Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 4,017,860 A→G 8.5% I99V (ATA→GTA)  PP_3545 → two‑component system sensor histidine kinase/response regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,017,8600AG 8.5% 131.9 / 3.0 47I99V (ATA→GTA) PP_3545two‑component system sensor histidine kinase/response regulator
Reads supporting (aligned to +/- strand):  ref base A (23/20);  new base G (2/2);  total (25/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.06e-01

GCGGCCGACCGCAGCATGCGCCTCTTGGCCATCAACCGCACGGCGCGCGAAACCTTCGAACGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGCTCAGCAGCGAATTCAGGGCGGCTACCTGTTCGCCTATGA  >  NC_002947/4017713‑4018005
                                                                                                                                                   |                                                                                                                                                 
gCGGCCGACCGCAGCATGCGCCTCTTGGCCATCAACCGCACGGCGCGCGAAACCTTCGAACGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGa                                                                                                                                                   <  5:226287/148‑1 (MQ=255)
  ggCCGACCGCAGCATGCGCCTCTTGGCCATCAACCGCACGGCGCGCGAAACCTTCGAACGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGatat                                                                                                                                                <  5:260640/149‑1 (MQ=255)
    ccGACCGCAGCATGCGCCTCTTGGCCATCAACCGCACGGCGCGCGAAACCTTCGAACGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATgg                                                                                                                                              <  3:364429/149‑1 (MQ=255)
      gACCGCAGCATGCGCCTCTTGGCCATCAACCGCACGGCGCGCGAAACCTTCGAACGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGcc                                                                                                                                            <  4:71421/149‑1 (MQ=255)
          gcagcaTGCGCCTCTTGGCCATCAACCGCACGGCGCGCGAAACCTTCGAACGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCgcgc                                                                                                                                        <  2:244507/149‑1 (MQ=255)
               aTGCGCATCTTGGCCATAAACCGCACGGCGCGCGAAACCTTCGAACCTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACGCGACTTCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACt                                                                                                                                   <  7:117171/149‑1 (MQ=255)
                      tctTGGCCATCAACCGCACGGCGCGCGAAACCTTCGAACGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAggg                                                                                                                            >  7:120548/1‑149 (MQ=255)
                        ttGGCCATCAACCGCACGGCGCGCGAAACCTTCGAACGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAggg                                                                                                                            <  7:118682/147‑1 (MQ=255)
                                  aCCGCACGGCGCGCGAAACCTTCGAACGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATc                                                                                                                <  7:308705/149‑1 (MQ=255)
                                       aCGGCGCGCGAAACCTTCGAACGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGacac                                                                                                           >  8:43474/1‑149 (MQ=255)
                                          gcgcgcGAAACCTTCGAACGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGt                                                                                                        >  3:244794/1‑149 (MQ=255)
                                           cgcgcgAAACCTTCGAACGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTc                                                                                                       <  2:372684/149‑1 (MQ=255)
                                            gcgcgAAACCTTCGAACGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCa                                                                                                      >  1:237292/1‑149 (MQ=255)
                                            gcgcgAAACCTTCGAACGTTACAGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCa                                                                                                      >  1:242460/1‑149 (MQ=255)
                                             cgcgAAACCTTCGAACGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCAc                                                                                                     <  6:48694/149‑1 (MQ=255)
                                                gAAACCTTCGAACGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAAGCCGACATCATGGGCCGCCTGGCCCAGATATGCCCGCGCATACTGGCAGGGGAAGCGGTCTTCGACACCGTCAACtt                                                                                                  >  6:243733/1‑149 (MQ=255)
                                                          aaCGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGG‑CACCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGACACCTTCGGGCTGgac                                                                                        >  3:180043/1‑148 (MQ=255)
                                                           aCGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGgacg                                                                                       <  8:120548/149‑1 (MQ=255)
                                                           aCGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGgac                                                                                        >  5:54520/1‑148 (MQ=255)
                                                            cGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGgacga                                                                                      <  4:351168/149‑1 (MQ=255)
                                                             gTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGGTATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGgacgac                                                                                     >  3:349534/1‑149 (MQ=255)
                                                             gTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGGTATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGgacgac                                                                                     >  3:344019/1‑149 (MQ=255)
                                                              ttACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGacgacg                                                                                    <  7:43474/149‑1 (MQ=255)
                                                                                             tACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGc                                                             >  3:201788/1‑141 (MQ=255)
                                                                                             tACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGc                                                             <  4:201788/141‑1 (MQ=255)
                                                                                                   ccccAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCt                                               >  6:267344/1‑149 (MQ=255)
                                                                                                    cccAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGt                                                   >  7:220769/1‑144 (MQ=255)
                                                                                                    cccAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGt                                                   <  8:220769/144‑1 (MQ=255)
                                                                                                    cccAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTc                                              >  1:222036/1‑149 (MQ=255)
                                                                                                    cccAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTc                                              >  3:71946/1‑149 (MQ=255)
                                                                                                    cccAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATAATTGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTc                                              >  1:227414/1‑149 (MQ=255)
                                                                                                         ttCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGc                                         >  6:189337/1‑149 (MQ=255)
                                                                                                          tCCTGACCGATCAACCCGACATCATGGG‑CACCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGCt                                        <  4:180043/148‑1 (MQ=255)
                                                                                                             tGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGCTcag                                     >  5:270843/1‑149 (MQ=255)
                                                                                                                   aTCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGCTCAGCAGCg                                >  3:75470/1‑148 (MQ=255)
                                                                                                                     cAACCCTACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCTTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGCTCAGCAGCGaa                              <  5:243733/148‑1 (MQ=255)
                                                                                                                      aaCCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGCTCAGCAGCGAAtt                            >  4:184489/1‑149 (MQ=255)
                                                                                                                        cccGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGCTCAGCAGCGAAtt                            >  1:203523/1‑147 (MQ=255)
                                                                                                                         ccGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGCTCAGCAGCGAATTCAg                         <  4:244794/149‑1 (MQ=255)
                                                                                                                          cGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGCTCAGCAGCGAATTCAgg                        >  8:10094/1‑149 (MQ=255)
                                                                                                                               tcatGGGCCGCCTGGCCCCGGTATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGCTCAGCAGCGAATTCAGggcggc                   <  4:344019/149‑1 (MQ=255)
                                                                                                                               tcatGGGCCGCCTGGCCCCGGTATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGCTCAGCAGCGAATTCAGggcggc                   <  4:349534/149‑1 (MQ=255)
                                                                                                                                catGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGCTCAGCAGCGAAtt                            >  3:45446/1‑139 (MQ=255)
                                                                                                                                catGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGCTCAGCAGCGAAtt                            <  4:45446/139‑1 (MQ=255)
                                                                                                                                    ggCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGCTCAGCAGCGAATTCAGGGCGGCTACCt              >  5:318933/1‑149 (MQ=255)
                                                                                                                                            ggCCCCGATATGGCCGCGCATACTCGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGCTCAGCAGCGAATTCAGGGCGGCTACCTGTTCGCCt      <  6:54520/149‑1 (MQ=255)
                                                                                                                                               cccGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGCTcagc                                    >  4:208794/1‑116 (MQ=255)
                                                                                                                                               cccGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGCTcagc                                    <  3:208794/116‑1 (MQ=255)
                                                                                                                                                ccGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGCTCAGCAGCGAATTCAGGGCGGCTACCTGTTCGCCTATGa  <  3:184489/149‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                                 
GCGGCCGACCGCAGCATGCGCCTCTTGGCCATCAACCGCACGGCGCGCGAAACCTTCGAACGTTACCGAGGCTTCGTGCCGCAGGTTGGCGACTACGTACCCCAGTTCCTGACCGATCAACCCGACATCATGGGCCGCCTGGCCCCGATATGGCCGCGCATACTGGCAGGGGAAGCGTTCATCGACACCGTCACCTTCGGGCTGGACGACGCACCACGCCACTACGAAATTCGCTACCACCCGTGGCTCGATGCTCAGCAGCGAATTCAGGGCGGCTACCTGTTCGCCTATGA  >  NC_002947/4017713‑4018005

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: ‑