Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 562,705 C→T 8.3% A144V (GCA→GTA)  rpsD → 30S ribosomal protein S4

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947562,7050CT 8.3% 137.0 / 2.3 48A144V (GCA→GTA) rpsD30S ribosomal protein S4
Reads supporting (aligned to +/- strand):  ref base C (20/24);  new base T (2/2);  total (22/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.26e-01

GAGTGCCGTCTGGATAACGTCGTTTACCGTATGGGCTTCGGCTCGACTCGTTCCGAGTCCCGTCAGCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTGACGTGGATGCTGCTAAAAAGTCGGGCGTTTTCAAGAACGTTCCTGCTCGCAGCGACCT  >  NC_002947/562557‑562846
                                                                                                                                                    |                                                                                                                                                
gAGTGCCGTCTGGATAACGTCGTTTACCGTATGGGCTTCGGCTCGACTCGTTCCGAGTCCCGTCAGCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGc                                                                                                                                                  >  4:102124/1‑149 (MQ=255)
 aGTGCCGTCTGGATAACGTCGTTTACCGTATGGGCTCCGGCTCGACTCGTTCCGAGTCCCGTCAGCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCa                                                                                                                                                 <  1:279209/149‑1 (MQ=255)
   tGCCGTCTGGATAACGTCGTTTACCGTATGGGCTTCGGCTCGACTCGTTCCGAGTCCCGTCAGCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGt                                                                                                                                               <  2:20674/149‑1 (MQ=255)
            gATAACGTCGTTTACCGTATGGGCTTCGGCTCGACTCGTTCCGAGTCCCGTCAGCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCgaga                                                                                                                                    >  4:51773/1‑148 (MQ=255)
             aTAACGTCGTTTACCGTATGGGCTTCGGCTCGACTCGTTCCGAGTCCCGTCAGCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCga                                                                                                                                      <  4:108148/145‑1 (MQ=255)
             aTAACGTCGTTTACCGTATGGGCTTCGGCTCGACTCGTTCCGAGTCCCGTCAGCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCga                                                                                                                                      >  3:108148/1‑145 (MQ=255)
                   tcgtTTACCGTATGGGCTTCGGCTCGACTCGTTCCGAGTCCCGTCAGCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTTTACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTg                                                                                                                            <  8:159804/149‑1 (MQ=255)
                                 ggCTTCGGCTCGACTCGTTCCGAGTCCCGTCAGCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCa                                                                                                               <  3:102124/148‑1 (MQ=255)
                                            gACTCGTTCCGAGTCCCGTCACCTGGTATCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGCAATCGCTGGGCCAGTTGCGCATTGTTCAAGccc                                                                                                   >  5:251433/1‑149 (MQ=255)
                                               tCGTTCCGAGTCCCGTCAGCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAGACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCtt                                                                                                 >  1:202176/1‑148 (MQ=255)
                                                   tCCGAGTCCCGTCAGCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACt                                                                                            >  1:14483/1‑149 (MQ=255)
                                                     cGAGTCCCGTCTGCTGGTTTCGCTCAAAGCGATCTGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTGCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACtgt                                                                                          <  1:311720/149‑1 (MQ=255)
                                                     cGAGTCCCGTCAGCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACtgt                                                                                          <  2:14483/149‑1 (MQ=255)
                                                      gAGTCCCGTCAGCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCga                                                                                                                                      >  1:43868/1‑104 (MQ=255)
                                                      gAGTCCCGTCAGCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCga                                                                                                                                      <  2:43868/104‑1 (MQ=255)
                                                           ccGTCAGCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTAGTCGCAGTCAATAGCGAGAGATCGCTGGGCCAGTTGCGAATTGTTCAAGCCCTTGAAGTGTgcg                                                                                       >  1:102233/1‑149 (MQ=255)
                                                            cGTCAGCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTACGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCa                                                                                   <  6:251433/149‑1 (MQ=255)
                                                              tCAGCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGc                                                                                 >  1:211388/1‑149 (MQ=255)
                                                                 gCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTg                                                                              >  1:163883/1‑149 (MQ=255)
                                                                 gCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTg                                                                              <  3:206722/149‑1 (MQ=255)
                                                                  cTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTgg                                                                             >  6:56365/1‑149 (MQ=255)
                                                                         cGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGt                                                                       <  3:51773/148‑1 (MQ=255)
                                                                           cacaAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGtt                                                                      >  1:153192/1‑147 (MQ=255)
                                                                            acaAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAg                                                                   >  6:17129/1‑149 (MQ=255)
                                                                              aaaGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTg                                                                 >  7:183814/1‑149 (MQ=255)
                                                                               aaGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTgg                                                                <  5:31729/149‑1 (MQ=255)
                                                                               aaGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTgg                                                                <  2:202176/149‑1 (MQ=255)
                                                                                       aGCGTAAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTGActt                                                        <  7:203288/149‑3 (MQ=255)
                                                                                           tCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTGACGTGGAt                                                    >  7:228844/1‑149 (MQ=255)
                                                                                             aaCGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTGACGTGGAtgc                                                  <  8:183814/149‑1 (MQ=255)
                                                                                               cGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTGACGTGGAtgctg                                                <  5:17129/149‑1 (MQ=255)
                                                                                               cGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTGACGTGGAtgctg                                                <  2:163883/149‑1 (MQ=255)
                                                                                                  tAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACtgt                                                                                          <  2:67885/104‑1 (MQ=255)
                                                                                                  tAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACtgt                                                                                          >  1:67885/1‑104 (MQ=255)
                                                                                                          tAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGTAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTGACGTGGATGCTGCTAAAAAGTCg                                     >  2:205484/1‑149 (MQ=255)
                                                                                                          tAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGTAGTC‑‑‑CGCGAGAAATCGCTGCGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTGACGTGGATGCTGCTAAAAAGTCg                                     >  2:210032/1‑149 (MQ=255)
                                                                                                          tAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTGACGTGGATGCTGCTAAAAAGTc                                      <  8:228844/148‑1 (MQ=255)
                                                                                                           aaaCATTCCATCCTACCAACTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCTCATTGTTCAAGCCATTGAACTCTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTTACGTGGATGCTGATAAAAAGTCgc                                    >  6:169024/1‑148 (MQ=255)
                                                                                                            aaCATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTGACGTGGATGCTGCTAAAAAGTCggg                                   <  2:211388/149‑1 (MQ=255)
                                                                                                                   cATCCTACCAAGTTCGTCCGGGTGACGTGGTCGTAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTGACGTGGATGCTGCTAAAAAGTCGGGCGtttt                             <  1:210032/148‑1 (MQ=255)
                                                                                                                   cATCCTACCAAGTTCGTCCGGGTGACGTGGTCGTAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTGACGTGGATGCTGCTAAAAAGTCGGGCGtttt                             <  1:205484/148‑1 (MQ=255)
                                                                                                                     tCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAGATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTGACGTGGATGCTGCTAAAAAGTCGGGCGTTTTCaa                          <  2:102233/149‑1 (MQ=255)
                                                                                                                     tCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTGACGTGGATGCTGCTAAAAAGTCGGGCGTTTTCaa                          <  5:56365/149‑1 (MQ=255)
                                                                                                                      ccTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGt                                                                  <  2:315498/108‑1 (MQ=255)
                                                                                                                      ccTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGt                                                                  >  1:315498/1‑108 (MQ=255)
                                                                                                                         aCCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTGACGTGGATGCTGCTAAAAAGTCGGGCGTTTTCAAGAAc                      >  3:210541/1‑149 (MQ=255)
                                                                                                                          ccAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCCCTGGGCCAGTTGAGCATTGTTCAAGCCCTTCAACTCTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTGACGTGGATGCTGCTAAAAAGTCGGGCGTTTTCAAGAACg                     >  5:225644/1‑149 (MQ=255)
                                                                                                                                 cGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTGACGTGGATGCTGCTAAAAAGTCGGGCGTTTTCAAGAACGTTCCTg               <  7:116812/148‑1 (MQ=255)
                                                                                                                                             gTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTGACGTGGATGCTGCTAAAAAGTCGGGCGTTTTCAAGAACGTTCCTGCTCGCAGCGACCt  >  2:3544/1‑149 (MQ=255)
                                                                                                                                                    |                                                                                                                                                
GAGTGCCGTCTGGATAACGTCGTTTACCGTATGGGCTTCGGCTCGACTCGTTCCGAGTCCCGTCAGCTGGTTTCGCACAAAGCGATCAGCGTCAACGGTAAGACTGTAAACATTCCATCCTACCAAGTTCGTCCGGGTGACGTGGTCGCAGTC‑‑‑CGCGAGAAATCGCTGGGCCAGTTGCGCATTGTTCAAGCCCTTGAACTGTGCGCCCAGCGTGGCCGCGTTGAGTGGGTTGACGTGGATGCTGCTAAAAAGTCGGGCGTTTTCAAGAACGTTCCTGCTCGCAGCGACCT  >  NC_002947/562557‑562846

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: ‑