Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,546,648	A→G	7.1%	F149F (TTT→TTC)	rpsA ←	ribosomal protein S1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,546,648	0	A	G	7.1%	167.9 / 3.2	56	F149F (TTT→TTC)	rpsA	ribosomal protein S1
Reads supporting (aligned to +/- strand):  ref base A (25/27);  new base G (2/2);  total (27/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

ATCGCCTTCATTTAAAGATTGTAATAATTGATCTTTTTTAGCATCGTTTTCTTCTTGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAACTACTTCTGTTACTTTCGCTTCGATGATTTCATTATTATCTAATTTT  >  CP000730/1546510‑1546786                                                                                                                                           |                                                                                                                                           aTCGCCTTCATTTAAAGATTGTAATAATTGATCTTTTTTAGCATCGTTTTCTTCTTGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCaaa                                                                                                                                          >  1:223401/1‑141 (MQ=255)  tCGCCTTCATTTAAAGATTGTAATAATTGATCTTTTTTAGCATCGTTTTCTTCTTGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAac                                                                                                                                         <  2:157233/141‑1 (MQ=255)   cGCCTTCATTTAAAGATTGTAATAATTGATCTTTTTTAGCATCGTTTTCTTCTTGTGCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAaca                                                                                                                                        >  2:695761/1‑141 (MQ=255)    gCCTTCATTTAAAGATTGTAATAATTGATCTTTTTTAGCATCGTTTTCTTCTTGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAacac                                                                                                                                       >  1:106922/1‑141 (MQ=255)             tAAAGATTGTAATAATTGATCTTTTTTAGCATCGTTTTCTTCTTGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATc                                                                                                                              <  1:232514/141‑1 (MQ=255)             tAAAGATTGTAATAATTGATCTTTTTTAGCATCGTTTTCTTCTTGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATc                                                                                                                              >  2:557832/1‑141 (MQ=255)                  aTTGTAATAATTGATCTTTTTTAGCATCGTTTTCTTCTTGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCaa                                                                                                                         <  1:609421/141‑1 (MQ=255)                    tGTAATAATTGATCTTTTTTAGCATCGTTTTCTTCTTGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATg                                                                                                                       <  2:59347/141‑1 (MQ=255)                     gTAATAATTGATCTTTTTTAGCATCGTTTTCTTCTTGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAAtta                                                                                                                      >  2:272406/1‑139 (MQ=255)                     gTAATAATTGATCTTTTTTAGCATCGTTTTCTTCTTGTTCAAATGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGa                                                                                                                      <  2:116368/141‑1 (MQ=255)                           atTGATCTTTTTTAGCATCGTTTTCTTCTTGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTg                                                                                                                <  1:688176/141‑1 (MQ=255)                           atTGATCTTTTTTAGCATCGTTTTCTTCTTGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTg                                                                                                                <  2:202160/141‑1 (MQ=255)                                tCTTTTTTATCATCGTTTTCTTCTTGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGaa                                                                                                           >  2:160926/1‑141 (MQ=255)                                       tAGCATCGTTTTCTTCTTGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTg                                                                                                    >  2:194110/1‑141 (MQ=255)                                        aGCATCGTTTTCTTCTTGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGa                                                                                                   <  2:139914/141‑1 (MQ=255)                                          cATCGTTCTCCTCTTGATCAACTGATTTACGGCTTAAAATGCCTCTATTATTTTCAGGATCCACTTATTCAACTTTAATACGAATTGTTTGTCCATCAACCACCTAGAAATCCTAAATGTAGTCTGTTGACATCAGTGAAg                                                                                                 >  2:708326/1‑141 (MQ=255)                                                  tcttctTGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACa                                                                                         >  2:368627/1‑141 (MQ=255)                                                   cttcttGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACaa                                                                                        >  1:31352/1‑141 (MQ=255)                                                   cttcttGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACaa                                                                                        >  1:253248/1‑141 (MQ=255)                                                      cttGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGCTCCAACTCCCCACACTTAATACCACTTGCTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAAc                                                                                     <  1:66091/141‑1 (MQ=255)                                                        tGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACct                                                                                   <  2:386735/141‑1 (MQ=255)                                                         gTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAGATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACctc                                                                                  <  2:217384/141‑1 (MQ=255)                                                         gTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACctc                                                                                  <  2:217350/141‑1 (MQ=255)                                                             aaCTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTg                                                                              >  1:449071/1‑141 (MQ=255)                                                                   tttACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTAc                                                                        <  1:289186/141‑1 (MQ=255)                                                                     tACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACAt                                                                      <  1:349617/141‑1 (MQ=255)                                                                     tACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACAt                                                                      <  1:303529/141‑1 (MQ=255)                                                                       cGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACGCTGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATca                                                                    >  1:673957/1‑141 (MQ=255)                                                                           ttAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATcaacaa                                                                <  1:79607/141‑1 (MQ=255)                                                                                 tGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCGAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACaaccaaac                                                          >  2:82331/1‑141 (MQ=255)                                                                                 tGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCGAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACaaccaaac                                                          >  2:82291/1‑141 (MQ=255)                                                                                    ctctATTATTTTCAGGATCCAATTTTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAaccac                                                       >  1:693437/1‑141 (MQ=255)                                                                                       tattatTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCtt                                                    <  1:520268/141‑1 (MQ=255)                                                                                           attTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAac                                                >  1:265767/1‑141 (MQ=255)                                                                                           attTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAac                                                <  2:38243/141‑1 (MQ=255)                                                                                              ttCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCCACAACCAAACCACCTTTAactac                                             >  1:693546/1‑141 (MQ=255)                                                                                              ttCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAactac                                             >  2:182746/1‑141 (MQ=255)                                                                                                       cAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAACTACTTCTATTAc                                    >  2:623528/1‑141 (MQ=255)                                                                                                            cttcAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAACTACTTCTGTTACTTTCg                               >  1:308224/1‑141 (MQ=255)                                                                                                              tcAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAGATTAGTGAGGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAACTACTTCTGTTACTTTCGCt                             >  2:704929/1‑141 (MQ=255)                                                                                                                aaCGTTCATACGAGTTGTTTGTCCATCAAACACAGAGAAATTCTCAATGAAGTCTGTTAAAATTAGTGAAGGTGGAACAAGATCTCTTTGTCCTACATCAACAACCAAACCGCCTTGAGCTACTTGTGTTAATATCGCTTc                           <  2:392142/141‑1 (MQ=255)                                                                                                                 aCTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACaacc                                                              >  2:392389/1‑105 (MQ=255)                                                                                                                 aCTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACaacc                                                              <  1:392389/105‑1 (MQ=255)                                                                                                                 aCTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAACTACTTCTGTTACTTTCGCTTCg                          >  2:114615/1‑141 (MQ=255)                                                                                                                      aaTACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAACTACTTCTGTTACTTTCGCTTCgatgat                     <  2:34664/141‑1 (MQ=255)                                                                                                                            aaTTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAACTACTTCTGTTACTTTCGCTTCGATGATTTCatt               <  1:194649/141‑1 (MQ=255)                                                                                                                                gtttgtCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAACTACTTCTGTTACTTTCGCTTCGATGATTTCAttatta           >  2:597239/1‑141 (MQ=255)                                                                                                                                 tttgtCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCg                                                                                              >  2:470547/1‑57 (MQ=255)                                                                                                                                 tttgtCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCg                                                                                              <  1:470547/57‑1 (MQ=255)                                                                                                                                  ttgtCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAACTACTTCTGTTACTTTCGCTTCGATGATTTCATTATTATc         <  1:326167/141‑1 (MQ=255)                                                                                                                                  ttgtCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAACTACTTCTGTTACTTTCGCTTCGATGATTTCATTATTATc         <  1:56173/141‑1 (MQ=255)                                                                                                                                  ttgtCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAACTACTTCTGTTACTTTCGCTTCGATGATTTCATTATTATc         <  1:540756/141‑1 (MQ=255)                                                                                                                                  ttgcCCATCAAACACAGAGCAATCCTCAATGACGTCTGTTGGAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAACTACTCCTGTTACTTTCGCTTCGATGATTTCATTATTATc         >  2:308717/1‑141 (MQ=255)                                                                                                                                    gtCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAACTACTTCTGTTACTTTCGCTTCGATGATTTCATTATTATCTa       >  1:433955/1‑141 (MQ=255)                                                                                                                                      ccATCGAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAACTACTTCTGTTACTTTCGCTTCGATGATTTCATTATTATCTAAt     <  1:82291/141‑1 (MQ=255)                                                                                                                                      ccATCGAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAACTACTTCTGTTACTTTCGCTTCGATGATTTCATTATTATCTAAt     <  1:82331/141‑1 (MQ=255)                                                                                                                                         tCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAACTACTTCTGTTACTTTCGCTTCGATGATTTCATTATTATCTAAtttt  <  1:129201/141‑1 (MQ=255)                                                                                                                                           |                                                                                                                                           ATCGCCTTCATTTAAAGATTGTAATAATTGATCTTTTTTAGCATCGTTTTCTTCTTGTTCAACTGCTTTACGGCTTAAAATGACTCTATTATTTTCAGGATCCAATTCTTCAACTTTAATACGAATTGTTTGTCCATCAAACACAGAGAAATCCTCAATGAAGTCTGTTGAAATTAGTGAAGCCGGAACAAAACCTCTTTGTCCTACATCAACAACCAAACCACCTTTAACTACTTCTGTTACTTTCGCTTCGATGATTTCATTATTATCTAATTTT  >  CP000730/1546510‑1546786

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑