Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,426,204	G→C	7.4%	E29Q (GAA→CAA)	PP_3919 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,426,204	0	G	C	7.4%	169.8 / 4.7	54	E29Q (GAA→CAA)	PP_3919	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (23/27);  new base C (2/2);  total (25/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.65e-01

CAGCAGCTGCGACTGACCACCAACCTGCCGCCACCGGCGGCGTGGAGACCATCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATCGACACCTTGCCGGTCGCACCAGCCCCACCACCAACGCCCGCCTGGACCCCTGAT  >  NC_002947/4426065‑4426347                                                                                                                                            |                                                                                                                                                cagcagCTGCGACTGACCACCAACCTGCCGCCACCGGCGGCGTGGAGACCATCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAgg                                                                                                                                          <  4:247124/147‑1 (MQ=255) cagcagCTGCGACTGACCACCAACCTGCCGCCACCGGCGGCGTGGAGACCATCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCt                                                                                                                                        >  5:187203/1‑149 (MQ=255) cagcagCTGCGACTGACCACCAACCTGCCGCCACCGGCGGCGTGGAGACCATCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCt                                                                                                                                        <  1:181188/149‑1 (MQ=255)  agcagcTGCGACTGACCACCAACCTGCCGCCACCGGCGGCGTGGAGACCATCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTg                                                                                                                                       <  1:262992/149‑1 (MQ=255)    cagcTGCGACTGACCACCAACCTGCCGCCACCGGCGGCGTGGAGACCATCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGc                                                                                                                                     <  2:256648/149‑1 (MQ=255)             cTGACCACCAACCTGCCGCCACCGGCGGCGTGGAGACCATCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTtcgtc                                                                                                                             >  5:105656/1‑148 (MQ=255)                accaccAACCTGCCGCCACCGGCGGCGTGGAGACCATCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCga                                                                                                                           >  1:133349/1‑147 (MQ=255)                  caccaACCTGCCGCCACCGGCGGCGTGGAGACCATCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGc                                                                                                                       >  2:173736/1‑149 (MQ=255)                     caACCTGCCGCCACCGGCGGCGTGGAGACCATCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCcgc                                                                                                                    >  2:314687/1‑149 (MQ=255)                         cTGCCGCCACCGGCGGCGTGGAGACCATCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCGCTTCGTCGAGAGCCgcggcg                                                                                                                >  5:351043/1‑149 (MQ=255)                         cTGCCGCCACCGGCGGCGTGGAGACCATCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCgaga                                                                                                                         <  1:169543/140‑1 (MQ=255)                         cTGCCGCCACCGGCGGCGTGGAGACCATCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCCTTGGCTAACAGAAAAATGCTGGCACTTAGTCgaga                                                                                                                         >  2:169543/1‑140 (MQ=255)                               ccACCGGCGGCGTGGAGACCATCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGcggccggc                                                                                                          <  2:133349/149‑1 (MQ=255)                                  ccGGCGGCGTGGAGACCATCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCGCTTCGTCGAGAGCCGCGGCGGCCGGCCAc                                                                                                       <  6:351043/149‑1 (MQ=255)                                           tGGAGACCATCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGgcc                                                                                              <  2:287169/149‑1 (MQ=255)                                               gaCCATCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAATAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCa                                                                                          <  1:277220/149‑1 (MQ=255)                                                  cATCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCCCTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTa                                                                                       >  7:283697/1‑149 (MQ=255)                                                   aTCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCa                                                                                          >  3:152444/1‑145 (MQ=255)                                                   aTCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCa                                                                                          <  4:152444/145‑1 (MQ=255)                                                       cATGAAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTAcgccc                                                                                  >  7:93905/1‑149 (MQ=255)                                                          ggAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTAcgcccgc                                                                                >  6:331983/1‑148 (MQ=255)                                                                 gAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCt                                                                        >  7:62057/1‑149 (MQ=255)                                                                       cTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAgcg                                                                   <  1:173736/148‑1 (MQ=255)                                                                                gAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGGGGCAGCGCCGTTGGCTAACAGAAAATGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGAt                                                         <  8:26076/149‑1 (MQ=255)                                                                                 aaGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATc                                                        <  6:187203/149‑1 (MQ=255)                                                                                 aaGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATc                                                        <  6:105656/149‑1 (MQ=255)                                                                                  agagCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTAcgc                                                                                    <  3:20410/120‑1 (MQ=255)                                                                                  agagCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTAcgc                                                                                    >  4:20410/1‑120 (MQ=255)                                                                                   gagCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATCGa                                                      <  8:93905/149‑1 (MQ=255)                                                                                         gtggCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATCGACACCtt                                                <  1:314687/149‑1 (MQ=255)                                                                                           ggCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATCGACACCTTGc                                              >  1:312534/1‑149 (MQ=255)                                                                                            gCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATCGACACCTTGc                                              <  5:331983/148‑1 (MQ=255)                                                                                              gATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATCGACACCTTGCCgg                                           >  2:134540/1‑149 (MQ=255)                                                                                                   ccGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCgtgg                                                             <  8:31193/126‑1 (MQ=255)                                                                                                   ccGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCgtgg                                                             >  7:31193/1‑126 (MQ=255)                                                                                                   ccGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATCGACACCTTGCCGGTCGCa                                      >  3:20095/1‑149 (MQ=255)                                                                                                   ccGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATCGACACCTTGCCGGTCGCa                                      >  6:19647/1‑149 (MQ=255)                                                                                                   ccGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACACAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAgcg                                                                   <  4:46616/120‑1 (MQ=255)                                                                                                   ccGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACACAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAgcg                                                                   >  3:46616/1‑120 (MQ=255)                                                                                                   ccGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACACAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAgcg                                                                   >  3:51503/1‑120 (MQ=255)                                                                                                   ccGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACACAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAgcg                                                                   <  4:51503/120‑1 (MQ=255)                                                                                                          cAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATCGACACCTTGCCGGTCGCAc                                     <  3:163829/143‑1 (MQ=255)                                                                                                          cAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATCGACACCTTGCCGGTCGCAc                                     >  4:163829/1‑143 (MQ=255)                                                                                                          cAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATCGACACCTTGCCGGTCGCACCAGc                                 <  6:34589/147‑1 (MQ=255)                                                                                                          cAAACCCCGGGCGTAGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGACGCTCAGCGGCGTGGGGATCGACACCTTGCCGGTCGCACCAGcac                               >  6:343167/1‑147 (MQ=255)                                                                                                             aCCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATCGACACCTTGc                                              >  7:71144/1‑131 (MQ=255)                                                                                                             aCCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATCGACACCTTGc                                              <  8:71144/131‑1 (MQ=255)                                                                                                                 cGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATCGACACCTTGCCGGTCGCACCAGCCccaccacc                        <  5:19647/149‑1 (MQ=255)                                                                                                                  gggCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATCGACACCTTGCCGGTCGCACCAGCCccaccacca                       <  8:62057/149‑1 (MQ=255)                                                                                                                        ggCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATCGACACCTTGCCGGTCg                                        <  6:245322/126‑1 (MQ=255)                                                                                                                        ggCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATCGACACCTTGCCGGTCg                                        >  5:245322/1‑126 (MQ=255)                                                                                                                           aGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGgcc                                                                                              <  3:32797/69‑1 (MQ=255)                                                                                                                           aGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGgcc                                                                                              >  4:32797/1‑69 (MQ=255)                                                                                                                                         aCAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATCGACACCTTGCCGGTCGCACCAGCCCCACCACCAACGCCCGCCTGGACCCCTGAt  <  2:312534/147‑1 (MQ=255)                                                                                                                                            |                                                                                                                                                CAGCAGCTGCGACTGACCACCAACCTGCCGCCACCGGCGGCGTGGAGACCATCCCATGGAAACCGAAATCCTTTCGGACGAAGAGCTGGTGGCGATCACCGGCTACAAACCCCGGGCGTGGCAGCGCCGTTGGCTAACAGAAAAAGGCTGGCACTTCGTCGAGAGCCGCGGCGGCCGGCCACTGGTTGGCCGCCAGTACGCCCGCCAGAAGCTCAGCGGCGTGGTGATCGACACCTTGCCGGTCGCACCAGCCCCACCACCAACGCCCGCCTGGACCCCTGAT  >  NC_002947/4426065‑4426347

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: ‑