Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,747,351 T→A 19.5% E53V (GAG→GTG)  PP_5473 ← LuxR family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,747,3510TA19.5% 65.1 / 7.3 35E53V (GAG→GTG) PP_5473LuxR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (7/20);  new base A (4/3);  total (12/23)
Fisher's exact test for biased strand distribution p-value = 1.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGCGCCAGGAGCGCCTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCC‑ACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACGAGAGCAGTTCGACGGCGAACC  >  NC_002947/1747206‑1747494
                                                                                                                                                  |                                                                                                                                                
gcgcgcCAGGAGCGCCTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCg                                                                                                                                               <  7:192518/149‑1 (MQ=255)
  gcgcCAGGAGCGCCTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGgc                                                                                                                                             <  4:35640/149‑1 (MQ=255)
   cgcCAGGAGCGCCTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCAGTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGGGCCGC‑GACGgcc                                                                                                                                            >  6:5164/1‑148 (MQ=255)
       aGGAGCGCCTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGCGCGCCGG‑AGCGgcgcacc                                                                                                                                        <  8:292429/149‑4 (MQ=25)
                      gtgtCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGCGACCGCCGCGcgccggagc                                                                                                                                 <  8:322870/142‑4 (MQ=21)
                      gtgtCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGCGACCGCCGCGcgccggagc                                                                                                                                 >  7:322870/1‑139 (MQ=21)
                         tCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATgg                                                                                                                       <  2:222155/148‑1 (MQ=255)
                            aCCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTc                                                                                                                   <  7:3873/149‑1 (MQ=255)
                             cgttCTCTTGGAAGGCGGGGTGCATTGTTGTCTGCTTGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAAGTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATgg                                                                                                                       <  4:29085/142‑1 (MQ=255)
                              cTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCgcggcg                                                                                                                            <  8:164590/138‑1 (MQ=255)
                              cTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑AACGGCGCCCGGCGGTCGCGgcgcccatcgg                                                                                                                    >  7:164590/1‑139 (MQ=21)
                               ttCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑ACCCGCGCCCGGCGGTCGCGGCGCATGGGGTCGCt                                                                                                                >  6:282759/1‑149 (MQ=255)
                                 ctctTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCt                                                                                                                <  8:107091/147‑1 (MQ=255)
                                       gAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCCCGCGGCGGTCGCGGCGCATGGGGTCGCAGGCGttta                                                                                                        >  4:287913/1‑147 (MQ=255)
                                                gggCATTGTTGTCTGCATGGATTATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGACCGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGgcat                                                                                               <  5:5164/147‑1 (MQ=255)
                                                 tGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGgcatg                                                                                              <  3:346959/149‑1 (MQ=255)
                                                    aTTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCCCCGC‑TACCGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTGGTTGATTGCGgcatgcat                                                                                           >  1:215222/1‑149 (MQ=17)
                                                        ttgtCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCgcggc                                                                                                                             >  3:57759/1‑111 (MQ=255)
                                                        ttgtCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCgcggc                                                                                                                             <  4:57759/111‑1 (MQ=255)
                                                           tCTGCAGGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCc‑aca                                                                                   <  2:274352/149‑1 (MQ=255)
                                                                                  ggtCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCGGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCC‑ACAAGACAGACCAGGGCGAGGCaga                                                             <  1:327053/148‑1 (MQ=255)
                                                                                   ggcAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCC‑ACAAGACAGACCAGGGCGAGGCAGAGc                                                           <  3:287913/147‑1 (MQ=255)
                                                                                      aGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGGCGCTGTCGTTGATGGCGGCATGCATTGCC‑ACAAGACAGACCAGGGCGAGGCAGAGCGGa                                                        <  5:282759/149‑1 (MQ=255)
                                                                                                   gAAGGCCTCGGGCTTACGAACGATTCGAACTTGGGCGGTGCGGCGC‑TCCGGCGCGCGGCGGGCGCGGCGCATGGGGTCGCTGTCGTTGATTGCGGCATGCATTGCCTACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGAtcttc                                            <  1:68716/149‑1 (MQ=21)
                                                                                                                             gAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCC‑ACAAGACAGACCAGGGCGAGGCAGAGCGGAGtgat                                                   >  7:78909/1‑115 (MQ=255)
                                                                                                                             gAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCC‑ACAAGACAGACCAGGGCGAGGCAGAGCGGAGtgat                                                   <  8:78909/115‑1 (MQ=255)
                                                                                                                                   gggCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCC‑ACAAGACAGACCAGGGCGAGGCaga                                                             <  3:70252/99‑1 (MQ=255)
                                                                                                                                    ggCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCC‑ACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACGAGAGCAGTTCGa           <  2:215222/148‑1 (MQ=255)
                                                                                                                                     cccatGCGCCGCGACCGCCGCGCGCCGG‑AGCGGCGCACGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCC‑ACAAGACAGACCGGGGCGAGGCAGAGCGGAGTGATGATCTTCTg                                          >  1:239331/5‑116 (MQ=25)
                                                                                                                                     cccatGCGCCGCGACCGCCGCGCGCCGG‑AGCGGCGCACGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCC‑ACAAGACAGACCCGGGCGAGGCAGAGCGGAGTGATGATCTTCTg                                          <  2:239331/112‑1 (MQ=25)
                                                                                                                                        gTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCC‑ACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTgg                                         <  4:229185/114‑1 (MQ=255)
                                                                                                                                        gTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCC‑ACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTgg                                         >  3:229185/1‑114 (MQ=255)
                                                                                                                                          gcgcCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCC‑ACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACGAGAGCAGtt              >  4:6733/1‑139 (MQ=255)
                                                                                                                                          gcgcCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCC‑ACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACGAGAGCAGtt              <  3:6733/139‑1 (MQ=255)
                                                                                                                                            gccgc‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCC‑ACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGAAGCTGGTATGGTATGCCGCCTCTGCTACGAGAGCAGTTCGACGGCGAAcc  >  1:300954/1‑149 (MQ=39)
                                                                                                                                                  |                                                                                                                                                
GCGCGCCAGGAGCGCCTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCC‑ACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACGAGAGCAGTTCGACGGCGAACC  >  NC_002947/1747206‑1747494

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑