Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,361,428 T→C 8.3% H164H (CAT→CAC)  phoP → two‑component system DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,361,4280TC 8.3% 130.6 / 2.2 48H164H (CAT→CAC) phoPtwo‑component system DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (23/21);  new base C (2/2);  total (25/23)
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

GCCGCTCCAGTGGTTTCACCCAGTCGACCATCGCCGCTGGCCCCTTGGTGCTTGACCTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGAAGTGCTGGTTGGCCGCCTGCGCCGCAAGCTTGAAGGCGAGCGCGGCTTCAAACCCATCGA  >  NC_002947/1361286‑1361568
                                                                                                                                              |                                                                                                                                            
gccgcTCCAGTGGTTTCACCCAGTCGACCATCGCCGCTGGCCCCTTGGTGCTTTAACTCAACCGCAAGCAGGCCACCCACGACGAAAAACCCTTGGCCCTGACCGCCTACGAATACCGCATACTCGAATACCAAATGCGCCACCACcag                                                                                                                                        >  2:158173/1‑149 (MQ=255)
       cAGTGGTTTCACCCAGTCGACCATCGCCGCTGGCCCCTTGGTGCTTGACCTCAACCGCAAGCAGGCCA‑CCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAggtggt                                                                                                                                >  7:240319/1‑149 (MQ=255)
        aGTGGTTTCACCCAGTCGACCATCGCCGCTGGCCCCTTGGTGCTTGACCTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAggtggt                                                                                                                                <  2:209402/149‑1 (MQ=255)
        aGTGGTTTCACCCAGTCGACCATCGCCGCTGGCCCCTTGGTGCTTGACCTCAACCGCAAGCAGGCCA‑CCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGgtggtg                                                                                                                               <  8:240319/149‑1 (MQ=255)
            gTTTCACCCAGTCGACCATCGCCGCTGGCCCCTTGGTGCTTGACCTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCACCACCTGCTGGTGATGGcg                                                                                                                            >  6:265047/1‑148 (MQ=255)
            gTTTCACCCAGTCGACCATCGCCGCTGGCCCCTTGGTGCTTGACCTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCACCACCTGCTGGTGATGGc                                                                                                                             <  1:158173/148‑1 (MQ=255)
             tttCACCCAGTCGACCATCGCCGCTGGCCCCTTGGTGCTTGACCTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCACCACCTGCTGGTGATGGcgc                                                                                                                           <  5:265047/149‑3 (MQ=255)
                 aCCCAGTCGACCATCGCCGCTGGCCCCTTGGTGCTTGACCTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCAt                                                                                                                                              >  8:49333/1‑126 (MQ=255)
                 aCCCAGTCGACCATCGCCGCTGGCCCCTTGGTGCTTGACCTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCAt                                                                                                                                              <  7:49333/126‑1 (MQ=255)
                   ccAGTCGACCATCGCCGCTGGCCCCTTGGTGCTTGACCTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATc                                                                                                                     <  1:66679/149‑1 (MQ=255)
                             aTCGCCGCTGGCCCCTTGGTGCTTGAGCTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGagg                                                                                                             >  5:342380/1‑145 (MQ=255)
                             aTCGCCGCTGGCCCCTTGGTGCTTGACCTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATg                                                                                                             >  2:94697/1‑147 (MQ=255)
                                 ccgcTGGCCCCTTGGTGCTTGACCTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAg                                                                                                       >  6:242129/1‑149 (MQ=255)
                                  cgcTGGCCCCTTGGTGCTTGACCTCAACCGCAAGCAGGCCCCCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGt                                                                                                      >  4:185535/1‑149 (MQ=255)
                                   gcTGGCCCCTTGGTGCTTGACCTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGtt                                                                                                     <  7:106374/149‑1 (MQ=255)
                                          ccTTGGTGCTTGACCTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTTGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTAcc                                                                                                >  3:65265/1‑147 (MQ=255)
                                           cTTGGTGCTTGACCTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAg                                                                                             <  5:242129/149‑1 (MQ=255)
                                           cTTGGTGCTTGACCTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAg                                                                                             <  2:39722/149‑1 (MQ=255)
                                           cTTGGTGCGTGACCTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAg                                                                                             <  8:254443/149‑1 (MQ=255)
                                            ttGGTGCTTGACCTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAggtggt                                                                                                                                >  8:33109/1‑113 (MQ=255)
                                              ggTGCTTGACCTCAACCGCAATCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGga                                                                                           <  7:313142/148‑1 (MQ=255)
                                               gTGCTTGACCTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGgag                                                                                          <  1:94697/148‑1 (MQ=255)
                                                       ccTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGtt                                                                                                     >  6:173220/1‑129 (MQ=255)
                                                          cAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACAGCCTACGAATACCTCATCCTCTAATACCTCATGCGCCATCACCAGCAGCTGGTGGCCAAGGATCGCCTGATCGACAAGTTCTAACCAGGAGAAGAAGAgcgc                                                                               >  4:265894/1‑148 (MQ=255)
                                                           aaCCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGa                                                                             >  3:316480/1‑149 (MQ=255)
                                                            aCCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGAc                                                                            <  7:57367/149‑1 (MQ=255)
                                                                cAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGAcccc                                                                         >  6:71925/1‑148 (MQ=255)
                                                                        ccACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACTAATACCGCATCCTCGAATTCCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATc                                                                <  3:265894/149‑1 (MQ=255)
                                                                         cACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATc                                                                >  8:91609/1‑148 (MQ=255)
                                                                                      cAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGaa                                                             >  3:282529/1‑138 (MQ=255)
                                                                                      cAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGaa                                                             <  4:282529/138‑1 (MQ=255)
                                                                                        aGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGAAGTGCTGGTTGgcc                                                <  4:316480/149‑1 (MQ=255)
                                                                                                         ccTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATc                                                                >  3:10806/1‑116 (MQ=255)
                                                                                                         ccTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATc                                                                <  4:10806/116‑1 (MQ=255)
                                                                                                          cTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGAAGTGCTGGTTgg                                                  >  6:70831/1‑129 (MQ=255)
                                                                                                          cTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGAAGTGCTGGTTGGCCGCCTGCGCCGCAAGCtt                               >  5:143473/1‑148 (MQ=255)
                                                                                                             cGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGAAGTGCTGGTTGGCCGCCTGCGCCGCAAGCTTGaa                            <  6:143473/148‑1 (MQ=255)
                                                                                                             cGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGAAGTGCTGGTTGGCCGCCTGCGCCGCAAGCTTGa                             <  3:185535/147‑1 (MQ=255)
                                                                                                             cGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGACACGAAGAGCGCGACCCCAATGTCATCGAAGTGCTGGTTGGCCGCCTGCGCCGCAAGCTTGa                             <  8:280193/147‑1 (MQ=255)
                                                                                                                 tACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGAAGTGCTGGTTGGCCGCCTGCGCCGCAAGCTTGAAGGCGa                       <  5:71925/149‑1 (MQ=255)
                                                                                                                   ccGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGAAGTGCTGGTTGGCCGCCTGCGCCGCAAGCTTGAAGGCGAgc                     >  3:129934/1‑149 (MQ=255)
                                                                                                                                   cTCCTGCCCCATCACGAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGAAGTGCTGGTTGGCCGCCTGCGCCGCAAGCTTGAAGGCGAGCGCgg                 <  8:311009/137‑1 (MQ=255)
                                                                                                                                   cTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGAAGTGCTGGTTGGCCGCCTGCGCCGCAAGc                                 <  6:26841/121‑1 (MQ=255)
                                                                                                                                   cTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGAAGTGCTGGTTGGCCGCCTGCGCCGCAAGc                                 >  5:26841/1‑121 (MQ=255)
                                                                                                                                   cTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGAAGTGCTGGTTGGCCGCCTGCGCCGCAAGCTTGAAGGCGAGCGCgg                 >  7:311009/1‑137 (MQ=255)
                                                                                                                                   cTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGAAGTGCTGGTTGGCCGCCTGCGCCGCAAGCTTGAAGGCGAGCGCGGCTTCAAACCCAt     <  7:91609/149‑1 (MQ=255)
                                                                                                                                   cTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGAAGTGCTGCTTGGCCGCCTGCGCCGCAAGCTTGAAGGCGAGCGCGGCTTCAAACCCAt     >  5:235628/1‑149 (MQ=255)
                                                                                                                                     cATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGAAGTGCTGGTTGGCCGCCTGCGCCGCAAGCTTGAAGGCGAGCGCGGCTTCAAACCCATc    >  6:332695/1‑148 (MQ=255)
                                                                                                                                     cATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGAAGTGCTGGTTGGCCGCCTGCGCCGCAAGCTTGAAGGCGAGCGCGGCTTCAAACCCATc    >  1:332688/1‑148 (MQ=255)
                                                                                                                                      aTGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGAAGTGCTGGTTGGCCGCCTGCGCCGCAAGCTTGAAGGCGAGCGCGGCTTCAAACCCATCGa  >  1:15273/1‑149 (MQ=255)
                                                                                                                                              |                                                                                                                                            
GCCGCTCCAGTGGTTTCACCCAGTCGACCATCGCCGCTGGCCCCTTGGTGCTTGACCTCAACCGCAAGCAGGCCACCCTCGACGAACAAGCCTTGGCCCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGCCATCACCAGCAGGTGGTGGCCAAGGATCGCCTGATGGAGCAGTTGTACCCAGGAGACGAAGAGCGCGACCCCAATGTCATCGAAGTGCTGGTTGGCCGCCTGCGCCGCAAGCTTGAAGGCGAGCGCGGCTTCAAACCCATCGA  >  NC_002947/1361286‑1361568

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑