Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,000,840	A→T	7.1%	R52R (CGT→CGA)	PP_2624 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,000,840	0	A	T	7.1%	158.8 / 3.4	56	R52R (CGT→CGA)	PP_2624	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (25/27);  new base T (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 = 7.17e-01

CGAAATCGTTGATGGACCTGAACTGCAGGTGGACGGCCAGCTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGCCTGCTCATCGCTGGTAGCGGGGACATACTTGATATTGACGCGTTCTTTCGGCGCAACGGATCCCG  >  NC_002947/3000692‑3000982                                                                                                                                                     |                                                                                                                                                cGAAATCGTTGATGGACCTGAACTGCAGGTGGACGGCCAGCTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGa                                                                                                                                                 >  8:70627/1‑149 (MQ=255) cGAAATCGTTGATGGA‑CTGAACTGCAGGTGGACGGCCAGCTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGAc                                                                                                                                                >  5:162080/1‑149 (MQ=255)            aTGGACCTGAACTGCAGGTGGACGGCCAGCTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCaa                                                                                                                                       <  2:65388/148‑1 (MQ=255)            aTGGACCTGAACTGCAGGTGGACGGCCAGCTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCaa                                                                                                                                       <  7:70627/148‑1 (MQ=255)                gacTGAACTGCAGGTGGACGGCCAGCTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAgcgc                                                                                                                                   <  6:162080/146‑1 (MQ=255)                  cTGAACTGCAGGTGGACGGCCAGCTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACg                                                                                                                                >  6:330898/1‑149 (MQ=255)                  cTGAACTCCAGGTGGACGGCCAGCTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACg                                                                                                                                >  7:367599/1‑149 (MQ=255)                       cTGCAGGTGGACGGCCAGCTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGt                                                                                                                           >  6:405417/1‑149 (MQ=255)                             gTGGACGGCCAGCTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑c                                                                                                                      >  4:52553/1‑147 (MQ=255)                               ggACGGCCAGCTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAgg                                                                                                                  <  3:52553/149‑1 (MQ=255)                                gACGGCCAGCTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGc                                                                                                                 >  4:303497/1‑149 (MQ=255)                                  cGGCCAGCTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGcc                                                                                                                >  6:188738/1‑148 (MQ=255)                                    gCCAGCTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACATGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGaa                                                                                                             <  8:66777/149‑1 (MQ=255)                                     ccAGCTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑c                                                                                                                      <  6:376603/139‑1 (MQ=255)                                     ccAGCTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑c                                                                                                                      >  5:376603/1‑139 (MQ=255)                                         cTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGTCGGTCCTc                                                                                                                                         >  7:75879/1‑117 (MQ=255)                                         cTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGTCGGTCCTc                                                                                                                                         <  8:81592/117‑1 (MQ=255)                                         cTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGTCGGTCCTc                                                                                                                                         <  8:75879/117‑1 (MQ=255)                                         cTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGTCGGTCCTc                                                                                                                                         >  7:81592/1‑117 (MQ=255)                                         cTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGc                                                                                                        >  3:189027/1‑149 (MQ=255)                                            ggTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGccc                                                                                                      <  3:303497/148‑1 (MQ=255)                                            ggTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGcc                                                                                                       <  5:188738/147‑1 (MQ=255)                                            ggTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGcc                                                                                                       <  8:154184/147‑1 (MQ=255)                                                tCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCccagcac                                                                                                 <  4:189027/149‑1 (MQ=255)                                                  cGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCCTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATTACCTGACGCTACTCAAGCGCACCGCAGTAAT‑CCAGGCCGAAGTCGCccagcacc                                                                                                >  8:254083/1‑148 (MQ=25)                                                             cGAGCCTGGACGGTACCGTCACGTCCAGTCGCACTTTGGCGTCGTTCAACAGGCTGTTGAATGTATGTTTATATAAGCTCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCTAAGTCGCCCAGAACCAGCATCTTGTGc                                                                                    <  8:367599/149‑1 (MQ=255)                                                                gCCTGGACGTGACGGTACCGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATc                                                                                          >  1:148156/1‑140 (MQ=21)                                                                gCCTGGACGTGACGGTACCGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATc                                                                                          <  2:148156/140‑1 (MQ=21)                                                                  cTGGACGTGACGGTACCGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAg                                                                               <  3:372343/149‑1 (MQ=18)                                                                  cTGGACGTGACGGTACCGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAg                                                                               >  4:372343/1‑149 (MQ=18)                                                                  cTGGACGGTACCGTCACGTCCAGGCTCGCATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCgg                                                                                  >  8:189409/1‑146 (MQ=255)                                                                  cTGGACGGTACCGTCACGTCCAGGCTCGCATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCa                                                                                <  7:189409/148‑1 (MQ=255)                                                                        ggTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCAc                                                                         <  5:330898/149‑1 (MQ=255)                                                                        ggTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCAACAGCATCTTGTGCGGCAGCTCCAc                                                                         <  7:254083/149‑1 (MQ=255)                                                                              gTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGc                                                                   <  5:405417/149‑1 (MQ=255)                                                                                 aCGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGCCTg                                                                >  6:190498/1‑149 (MQ=255)                                                                                    tCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGCCTGCt                                                              >  8:283741/1‑148 (MQ=255)                                                                                      cAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGCCTGCTCAt                                                           <  1:369420/149‑1 (MQ=255)                                                                                             acaTTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACTTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGccc                                                                                                      <  1:86215/99‑1 (MQ=255)                                                                                             acaTTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGccc                                                                                                      >  2:86215/1‑99 (MQ=255)                                                                                               aTTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGCCTGCTCATCGCTGGTAg                                                  >  6:380835/1‑149 (MQ=255)                                                                                                    cgtcgtTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGCCTGCTCATCGCTGGTAGCggg                                              >  3:245839/1‑148 (MQ=255)                                                                                                         ttCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCgg                                                                                  >  7:226003/1‑107 (MQ=255)                                                                                                         ttCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCgg                                                                                  <  8:226003/107‑1 (MQ=255)                                                                                                           cAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGCCTGc                                                               <  6:168090/124‑1 (MQ=255)                                                                                                           cAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGCCTGc                                                               >  5:168090/1‑124 (MQ=255)                                                                                                                cGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGCCTGCTCATCGCTGGTAGCGGGGACATACTTGata                                 <  5:380835/149‑1 (MQ=255)                                                                                                                     ttGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTc                                                                      <  6:155244/107‑1 (MQ=255)                                                                                                                     ttGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGCCTGCTCATCGCTGGTAGCGGGGACATACTTGATATTGa                             <  4:245839/148‑1 (MQ=255)                                                                                                                        aaTGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGCCTGCTCATCGCTGGTAGCGGGGACATACTTGATATTGAcgcg                         >  6:160749/1‑149 (MQ=255)                                                                                                                                          cgcATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGCCTGCTCATCGCTGGTAGCGGGGACATACTTGATATTGACGCGTTCTTTCGGCGCAACgg        <  7:283741/148‑1 (MQ=255)                                                                                                                                           gcATGACCTGACGGTCCTCAAGCGCACGGCTGTCATACCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGCCTGCTCATCGCTg                                                      >  1:273466/1‑102 (MQ=255)                                                                                                                                           gcATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGCCTGCTCATCGCTg                                                      <  2:273466/101‑1 (MQ=255)                                                                                                                                           gcATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGCCTGCTCATCGCTGGTAGCGGGGACATACTTGATATTGAcgc                          <  2:298658/129‑1 (MQ=255)                                                                                                                                           gcATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGCCTGCTCATCGCTGGTAGCGGGGACATACTTGATATTGAcgc                          >  1:298658/1‑129 (MQ=255)                                                                                                                                               gACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGCCTGCTCATCGCTGGTAGCGGGGCCATAGGTGATATTGACGCGTTCTTTGGGCGCAGCGGagcgcg  >  4:302599/1‑144 (MQ=21)                                                                                                                                               gACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGCCTGCTCATCGCTGGTAGCGGGGACATACTTGATATTGACGCGTTCTTTCGGCGCAACGGATccag  >  4:72105/1‑147 (MQ=255)                                                                                                                                                     |                                                                                                                                                CGAAATCGTTGATGGACCTGAACTGCAGGTGGACGGCCAGCTCGGTATCCGGGGCGGTGCCGAGCCTGGACGGTACCGTCACGTCCAGGCTCACATTGGCGTCGTTCAACACGCTGTTGAATGTATGTTTATCGATGCGCATGACCTGACGGTCCTCAAGCGCACGGCTGTCAT‑CCAGGCCGAAGTCGCCCAGCACCAGCATCTTGTGCGGCAGCTCCACCTCAGCCTGCTCATCGCTGGTAGCGGGGACATACTTGATATTGACGCGTTCTTTCGGCGCAACGGATCCCG  >  NC_002947/3000692‑3000982

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: ‑