134.7 / 2.3 46L254Q (CTG→CAG) PP_2390LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (22/20);  new base A (2/2);  total (24/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGCGAATGGATGCGCTGGACATCAGCATCGACCAGGGGCAGGTGTTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAGCGCGGCAGATGCACAAGCTGCGTGACTTCCTGCTCGGCCAGGTACCGCCGCTGGCCTACAAGGAC  >  NC_002947/2728888‑2729172
                                                                                                                                                  |                                                                                                                                           
gcgcGAATGGATGCGCTGGACATCAGCATCGACCAGGGGCAGGTGTTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTg                                                                                                                                            <  1:80364/147‑1 (MQ=255)
gcgcGAATGGATGCGCTGGACATCAGCATCGACCAGGGGCAGGTGTTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTg                                                                                                                                            <  2:239775/147‑1 (MQ=255)
  gcgAATGGATGCGCTGGACATCAGCATCGACCAGGGGCAGGTGTTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCa                                                                                                                                        >  5:14968/1‑149 (MQ=255)
  gcgAATGGATGCGCTGGACATCAGCATCGACCAGGGGCAGGTGTTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCa                                                                                                                                        >  5:10436/1‑149 (MQ=255)
             cgcTGGACATCAGCATCGACCAGGGGCAGGTGTTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCGGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCaa                                                                                                                              <  8:44851/148‑1 (MQ=255)
               cTGGACATCAGCATCGACCAGGGGCAGGTGTTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCt                                                                                                                                             <  3:222495/131‑1 (MQ=255)
               cTGGACATCAGCATCGACCAGGGGCAGGTGTTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCt                                                                                                                                             >  4:222495/1‑131 (MQ=255)
                  gACATCAGCATCGACCAGGGGCAGGTGTTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCAt                                                                                                                          <  6:14968/147‑1 (MQ=255)
                  gACATCAGCATCGACCAGGGGCAGGTGTTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCAt                                                                                                                          <  6:10436/147‑1 (MQ=255)
                  gACATCAGCATCGACCAGGGGCAGGTGTTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGc                                                                                                                        >  2:261567/1‑149 (MQ=255)
                     aTCAGCATCGACCAGGGGCAGGTGTTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCCGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGt                                                                                                                     >  8:194813/1‑149 (MQ=255)
                       cAGCATCGACCAGGGGCAGGTGTTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTgg                                                                                                                   >  2:163326/1‑149 (MQ=255)
                              gACCAGGGGCAGGTGTTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCGAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCg                                                                                                             <  8:119722/148‑1 (MQ=255)
                                 cAGGGGCAGGTGTTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGa                                                                                                         >  6:156054/1‑149 (MQ=255)
                                   ggggCAGGTGTTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACg                                                                                                       >  8:124881/1‑149 (MQ=255)
                                    gggCAGGTGTTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACgg                                                                                                      <  1:261567/149‑1 (MQ=255)
                                     ggCAGGTGTTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGt                                                                                                     >  2:204749/1‑149 (MQ=255)
                                          gtgtTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTtacta                                                                                                <  5:156054/149‑1 (MQ=255)
                                            gtTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACa                                                                                              >  6:317951/1‑149 (MQ=255)
                                                      cTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCTAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGc                                                                                                                                     >  6:256390/1‑100 (MQ=255)
                                                      cTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCTAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGc                                                                                                                                     <  5:256390/100‑1 (MQ=255)
                                                                gCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGc                                                                          >  7:128615/1‑149 (MQ=255)
                                                                       ggCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCaaaa                                                                    <  4:240970/148‑1 (MQ=255)
                                                                        gccgccCAGCAAGGCTTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAgc                                                                  >  7:33059/1‑149 (MQ=255)
                                                                         ccgccCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAgcg                                                                 >  6:225388/1‑149 (MQ=255)
                                                                            cccAGCAAGGCCTGGGCATTTCAGCGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAgcgc                                                                <  6:54851/147‑1 (MQ=255)
                                                                            cccAGCAAGGCCTGGGCATTTCAGAGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAgcgc                                                                >  5:54851/1‑147 (MQ=255)
                                                                              cAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAGCGCgg                                                              >  7:256555/1‑147 (MQ=255)
                                                                                  aaGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAGCGCGGCAGATg                                                        <  7:124881/149‑1 (MQ=255)
                                                                                     gCCTGGGCATTTCAGTGGTCTATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑TCCTGGTCACGCCTTTCAAGCATGCCGTGGCCTCCGGCGACGGTTACTACTTGACCTGGCTCAAGGCCAGCCCAAAAGCGCGGCAGATGcac                                                     <  1:89978/149‑1 (MQ=255)
                                                                                       cTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAGCGCGGCAGATGcac                                                     >  2:226422/1‑147 (MQ=255)
                                                                                        tGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAGCGCGGCAGATGCACAAg                                                  >  3:118759/1‑149 (MQ=255)
                                                                                              tttCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAGGCGCGGCAGATGCACAAGCTGCGt                                            <  5:317951/149‑1 (MQ=255)
                                                                                                       tCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAGCGCGGCAGATGCACAAGCTGCGTGACTTCCTg                                   >  5:242593/1‑149 (MQ=255)
                                                                                                       tCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAGCGCGGCAGATGCACAAGCTGCGTGACTTCCTg                                   <  5:225388/149‑1 (MQ=255)
                                                                                                               gTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAGCGCGGCAGATGCACAAGCTGCGTGACTTCCTGCTCGGc                             >  4:288781/1‑147 (MQ=255)
                                                                                                                tACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAGCGCGGCAGATGCACAAGCTGCGTGACTTCCTGCTCGGCCAg                          >  8:275332/1‑149 (MQ=255)
                                                                                                                      ccAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAGCGCGGCAGATGCACAAGCTGCGTGACTTCCTGCTCGGCCAGGTAccg                    >  4:46164/1‑149 (MQ=255)
                                                                                                                       cAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAGCGCGGCAGATGCACAAGCTGCGTGACTTCCTGCTCGGCCAGGTAccgc                   <  8:128615/149‑1 (MQ=255)
                                                                                                                        aGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTtac                                                                                                  >  8:162413/1‑69 (MQ=255)
                                                                                                                        aGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTtac                                                                                                  <  7:162413/69‑1 (MQ=255)
                                                                                                                            gtgACCAGGCGCCCGGCG‑GCCAGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAGAGCGGCAGATGCACAAGCTGCGTGACTTCCTGCTCGGCCAGGTACCGCCGCTg              >  4:38962/3‑149 (MQ=255)
                                                                                                                             cGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAGCGCGGCAGATGCACAAGCTGCGTGACTTCCTGCTCGGCCAGGTACCGCCGCTgg             <  3:203057/149‑1 (MQ=255)
                                                                                                                             cGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAGCGCGGCAGATGCACAAGCTGCGTGACTTCCTGCTCGGCCAGGTACCGCCGCTgg             <  1:226422/149‑1 (MQ=255)
                                                                                                                                  caggcgcccGGCGGCCAGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCaaaa                                                                    >  5:19758/5‑90 (MQ=255)
                                                                                                                                  caggcgcccGGCGGCCAGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCaaaa                                                                    <  6:19758/86‑1 (MQ=255)
                                                                                                                                     ccgccgGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAGCGCGGCAGATGCACAAGCTGCGTGACTTCCTGCTCGGCCAGGTACCGCCGCTGGCCTACAAg     <  1:204749/149‑1 (MQ=255)
                                                                                                                                         ccggcggcCAGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAGCGCGGCAGATGCACAAGCTGCGTTACTTCCTGCTCGGCCAGGTACCGCCGCTGGCCTACAAGGAc  <  3:38962/143‑1 (MQ=255)
                                                                                                                                                  tGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAGCGCGGCAGATGCACAAGCTGCGTGACTTCCTGCTCGGCCAGGTACCGCCGCTGGCCTACAAGGa   >  6:264713/1‑139 (MQ=255)
                                                                                                                                                  tGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAGCGCGGCAGATGCACAAGCTGCGTGACTTCCTGCTCGGCCAGGTACCGCCGCTGGCCTACAAGGa   <  5:264713/139‑1 (MQ=255)
                                                                                                                                                  |                                                                                                                                           
GCGCGAATGGATGCGCTGGACATCAGCATCGACCAGGGGCAGGTGTTCGATACCCTCGACCAGGGCATATCGGCCGCCCAGCAAGGCCTGGGCATTTCAGTGGTCGATCTGGTACTGGCCAGCACCGACCTGGCCGCCGGGC‑GCCTGGTCACGCCTTTCAAGCATGCCGTGGCCACCGGCGACGGTTACTACATGACCTGGCTCAAGGCCAGCCCAAAAGCGCGGCAGATGCACAAGCTGCGTGACTTCCTGCTCGGCCAGGTACCGCCGCTGGCCTACAAGGAC  >  NC_002947/2728888‑2729172

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑