Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 2,810,100 G→T 12.1% M169I (ATG→ATT) ‡ thrS → threonine‑‑tRNA ligase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029472,810,1000GT12.1% 145.2 / 11.3 58M169I (ATG→ATT) ‡thrSthreonine‑‑tRNA ligase
Reads supporting (aligned to +/- strand):  ref base G (24/27);  new base T (3/4);  total (27/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.11e-01

GCGCATGATGGAGCTGATTGAAAAAGACTACGACGTGGTCAAGAAAATGACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACTGGCGTGGCGATGCCAAGAACGAGCAGCTTCAGCGCGT  >  NC_002947/2809959‑2810243
                                                                                                                                             |                                                                                                                                               
gcgcATGATGGAGCTGATTGAAAAAGACTACGACGTGGTCAAGAAAATGACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGt                                                                                                                                          <  4:94031/149‑1 (MQ=255)
 cgcATGATGGAGGTGATTGAAAAAGACTTCGACGTGGTCAAGAAAATGACCCCGCGCGCCGAAGTCATCGATGTGTTCACGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATTCCGGATGAACAGGCCCATGGCCTGtt                                                                                                                                         <  6:443486/149‑2 (MQ=255)
   cATGATGGAGCTGATTGAAAAAGACTACGACGTGGTCAAGAAAATGACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGtac                                                                                                                                        >  5:406948/1‑148 (MQ=255)
    atgatgGAGCTGATTGAAAAAGACTACGACGTGGTCAAGAAAATGACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGtacta                                                                                                                                      <  5:171312/149‑1 (MQ=255)
    atgatgGAGCTGAATGAAAAAGACTACGACGTGGTCAAGAAAATGACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGGGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCCATGGCCTGttcat                                                                                                                                      <  7:399526/149‑5 (MQ=255)
     tgatgGAGCTGATTGAAAAAGACTACGACGTGGTCAAGAAAATGACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCCATGGCCTGttcatc                                                                                                                                     <  7:56949/149‑6 (MQ=255)
        tgGAGCTGATTGAAAAAGACTACGACGTGGTCAAGAAAATGACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCAc                                                                                                                                  <  1:117748/149‑1 (MQ=255)
                 ttGAAAAAGACTACGACGTGGTCAAGAAAATGACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATAc                                                                                                                         <  4:378901/149‑1 (MQ=255)
                    aaaaaGACTACGACGTGGTCAAGAAAATGACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGt                                                                                                                       <  8:311075/148‑1 (MQ=255)
                    aaaaaGACTACGACGTGGTCAAGAAAATGACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTc                                                                                                                      >  6:202026/1‑149 (MQ=255)
                         gACTACGACGTGGTCAAGAAAATGACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACAt                                                                                                                 <  2:426737/149‑1 (MQ=255)
                                acgTGGTCAAGAAAATGACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACgaa                                                                                                                               <  1:386456/128‑1 (MQ=255)
                                acgTGGTCAAGAAAATGACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACgaa                                                                                                                               >  2:386456/1‑128 (MQ=255)
                                      tCAAGAAAATGACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCg                                                                                                    <  5:114092/149‑1 (MQ=255)
                                        aaGAAAATGACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCa                                                                                                  >  1:254820/1‑149 (MQ=255)
                                        aaGAAAATGACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCa                                                                                                  >  7:406539/1‑149 (MQ=255)
                                        aaGAAAATGACCCCGCGCGCCGAAGTCAACGATGTGTTCAAGGCCCGTGGCGAAGACAAAAAGAGGGGGCGGGTGGAAGAAATGCCGGATAAAAAGGCCAAGGGACGGGACGACACCGAAAAAAACGGCGACAAGGGCGGGGGGCCGcc                                                                                                  >  2:391165/1‑148 (MQ=255)
                                           aaaaTGACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGt                                                                                               >  5:319024/1‑149 (MQ=255)
                                                gACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACAtgtg                                                                                                              <  3:359384/129‑1 (MQ=255)
                                                gACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACAtgtg                                                                                                              >  4:359384/1‑129 (MQ=255)
                                                  ccccGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTCGCGAAGACTAAAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACCTGTGAAGTGGCCCGCACGTGCCGAac                                                                                        >  6:6614/1‑149 (MQ=255)
                                                           ccGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTc                                                                               <  4:95222/149‑1 (MQ=255)
                                                                       aTGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTc                                                                   <  6:406948/149‑1 (MQ=255)
                                                                         gtgtTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTcc                                                                              <  7:78073/136‑1 (MQ=255)
                                                                         gtgtTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTcc                                                                              >  8:78073/1‑136 (MQ=255)
                                                                          tgtTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAg                                                                <  4:428121/149‑1 (MQ=255)
                                                                            ttCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCt                                                              >  8:338522/1‑149 (MQ=255)
                                                                             tCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCa                                                                                                  >  7:279033/1‑112 (MQ=255)
                                                                             tCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCa                                                                                                  <  8:279033/112‑1 (MQ=255)
                                                                              cAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATTCGTCGACATGTGCCGTGGCCCGCAAGTGCCGAACACCCGCTTCCTCAAGGCATTAAAggata                                                            >  8:269457/1‑145 (MQ=255)
                                                                                           gAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCAGTCAAGCTGACCAAGCTGTCCgg                                               >  4:130746/1‑149 (MQ=255)
                                                                                                 tACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCGCGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTa                                         >  6:263838/1‑149 (MQ=255)
                                                                                                 tACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTa                                         >  7:111267/1‑149 (MQ=255)
                                                                                                   cAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTAc                                        <  8:111267/148‑1 (MQ=255)
                                                                                                   cAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACt                                       >  5:280187/1‑149 (MQ=255)
                                                                                                      gCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACtggc                                    >  7:328141/1‑149 (MQ=255)
                                                                                                      gCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCGGTCCGGCGCCTACtggc                                    >  6:347636/1‑149 (MQ=255)
                                                                                                          cGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACtggcgtgg                                <  8:406539/149‑1 (MQ=255)
                                                                                                            tCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACaggcgtggc                               >  3:381325/1‑148 (MQ=255)
                                                                                                               ggTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACTGGCGTGGCGATg                           >  7:300378/1‑149 (MQ=255)
                                                                                                                gTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACTGGCGTGGCGAt                            <  6:319024/147‑1 (MQ=255)
                                                                                                                 tCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACTGGCGTGGCGATGcc                         <  8:300378/149‑1 (MQ=255)
                                                                                                                      gACATGCCGTATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACTGGCGTGGCGATGCCAAGaa                    <  7:269457/149‑1 (MQ=255)
                                                                                                                      gACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACTGGCGTGGCGATGCCAAGaa                    <  4:381325/149‑1 (MQ=255)
                                                                                                                      gACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACTGGCGTGGCGATGCCAAGaa                    <  7:121758/149‑1 (MQ=255)
                                                                                                                       aCATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCGCGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACTGGCGTGGCGATGCCAAGAAc                   <  5:263838/149‑1 (MQ=255)
                                                                                                                       aCATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACTGGCGTGGCGATGCCAAGAAc                   <  1:391165/149‑1 (MQ=255)
                                                                                                                        cATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCAGTGGCCCGCACGTGCCGAACACCAGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACTGGCGTGGCGATGCCAAGAAc                   <  2:340721/148‑1 (MQ=255)
                                                                                                                            ccGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACTGGCGTGGCGATGCCAAGAACGagc               <  5:202026/148‑1 (MQ=255)
                                                                                                                             tggtagtaCAGGCCCATGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACTGGTGTGGCGATGCCAAGAACGagcag             >  3:210856/8‑149 (MQ=255)
                                                                                                                               gATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACTGGCGTGGCGATGCCAAGAACGag                >  3:362954/1‑144 (MQ=255)
                                                                                                                               gATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACTGGCGTGGCGATGCCAAGAACGag                <  4:362954/144‑1 (MQ=255)
                                                                                                                                 agtaCAGGCCCATGGCCTGTACTACCACGAAGAATACGTCGACATGTGCTGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACTGGCGTGGCGATGCCAAGAACGagcagc            <  6:139179/143‑1 (MQ=255)
                                                                                                                                 agtaCAGGCCCATGGCCTGTACTACCACGAAGAATACGTCGACATGTGCTGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACTGGCGTGGCGATGCCAAGAACGagcagc            >  5:139179/4‑146 (MQ=255)
                                                                                                                                   taCAGGCCCATGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACTGGCGTGGCGATGCCAAGAACGAGCAGCtt          >  8:183888/2‑146 (MQ=255)
                                                                                                                                        gCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACTGGCGTGGCGATGCCAAGAACGAGCAGCTTCAGCGCgt  >  1:317055/1‑149 (MQ=255)
                                                                                                                                          cATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGc                                                      <  6:358661/95‑1 (MQ=255)
                                                                                                                                          cATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGc                                                      >  5:358661/1‑95 (MQ=255)
                                                                                                                                             |                                                                                                                                               
GCGCATGATGGAGCTGATTGAAAAAGACTACGACGTGGTCAAGAAAATGACCCCGCGCGCCGAAGTCATCGATGTGTTCAAGGCCCGTGGCGAAGACTACAAGCTGCGTCTGGTCGAAGACATGCCGGATGAACAGGCCATGGGCCTGTACTACCACGAAGAATACGTCGACATGTGCCGTGGCCCGCACGTGCCGAACACCCGCTTCCTCAAGGCATTCAAGCTGACCAAGCTGTCCGGCGCCTACTGGCGTGGCGATGCCAAGAACGAGCAGCTTCAGCGCGT  >  NC_002947/2809959‑2810243

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: ‑