Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,531,010 A→C 8.6% R421R (CGT→CGG)  braE ← high‑affinity branched‑chain amino acid ABC transporter permease BraE

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,531,0100AC 8.6% 132.2 / 2.4 46R421R (CGT→CGG) braEhigh‑affinity branched‑chain amino acid ABC transporter permease BraE
Reads supporting (aligned to +/- strand):  ref base A (22/20);  new base C (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 = 9.36e-01

GCAAATATCTGGTTGCGCCGGACCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAACGCCGCGATGACCACACCCACGGTC  >  NC_002947/5530862‑5531148
                                                                                                                                                    |                                                                                                                                            
gCAAATATCTGGTTGCGCCGGACCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATa                                                                                                                                              >  1:35534/1‑149 (MQ=255)
  aaaTATCTGGTTGCGCCGGACCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACg                                                                                                                                            <  4:167837/149‑1 (MQ=255)
  aaaTATCTGGTTGCGCCGGACCTTCAGGCTGACGTCACTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGCCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACg                                                                                                                                            >  1:214352/1‑149 (MQ=255)
    atatCTGGTTGCGCCGGACCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATCCgta                                                                                                                                          >  7:4270/1‑147 (MQ=255)
    atatCTGGTTGCGCCGGACCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGa                                                                                                                                          >  4:280168/1‑149 (MQ=255)
       tCTGGTTGCGCCGGACCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGAt                                                                                                                                         >  7:291260/1‑147 (MQ=255)
            ttGCGCCGGACCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATCCGTATCAGccgt                                                                                                                                  <  1:186003/149‑3 (MQ=255)
              gcgcCGGACCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCAcg                                                                                                                                >  5:144260/1‑149 (MQ=255)
                     aCCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGc                                                                                                                         <  5:295306/149‑1 (MQ=255)
                               tGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACTGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGatcatc                                                                                                                >  6:59576/1‑148 (MQ=255)
                               tGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGATGATACGGATCAGCCCACGCGGTCGCCAGatcatca                                                                                                               >  3:169720/1‑149 (MQ=255)
                                 aCGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACTGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGatcatc                                                                                                                <  5:59576/146‑1 (MQ=255)
                                      gCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATcatcagca                                                                                                         <  5:83970/148‑1 (MQ=255)
                                            cgcCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATcatcagcaccatcag                                                                                                  >  3:80444/1‑149 (MQ=255)
                                                   aTGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGcc                                                                                            <  8:291260/148‑1 (MQ=255)
                                                     gCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATcatcagcaccatcag                                                                                                  <  1:300585/140‑1 (MQ=255)
                                                     gCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATcatcagcaccatcag                                                                                                  >  2:300585/1‑140 (MQ=255)
                                                      ccACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGaa                                                                                         >  6:165861/1‑148 (MQ=255)
                                                      ccACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGaa                                                                                         <  5:165861/148‑1 (MQ=255)
                                                       cACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGatcat                                                                                                                 <  6:303765/123‑1 (MQ=255)
                                                       cACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGatcat                                                                                                                 >  5:303765/1‑123 (MQ=255)
                                                            aaCTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACagcag‑‑c                                                                                <  2:107541/149‑1 (MQ=255)
                                                               tGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATcatcag                                                                                                           <  3:165490/121‑1 (MQ=255)
                                                               tGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATcatcag                                                                                                           >  4:165490/1‑121 (MQ=255)
                                                                       caGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTc                                                                     >  5:304234/1‑149 (MQ=255)
                                                                            tGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGatcatc                                                                                                                <  5:195485/103‑1 (MQ=255)
                                                                            tGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGatcatc                                                                                                                >  6:195485/1‑103 (MQ=255)
                                                                                  ccGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTgc                                                          <  3:280168/149‑1 (MQ=255)
                                                                                   cGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTgcg                                                         >  8:173884/1‑149 (MQ=255)
                                                                                   cGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTgcg                                                         <  4:80444/149‑1 (MQ=255)
                                                                                     agagaATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTgcg                                                         >  1:67166/1‑147 (MQ=255)
                                                                                            gATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTGCGCAGCAGTTc                                                >  7:187809/1‑149 (MQ=255)
                                                                                               atCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCgg                                             >  2:254243/1‑149 (MQ=255)
                                                                                                tcgtcgCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGgc                                            <  2:35534/149‑1 (MQ=255)
                                                                                                tcgtcgCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGgc                                            <  7:173884/149‑1 (MQ=255)
                                                                                                            gcgcCACTCCTTTACGTGGGGTCACACCGTTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAg                                 >  7:249151/1‑148 (MQ=255)
                                                                                                                      tttACGTGGGGTCACACCGTTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAAcgccg                      <  8:249151/149‑1 (MQ=255)
                                                                                                                      tttACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAAc                          >  6:193568/1‑145 (MQ=255)
                                                                                                                      tttACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAAc                          <  5:193568/145‑1 (MQ=255)
                                                                                                                         aCGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAACGCCGCGa                   >  7:64537/1‑149 (MQ=255)
                                                                                                                         aCGGGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCCGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGTACACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAAcgccg                      <  1:254243/148‑1 (MQ=255)
                                                                                                                          cGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAACGCCGCGAt                  <  4:169720/149‑1 (MQ=255)
                                                                                                                          cGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAACGCCGCGAt                  <  8:64537/149‑1 (MQ=255)
                                                                                                                               ggTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAACGCCGCGATGACca             >  8:98051/1‑149 (MQ=255)
                                                                                                                                     acCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGAACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAACGCCGCGATGACCACACCCa       >  6:100570/1‑149 (MQ=255)
                                                                                                                                        gcgtgggCTGATCCGTATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAACGCCGCGATGACCACACCCACgg    >  6:76530/6‑149 (MQ=255)
                                                                                                                                          gtgggCTGATCCGTATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAACGCCGCGATGACCACACCCACGGTc  <  5:76530/146‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                            
GCAAATATCTGGTTGCGCCGGACCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAG‑‑CACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAACGCCGCGATGACCACACCCACGGTC  >  NC_002947/5530862‑5531148

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: ‑