Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,655,763	T→A	8.0%	L220M (TTG→ATG)	PP_4118 →	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,655,763	0	T	A	8.0%	139.7 / 2.8	50	L220M (TTG→ATG)	PP_4118	membrane protein
Reads supporting (aligned to +/- strand):  ref base T (26/20);  new base A (2/2);  total (28/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.56e-01

CGGCCTGTTCGTGTTCTCCGACAGCCTGATCGGCATCGACCGCTTCATCAGCCCGTTCGCCGCCGCACCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTT‑TACAAGGCGCAGAACAGCGAAATTCGAGCGCAGCAGTTCAAATGATATTA  >  NC_002947/4655615‑4655900                                                                                                                                                     |                                                                                                                                            cGGCCTGTTCGTGTTCTCCGACAGCCTGATCGGCATCGACCGCTTCATCAGCCCGTTCGCCGCCGCACCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCAGCGCTTCATCAGTAGGTCATCGCTCAGCCGATAAAGTAt                                                                                                                                             >  4:65478/1‑149 (MQ=255)     cTGTTCGTGTTCTCCGACAGCCTGATCGGCATCGACCGCTTCATCAGCCCGTTCGCCGCCGCACCGTACCTGATCCTCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAc                                                                                                                                         >  2:80387/1‑149 (MQ=255)           gtgtTCTCCGACAGCCTGATCGGCATCGACCGCTTCATCAGCCCGTTCGCCGCCGCACCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCagag                                                                                                                                  >  2:180561/1‑149 (MQ=255)                ctcCGACAGCCTGATCGGCATCGACCGCTTCATCAGCCCGTTCGCCGCCGCACCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGa                                                                                                                                          <  1:132028/137‑1 (MQ=255)                ctcCGACAGCCTGATCGGCATCGACCGCTTCATCAGCCCGTTCGCCGCCGCACCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGa                                                                                                                                          >  2:132028/1‑137 (MQ=255)                    gACAGCCTGATCGGCATCGACCGCTTCATCAGCCCGTTCGCCGCCGCACCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTgcgcg                                                                                                                         <  7:5745/149‑1 (MQ=255)                              tCGGCATCGACCGCTTCATCAGCCCGTTCGCCGCCGCACCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGAcc                                                                                                                  >  4:126710/1‑146 (MQ=255)                              tCGGCATCGACCGCTTCATCAGCCCGTTCGCCGCCGCACCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGAcc                                                                                                                  >  2:189065/1‑146 (MQ=255)                                 gCATCGACCGCTTCATCAGCCCGTTCGCCGCCGCACCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAgc                                                                                                            >  6:63447/1‑149 (MQ=255)                                      gACCGCTTCATCAGCCCGTTCGCCGCCGCACCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAgctgc                                                                                                         >  8:91011/1‑147 (MQ=255)                                       aCCGCTTCATCAGCCCGTTCGCCGCCGCACCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGACACCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTa                                                                                                       <  1:43019/149‑1 (MQ=255)                                       aCCGCTTCATCAGCCCGTTCGCCGCCGCACCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAgctgc                                                                                                         >  2:43019/1‑146 (MQ=255)                                                    cccGTTCGCCGCCGCACCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGaa                                                                                                    >  5:299780/1‑138 (MQ=255)                                                    cccGTTCGCCGCCGCACCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGaa                                                                                                    <  6:299780/138‑1 (MQ=255)                                                                 gcACCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTAtt                                                                                                                                            <  1:30758/86‑1 (MQ=255)                                                                 gcACCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTAtt                                                                                                                                            >  2:30758/1‑86 (MQ=255)                                                                   aCCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTAATGAC‑CCAGAGCGGTGCGCGCAGGACCgag                                                                                                               <  2:270667/112‑1 (MQ=255)                                                                   aCCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTAATGAC‑CCAGAGCGGTGCGCGCAGGACCgag                                                                                                               <  2:274250/112‑1 (MQ=255)                                                                   aCCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTAATGAC‑CCAGAGCGGTGCGCGCAGGACCgag                                                                                                               >  1:270667/1‑112 (MQ=255)                                                                   aCCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTAATGAC‑CCAGAGCGGTGCGCGCAGGACCgag                                                                                                               >  1:274250/1‑112 (MQ=255)                                                                     cGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAggg                                                                        <  7:96025/149‑1 (MQ=255)                                                                             atcatcCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGc                                                                >  6:261642/1‑149 (MQ=255)                                                                                      gCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAAc                                                       >  7:68821/1‑149 (MQ=255)                                                                                          aCTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACtt‑t                                                   >  5:184645/1‑148 (MQ=255)                                                                                           cTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTT‑Ta                                                  >  5:220573/1‑148 (MQ=255)                                                                                           cTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTT‑Ta                                                  >  1:151374/1‑148 (MQ=255)                                                                                              gCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGtttttt                                                                                         >  4:34464/1‑107 (MQ=255)                                                                                              gCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGtttttt                                                                                         <  3:34464/107‑1 (MQ=255)                                                                                              gCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTT‑TACAAg                                              >  5:199373/1‑149 (MQ=255)                                                                                                 cGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTT‑TACAAGgcg                                           <  6:220573/149‑1 (MQ=255)                                                                                                  ggCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTT‑TACAAGgcg                                           >  4:149796/1‑148 (MQ=255)                                                                                                  ggCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTT‑TACAAGgc                                            <  3:126710/147‑1 (MQ=255)                                                                                                    ccAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCACCAGATGAACTT‑TACAAGgcg                                           >  6:192571/1‑146 (MQ=255)                                                                                                     cAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTT‑TACAAGGCGCAGa                                       <  8:68821/149‑1 (MQ=255)                                                                                                     cAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTT‑TACAAGGCGCAGa                                       <  1:189065/149‑1 (MQ=255)                                                                                                      aaTGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTttg                                                                                       <  1:280820/101‑1 (MQ=255)                                                                                                      aaTGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTttg                                                                                       >  2:280820/1‑101 (MQ=255)                                                                                                             cATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTT‑TACAAGGCGCAGAACAGCGa                                >  6:304748/1‑148 (MQ=255)                                                                                                                 gCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTT‑TACAAGGCGCAGAACAGCGAAATTc                           <  8:55085/149‑1 (MQ=255)                                                                                                                   ttCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAAc                                                                                                   >  4:275527/1‑76 (MQ=255)                                                                                                                   ttCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAAc                                                                                                   <  3:275527/76‑1 (MQ=255)                                                                                                                    tcatcaGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCGAGTAGGGGGAATCGCCAGATGAACTT‑TACAAGGCGCAGAACAGCGAAATTCGAg                        >  7:246837/1‑149 (MQ=255)                                                                                                                    tcatcaGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTT‑TACAAGGCGCAGAACAGCGAAATTCGAg                        >  8:118737/1‑149 (MQ=255)                                                                                                                     catcaGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGtt                                                                                             >  2:99864/1‑80 (MQ=255)                                                                                                                     catcaGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGtt                                                                                             <  1:99864/80‑1 (MQ=255)                                                                                                                     catcaGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTT‑TACAAGGCGCAGAACAGCGAAATTCGa                         <  1:180561/147‑1 (MQ=255)                                                                                                                     catcaGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTT‑TACAAGGCGCAGAACAGCGAAATTCGa                         <  6:184645/147‑1 (MQ=255)                                                                                                                                    gCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGTAAGTAGGGGGAATCGCCAGATGAACTT‑TACAAGGCGCAGAACAGCGAAATTCGAGCGCAGCAGTTCAAAt         <  7:50296/148‑1 (MQ=255)                                                                                                                                       cAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTT‑TACAAGgcg                                           <  6:16864/111‑1 (MQ=255)                                                                                                                                       cAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTT‑TACAAGgcg                                           >  5:16864/1‑111 (MQ=255)                                                                                                                                        aaCCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTT‑TACAAGGCGCAGAACAGCGAAATTCGAGCGCAGCAGTTCAAATGat      <  5:63447/147‑1 (MQ=255)                                                                                                                                          ccGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTT‑TACAAGGCGCAGAACAGCGAAATTCGAGCGCAGCAGTTCAAATGATatt   >  4:309551/1‑148 (MQ=255)                                                                                                                                           cGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTTCTACAAGGCGCAGAACAGCGAAATTCGAGCGCAGCAGTTCAAATGATatta  <  1:80387/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                            CGGCCTGTTCGTGTTCTCCGACAGCCTGATCGGCATCGACCGCTTCATCAGCCCGTTCGCCGCCGCACCGTACCTGATCATCCTCGCCTACTGGCTCGGCCAATGGGCCATCGCTTCATCAGTCGGTCATCGCTCAACCGATAAAGTATTGAC‑CCAGAGCGGTGCGCGCAGGACCGAGAGCTGCTAGAACAAGGTTTTTTTGCAATTGCAAGTAGGGGGAATCGCCAGATGAACTT‑TACAAGGCGCAGAACAGCGAAATTCGAGCGCAGCAGTTCAAATGATATTA  >  NC_002947/4655615‑4655900

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: ‑