Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,338,796	C→T	8.1%	P197S (CCG→TCG)	PP_2055 →	isomerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,338,796	0	C	T	8.1%	137.4 / 3.7	49	P197S (CCG→TCG)	PP_2055	isomerase
Reads supporting (aligned to +/- strand):  ref base C (22/23);  new base T (2/2);  total (24/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

GGCGATCGATGGGGTACCGGGCACTGCCGCCCCGGTGCATCTGACCTTCCTCGACGCGGTCGGCAGCAAGACCGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCTGAAGGCCGGAAAGGCCATGGGCCTGGGCGATGTCAGTGGCAT  >  NC_002947/2338648‑2338944                                                                                                                                                     |                                                                                                                                                     ggCGATCGATGGGGTACCGGGCACTGCCGCCCCGGTGCATCTGACCTTCCTCGACGCGGTCGGCAGCAAGACCGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGc                                                                                                                                                      >  1:152309/1‑149 (MQ=255)    gatcgatGGGGTACCGGGCACTGCCGCCCCGGTGCATCTGACCTTCCTCGACGCGGTCGGCAGCAAGACCGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCga                                                                                                                                                   <  7:269998/149‑1 (MQ=255)        gatGGGGTACCGGGCACTGCCGCCCCGGTGCATCTGACCTTCCTCGACGCGGTCGGCAGCAAGACCGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGGCATGGCCATGTCgatgc                                                                                                                                                <  5:250246/148‑2 (MQ=255)          tGGGGTACCGGGCACTGCCGCCCCGGTGCATCTGACCTTCCTCGACGCGGTCGGCAGCAAGACCGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATgg                                                                                                                                             >  7:204691/1‑149 (MQ=255)            gggTACCGGGCACTGCCGCCCCGGTGCATCTGACCTTCCTCGACGCGGTCGGCAGCAAGACCGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGGCATGGCCATGTCgatgcag                                                                                                                                              <  3:2139/146‑4 (MQ=255)            gggTACCGGGCACTGCCGCCCCGGTGCATCTGACCTTCCTCGACGCGGTCGGCAGCAAGACCGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGGCATGGCCATGTCgatgcag                                                                                                                                              >  4:2139/1‑143 (MQ=255)                 ccGGGCACTGCCGCCCCGGTGCATCTGACCTTCCTCGACGCGGTCGGCAGCAAGACCGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTgg                                                                                                                                       <  5:69467/148‑1 (MQ=255)                  cGGGCACTGCCGCCCCGGTGCATCTGACCTTCCTCGACGCGGTCGGCAGCAAGACCGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAg                                                                                                                                     <  8:252478/149‑1 (MQ=255)                    ggCACTGCCGCCCCGGTGCATCTGACCTTCCTCGACGCGGTCGGCAGCAAGACCGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGgc                                                                                                                                   >  1:41353/1‑149 (MQ=255)                              ccccGGTGCATCTGACCTTCCTCGACGCGGTCGGCAGCAAGACCGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTg                                                                                                                         <  3:329215/149‑1 (MQ=255)                                 cGGTGCATCTGACCTTCCTCGACGCGGTCGGCAGCAAGACCGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGgt                                                                                                                      <  2:152309/149‑1 (MQ=255)                                                   tCGACGCGGTCGGCAGCAAGACCGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAAcc                                                                                                    >  3:142091/1‑149 (MQ=255)                                                      aCGCGGTCGGCAGCAAGACCGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCg                                                                                                 <  2:322851/149‑1 (MQ=255)                                                       cgcgGTCGGCAGCAAGACCGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACAAGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCgg                                                                                                <  6:329966/149‑1 (MQ=255)                                                               gcagcaAGACCGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTg                                                                                        >  4:213558/1‑149 (MQ=255)                                                                       aCCGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCaa                                                                                <  3:213558/149‑1 (MQ=255)                                                                         cGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCaa                                                                                >  1:224795/1‑147 (MQ=255)                                                                         cGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCaa                                                                                >  3:31896/1‑147 (MQ=255)                                                                         cGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACa                                                                              <  5:201311/149‑1 (MQ=255)                                                                           gCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAgc                                                                            <  5:239628/149‑1 (MQ=255)                                                                                       ccACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGCCGCCCACAGCGCGCTGCTCGaa                                                                >  7:115374/1‑149 (MQ=255)                                                                                       ccACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGaa                                                                >  8:215116/1‑149 (MQ=255)                                                                                        cACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAAc                                                               >  8:202893/1‑149 (MQ=255)                                                                                        cACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAAc                                                               <  8:204691/149‑1 (MQ=255)                                                                                          cGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGc                                                             <  2:244959/149‑1 (MQ=255)                                                                                             gCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGACACCCCGGCTCAGCTGGCCGCCACCCGCGCGCTGCTCGAACGCCTg                                                          >  2:314458/1‑149 (MQ=255)                                                                                             gCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGc                                                                                   <  7:99941/124‑1 (MQ=255)                                                                                             gCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGc                                                                                   >  8:99941/1‑124 (MQ=255)                                                                                               aaGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTgg                                                         >  4:18302/1‑148 (MQ=255)                                                                                                    ccAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGaa                                                                >  6:96597/1‑136 (MQ=255)                                                                                                    ccAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGaa                                                                <  5:96597/136‑1 (MQ=255)                                                                                                           gTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCt                                            >  1:300081/1‑149 (MQ=255)                                                                                                                   tGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGc                                                     <  3:255515/132‑1 (MQ=255)                                                                                                                   tGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGc                                                     >  4:255515/1‑132 (MQ=255)                                                                                                                         gCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCTGAAGGCCGGAAAgg                              >  6:270878/1‑149 (MQ=255)                                                                                                                           cGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCTGAAGGCCGGAAAGGcc                            <  4:142091/149‑1 (MQ=255)                                                                                                                                aCCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCTGAAACCCCGGCTCAGCTGGACGCCAACAGAGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCTGAAGGCCGGAAAGGCCATgg                        <  4:31896/148‑1 (MQ=255)                                                                                                                                  cTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCTGAAGGCCGGAAAGGCCATGGGcc                     >  3:219405/1‑149 (MQ=255)                                                                                                                                    tcATCGGCATGGCCATGTCGATGATGGTTGTGGAGGCCAGCCAGTTGGGAGTCAGCCGCTCGGAACCCCAGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGACCGCCTGGAAGCGTTGCGCCTGAAGCCCGGAAAGGCCATGGGCCTg                   >  7:268367/2‑149 (MQ=255)                                                                                                                                     cATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCTGAAGGCCGGAAAGGCCATGGGCCTgg                  >  4:246360/1‑149 (MQ=255)                                                                                                                                      aTCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCTGAAGGCCGGAAAGGCCATGGGCCTggg                 <  3:305057/149‑1 (MQ=255)                                                                                                                                       tCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCTGAAGGCCGGAAAGGCCATGGGCCTGGGc                >  8:163457/1‑149 (MQ=255)                                                                                                                                         gACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCTGAAGGCCGGAAAGGCCATGGGCCTGGGCGa              <  2:41353/149‑1 (MQ=255)                                                                                                                                          aCATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCTGAAGGCCGGAAAGGCCATGGGCCTGGGCGAt             >  8:42352/1‑149 (MQ=255)                                                                                                                                            aTGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCTGAAGGCCGGAAAGGCCATGGGCCTGGGCGATGt           <  3:84055/149‑1 (MQ=255)                                                                                                                                            aTGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCTGAAGGCCGGAAAGGCCATGGGCCTGGGCGATGt           >  4:84055/1‑149 (MQ=255)                                                                                                                                              ggCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCTGAAGGCCGGAAAGGCCATGGGCCTGGGCGATGt           >  4:41229/1‑147 (MQ=255)                                                                                                                                               gCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCTGAAGGCCGGAAAGGCCATGGGCCTGGGCGATGTCAg        <  5:270878/149‑1 (MQ=255)                                                                                                                                                 cATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCTGAAGGCCGGAAAGGCCATGGGCCTGGGCGATGTCAGTg      <  4:219405/149‑1 (MQ=255)                                                                                                                                                 cATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCTGAAGGCCGGAAAGGCCATGGGCCTGGGCGATGTCAGTg      <  3:18302/149‑1 (MQ=255)                                                                                                                                                     ccGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCTGAAGGCCGGAAAGGCCATGGGCCTGGGCGATGTCAGTGGCAt  >  2:327394/1‑149 (MQ=255)                                                                                                                                                     ccGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCGCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCTGAAGGCCGGAAAGGCCATGGGCCTGGGCGATGTCAGTGGCAt  <  6:51230/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                     GGCGATCGATGGGGTACCGGGCACTGCCGCCCCGGTGCATCTGACCTTCCTCGACGCGGTCGGCAGCAAGACCGGCAAGCTGTTCCCCACGGGCAAGGCCCAGGACGTGATTGATGGCGTGCCGGTGACCTGCATCGACATGGCCATGCCGATGATGGTTGTGGAGGCCAGCCAGTTGGGTGTCAGCGGCTCGGAAACCCCGGCTCAGCTGGACGCCAACAGCGCGCTGCTCGAACGCCTGGAAGCGTTGCGGCTGAAGGCCGGAAAGGCCATGGGCCTGGGCGATGTCAGTGGCAT  >  NC_002947/2338648‑2338944

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: ‑