Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,311,314	T→A	10.0%	F12I (TTT→ATT) ‡	PP_3784 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,311,314	0	T	A	10.0%	126.6 / 5.9	50	F12I (TTT→ATT) ‡	PP_3784	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (24/21);  new base A (3/2);  total (27/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.37e-01

GACACAACCGCGTGCGCTCGCAAACCACTCGTGGCAAGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATCCAGCAACGAACAGGCACCACTTGGCGTGCTGCGTCTTGTCGTGGCAGTGAG  >  NC_002947/4311166‑4311462                                                                                                                                                     |                                                                                                                                                      gACACAACCGCGTGCGCTCGCAAACCACTCGTGGCAAGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCAt                                                                                                                                                       >  8:155186/1‑149 (MQ=255)  acacAACCGCGTGCGCTCGCAAACCACTCGTGGCAAGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCAtt                                                                                                                                                      <  6:298758/149‑1 (MQ=255)   cacaACCGCGGGAGCTCGCAAACCACTCGTGGCATGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCAttt                                                                                                                                                     <  8:65272/149‑1 (MQ=255)      aaCCGCGTGCGCTCGCAAACCACTCGTGGCAAGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCg                                                                                                                                                  >  3:356575/1‑149 (MQ=255)      aaCCGCGTGCGCTCGCAAACCACTCGTGGCAAGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCg                                                                                                                                                  >  1:325300/1‑149 (MQ=255)           cgTGCGCTCGCAAACCACTCGTGGCAAGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCAAATGCGTTGcc                                                                                                                                             <  7:330724/149‑1 (MQ=255)           atctcgcTCGCAAACCACTCGTGGCAAGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCAAATGCGTTGcc                                                                                                                                             <  1:345426/145‑1 (MQ=255)               cgcTCGCAAACCACTCGTGGCAAGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTc                                                                                                                                        <  5:272320/149‑1 (MQ=255)                gcTCGCAAACCACTCGTGGCAAGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCAAATGCGTTGcc                                                                                                                                             >  2:345426/1‑144 (MQ=255)                 cTCGCAAACCACTCGTGGCAAGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGc                                                                                                                                      <  7:155186/149‑1 (MQ=255)                  tCGCAAACCACTCGTGGCAAGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGcctccttc                                                                                                                                       >  2:306801/1‑142 (MQ=255)                     cAAACCACTCGTGGCAAGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGAATTCCCTCCGTGGGCAACGCATTTTCGTTGCC‑CTACGCCGGc                                                                                                                                  >  2:184284/1‑149 (MQ=255)                      aaaCCACTCGTGGCAAGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGct                                                                                                                                 >  4:332034/1‑149 (MQ=255)                         ccACTCGTGGCAAGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCtctc                                                                                                                              <  2:325300/149‑1 (MQ=255)                             tCGTGGCAAGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGtca                                                                                                                          >  6:88633/1‑149 (MQ=255)                             tCGTGGCAAGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGtca                                                                                                                          >  4:309849/1‑149 (MQ=255)                                  gCAAGGCGTTTAACCGATTTCCGTAACGCTCTGGGCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCA‑CTTCGCCGGCTCTCGTCATCAAt                                                                                                                     <  1:184284/149‑1 (MQ=255)                                  gCAAGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAAt                                                                                                                     <  4:356575/149‑1 (MQ=255)                                    aaGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATtc                                                                                                                   <  3:332034/149‑1 (MQ=255)                                    aaGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGAC‑CTTCGCCGGCTCTCGTCATCAAtt                                                                                                                    >  8:289112/1‑148 (MQ=255)                                               cgcaaTTCCGTACCGCTCTGCCCCCCGAATCTATTGCGCGCCCTCCGGTCAGTTAAAGTAACATCATCAATGGCTAACAGCTTCCCCTCGGGGGGCAACGCTTTTGGGTTGCC‑CTCCGCCGGCTCTCGTCATCAATTCATCAGTGCCAc                                                                                                        <  4:11648/146‑1 (MQ=255)                                                cGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTCCGCCGGCTCTCGTCATCAATTCATCAGTGCCAc                                                                                                        >  3:11648/1‑148 (MQ=255)                                                                       ccGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGacac                                                                                         <  3:13337/140‑1 (MQ=255)                                                                       ccGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGacac                                                                                         >  4:13337/1‑140 (MQ=255)                                                                               aTTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACTCCTGACACATTCAGCgactgacttt                                                                        >  4:206491/1‑147 (MQ=255)                                                                                ttGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGa                                                                                            <  3:307356/128‑1 (MQ=255)                                                                                ttGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGa                                                                                            >  4:307356/1‑128 (MQ=255)                                                                                                   tGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATcc                                                    <  7:289112/149‑1 (MQ=255)                                                                                                          aaGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATCCAGCAAc                                              >  5:208204/1‑148 (MQ=255)                                                                                                                 tcaATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATcc                                                    <  8:331625/135‑1 (MQ=255)                                                                                                                 tcaATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATcc                                                    >  7:331625/1‑135 (MQ=255)                                                                                                                  caATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATc                                                     <  4:278488/133‑1 (MQ=255)                                                                                                                  caATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATc                                                     >  3:278488/1‑133 (MQ=255)                                                                                                                    aTGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTc                                                                                     <  5:125633/99‑1 (MQ=255)                                                                                                                    aTGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTc                                                                                     >  6:125633/1‑99 (MQ=255)                                                                                                                         tAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATCCAGCAACGAACAGGCACCACTTg                              >  5:203113/1‑149 (MQ=255)                                                                                                                           aCAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATc                                                     >  6:210163/1‑124 (MQ=255)                                                                                                                           aCAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATc                                                     <  5:210163/124‑1 (MQ=255)                                                                                                                              gCATTCCCTCCGGGGGCAACGCATTTGCGTTGCCACTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATCCAGCAACGAACAGGCACCACTTGGCGt                          >  1:47640/1‑149 (MQ=255)                                                                                                                               cATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATCCAGCAACGAACAGGCACCACTTGGCGtgc                        >  5:343927/1‑149 (MQ=255)                                                                                                                                    ccTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTgc                                                            <  7:109404/108‑1 (MQ=255)                                                                                                                                    ccTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTgc                                                            >  8:109404/1‑108 (MQ=255)                                                                                                                                     cTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCGTGTCGCAATCATTGCCGCCATCCAGCAACGAACAGGCACCACTTGGCGTGCTGCGTc                  <  2:47640/149‑1 (MQ=255)                                                                                                                                         gggggCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATCCAGCAACGAACAgg                                       <  7:171720/124‑1 (MQ=255)                                                                                                                                         gggggCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATCCAGCAACGAACAgg                                       >  8:171720/1‑124 (MQ=255)                                                                                                                                           gggCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATCCAGCAACGAACAGGCACCACTTGGCGTGCTGCGTCTTGTCg            <  6:208204/149‑1 (MQ=255)                                                                                                                                            ggCAACGCAAATGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATCCAGCAACGAACAGGCACCACTTGGCGTGCTGCGTCTTGTCGt           >  2:345873/1‑149 (MQ=255)                                                                                                                                             gCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGGGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCCTCCAGCAACGAACAGGCACCACTTGGCGTGCTGCGTCTTGTCGTg          <  5:88633/149‑1 (MQ=255)                                                                                                                                             gCAACGCAAATGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACAGCCTGTCGCAATCATTGCCGCCATTCAGCAACGAACAGGCACCACTTGGCGTGCTGCGTCTTGTCGTg          >  6:44021/1‑149 (MQ=255)                                                                                                                                              cAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATCCAGCAACGAACAGGCACCACTTGGCGTGCTGCGTCTTGTCGTgg         <  6:203113/149‑1 (MQ=255)                                                                                                                                                aCGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATCCAGCAACGAACAGGCACCACTTGGCGTGCTGCGTCTTGTCGTgg         >  1:28277/1‑147 (MQ=255)                                                                                                                                                aCGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATAATTGCCGCCATCCAGCAACGAACAGGCACCACTTGGCGTGCTGCGTCTTGTCGTGGCa       >  7:294714/1‑149 (MQ=255)                                                                                                                                                    aTTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATCCAGCAACGAACAGGCACCACTTGGCGTGCTGCGTCTTGTCGTGGCAGTGa   <  2:28277/149‑1 (MQ=255)                                                                                                                                                     tttGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATCCAGCAACGAACAGGCACCACTTGGCGTGCTGCGTCTTGTCGTGGCAGTGAg  >  3:133214/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                      GACACAACCGCGTGCGCTCGCAAACCACTCGTGGCAAGGCGTTTAACCGAATTCCGTAACGCTCTGGCCCCCGAATCGATTGCGCGCCCTCCCGTCAGTGAAAGGAAGATCATCAATGGCTAACAGCATTCCCTCCGGGGGCAACGCATTTGCGTTGCC‑CTTCGCCGGCTCTCGTCATCAATTCATCAGTGCCACGTGTACGCCTGACACATTCAGCGACTGCCTGTCGCAATCATTGCCGCCATCCAGCAACGAACAGGCACCACTTGGCGTGCTGCGTCTTGTCGTGGCAGTGAG  >  NC_002947/4311166‑4311462

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: ‑