Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,097,121	T→C	9.1%	V42A (GTT→GCT)	PP_2705 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,097,121	0	T	C	9.1%	149.7 / 5.4	55	V42A (GTT→GCT)	PP_2705	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (27/23);  new base C (3/2);  total (30/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.90e-01

GCTCTGAGCCGAAGCGCGTCGTGACAGGCTTCATCCCGTTATCGTCGCTCTGGCGATTCACACCGACGGACCAGGCTCGGTCCAAAGAGGGTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCACCAGGTTTCAGAACCAGTGCCAGCTGTTTTATGCCGAAGT  >  NC_002947/3096977‑3097262                                                                                                                                                   |                                                                                                                                              gCTCTGAGCCGAAGCGCGTCGTGACAGGCTTCATCCCGTTATCGTCGCTCTGGCGATTCACACCGACGGACCAGGCTCGGTCCAAAGAGGGTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGaa                                                                                                                                           <  5:266745/149‑1 (MQ=255)           gAAGCGCGTCGTGACAGGCTTCATCCCGTTATCGTCGCTCTGGCGATTCACACCGACGGACCAGGCTCGGTCCAAAGAGGGTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGCTTCAACctgctgca                                                                                                                                 <  8:137893/149‑3 (MQ=255)                   tcgtGACAGGCGTCATCCCGGTTTCGTCGCTCGTGCGATTCAAACCGACGGACCAGGCTCGGGCCCAACTCGGTGCTGCAATGGCGTCTATCGAGTACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGta                                                                                                                          <  1:251659/149‑1 (MQ=255)                          aGGCTTCATCCCGTTATCGTCGCTCTGGCGATTCACACCGACGGACCAGGCTCGGTCCAAAGAGGGTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGt                                                                                                                  >  1:245014/1‑149 (MQ=255)                            gCTTCATCCCGTTATCGTCGCTCTGGCGATTCACACCGACGGACCAGGCTCGGTCCAAAGAGGGTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAGGGGGCTGCCAGCAGGCTTCAACctgctgcagc                                                                                                                               >  2:250601/1‑131 (MQ=255)                            gCTTCATCCCGTTATCGTCGCTCTGGCGATTCACACCGACGGACCAGGCTCGGTCCAAAGAGGGTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAGGGGGCTGCCAGCAGGCTTCAACctgctgcagc                                                                                                                               <  1:250601/135‑5 (MQ=255)                                  tCCCGTTATCGTCGCTCTGGCGATTCACACCGACGGACCAGGCTCGGTCCAAAGAGGGTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCgg                                                                                                          >  6:108602/1‑149 (MQ=255)                                   cccGTTATCGTCGCTCTGGCGATTCACACCGACGGACCAGGCTCGGTCCAAAGAGGGTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGCCGTATACCTCGTCACAGCGGc                                                                                                         >  8:209392/1‑149 (MQ=255)                                            gtcgCTCTGGCGATTCACACCGACGGACCAGGCTCGGTCCAAAGAGGGTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGaa                                                                                                 <  5:108602/148‑1 (MQ=255)                                               gCTCTGGCGATTCACACCGACGGACCAGGCTCGGTCCAAAGAGGGTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGcc                                                                                             >  8:250807/1‑149 (MQ=255)                                                     gCGATTCACACCGACGGACCAGGCTCGGTCCAAAGAGGGTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTcgcg                                                                                        <  7:250807/148‑1 (MQ=255)                                                              acCGACGGACCAGGCTCGGTCCAAAGAGGGTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAg                                                                                                >  4:143811/1‑131 (MQ=255)                                                              acCGACGGACCAGGCTCGGTCCAAAGAGGGTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAg                                                                                                <  3:143811/131‑1 (MQ=255)                                                                    ggACCAGGCTCGGTCCAAAGATGGTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGaa                                                                                                 <  6:85693/124‑1 (MQ=255)                                                                               ggTCCAAAGAGGGTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGa                                                              >  6:142548/1‑148 (MQ=255)                                                                                gTCCAAAGAGGGTGCTGCAATGGCGACAATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGAGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGaaa                                                            >  1:183456/1‑149 (MQ=255)                                                                                    aaaGAGGGTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGAc                                                                               >  6:153105/1‑126 (MQ=255)                                                                                    aaaGAGGGTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGAc                                                                               <  5:153105/126‑1 (MQ=255)                                                                                         gggTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCAtt                                                                <  6:220875/136‑1 (MQ=255)                                                                                         gggTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCAtt                                                                >  5:220875/1‑136 (MQ=255)                                                                                          ggTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAACCCGCCAACcg                                                  >  8:306520/1‑149 (MQ=255)                                                                                          ggTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGACACCcg                                                  >  8:20519/1‑149 (MQ=255)                                                                                            tgctgcAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACcgc                                                 >  7:308557/1‑148 (MQ=255)                                                                                               tgcAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGa                                               >  3:229376/1‑147 (MQ=255)                                                                                               tgcAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGa                                               <  4:229376/147‑1 (MQ=255)                                                                                                gcAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATAcc                                                                                                                      >  8:44105/1‑75 (MQ=255)                                                                                                gcAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATAcc                                                                                                                      <  7:44105/75‑1 (MQ=255)                                                                                                gcAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGAttt                                            >  7:98738/1‑149 (MQ=255)                                                                                                   aTGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCAc                                         <  5:142548/149‑1 (MQ=255)                                                                                                        gACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCACCAGGt                                    >  2:33455/1‑149 (MQ=255)                                                                                                             tCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCg                                                                                                                            <  1:286407/56‑1 (MQ=255)                                                                                                             tCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCg                                                                                                                            >  2:286407/1‑56 (MQ=255)                                                                                                             tCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCACCAGGttt                                  >  3:110897/1‑146 (MQ=255)                                                                                                                a‑cacCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCACCAGGTTTCa                                >  4:183717/1‑145 (MQ=255)                                                                                                                a‑cacCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCACCAGGTTTCa                                <  3:183717/145‑1 (MQ=255)                                                                                                                a‑cacCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCACCAGGTTTCAGAAc                            <  7:209392/149‑1 (MQ=255)                                                                                                                     cGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCACCCGCGAt                                              >  8:254181/1‑127 (MQ=255)                                                                                                                       agaACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCg                                                                             <  1:257192/94‑1 (MQ=255)                                                                                                                       agaACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCg                                                                             >  2:257192/1‑94 (MQ=255)                                                                                                                             ttGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCACCAGGTTTCAGAACCAGTGCCAGCTg                >  2:128349/1‑149 (MQ=255)                                                                                                                                 aaaGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGa                                               <  5:306038/114‑1 (MQ=255)                                                                                                                                 aaaGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGa                                               >  6:306038/1‑114 (MQ=255)                                                                                                                                 aaaGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCACCAGGTTTCa                                <  4:111790/129‑1 (MQ=255)                                                                                                                                 aaaGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCACCAGGTTTCa                                >  3:111790/1‑129 (MQ=255)                                                                                                                                 aaaGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCACCAGGTTTCAGAACCAGt                        >  6:86536/1‑137 (MQ=255)                                                                                                                                 aaaGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCACCAGGTTTCAGAACCAGt                        <  5:86536/137‑1 (MQ=255)                                                                                                                                   aGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACGGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCACCAGGTTTCAGAACCAGTGCCAGCTGTTTTAt          <  5:143385/149‑1 (MQ=255)                                                                                                                                   aGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCACCAGGTTTCAGAACCAGTGCCAGCTGTTTTAt          <  8:308557/149‑1 (MQ=255)                                                                                                                                        ctgccagcagGCTTCAACCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCACCAGGTTTCAGAACCAGTGCCCGCTGTTTTATGcc       >  4:10774/5‑148 (MQ=255)                                                                                                                                           ccagcagGCTTCAACCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTTCCATTGAAACCGCCAACCGCGATTTCACCAGGTTTCAGAACCAGTGCCAGCTGTTTTATGCCGAAg   >  3:223001/2‑149 (MQ=255)                                                                                                                                            cagcagGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCACCAGGTTTCAGAACCAGTGCCAGCTGTTTTATGCCGAAGt  <  8:98738/149‑1 (MQ=255)                                                                                                                                              gcagGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCACCAGGTTTCAGAACCAGTGTCAGCTGttt             >  6:274344/1‑136 (MQ=255)                                                                                                                                              gcagGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCACCAGGTTTCAGAACCAGTGTCAGCTGttt             <  5:274344/136‑1 (MQ=255)                                                                                                                                                 ggTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAACCCGCCAACCGCGATTTCACCAGGTTTCAGAACCAGTGCCAGCTGTTTTa           >  6:331121/1‑135 (MQ=255)                                                                                                                                                 ggTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCACCAGGTTTCAGAACCAGTGCCAGCTGTTTTa           <  5:331121/135‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                              GCTCTGAGCCGAAGCGCGTCGTGACAGGCTTCATCCCGTTATCGTCGCTCTGGCGATTCACACCGACGGACCAGGCTCGGTCCAAAGAGGGTGCTGCAATGGCGACTATCGA‑CACCGAGAACCTTGCAAAGGGGCTG‑CAGCAGGTTGAAGCCTGCTGGCAGGCGTATACCTCGTCACAGCGGCTTGTCGAAGGCCTCGCGGGCAGCGACCGGAGCAGTGCCATTGAAACCGCCAACCGCGATTTCACCAGGTTTCAGAACCAGTGCCAGCTGTTTTATGCCGAAGT  >  NC_002947/3096977‑3097262

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: ‑