Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,357,747	G→A	12.0%	intergenic (+93/‑161)	PP_3831 → / → PP_3832	hypothetical protein/CsrA‑like carbon storage regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,357,747	0	G	A	12.0%	128.0 / 7.7	50	intergenic (+93/‑161)	PP_3831/PP_3832	hypothetical protein/CsrA‑like carbon storage regulator
Reads supporting (aligned to +/- strand):  ref base G (25/19);  new base A (4/2);  total (29/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.38e-01

GCCTTGCTGTTGTTTCTTCAGGCACTTGAGGAACAGGAGGACCATTGAGCTTGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAGAAGGAAGAGGGACAAGCTCCCGCCGCCGCGGCAACTAGCCCAGCGGACTTATACATCAC  >  NC_002947/4357607‑4357894                                                                                                                                             |                                                                                                                                                     gCCTTGCTGTTGTTTCTTCAGGCACTTGAGGAACAGGAGGACCATTGAGCTTGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTg                                                                                                                                              >  8:166711/1‑149 (MQ=255)  ccTTGCTGTTGTTTCTTCAGGCACTTGAGGAACAGGAGGACCATTGAGCTTGTCTATTCAGCCCATGATGAGAAGAAATTTCACATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGc                                                                                                                                             >  6:285069/1‑149 (MQ=255)   cTTGCTGTTGTTTCTTCAGGCAGTTGAGGAACAGGAGGACCATTGAGCTTGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGGGAGCACCTTGGCCGACAAACCGTCAACGGTTTgtc                                                                                                                                            <  1:306730/149‑3 (MQ=255)        tgttgtTTCTTCAGGCACTTGAGGAACAGGAGGACCATTGAGCTTGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTgg                                                                                                                                        >  2:210882/1‑148 (MQ=255)          ttgttTCTTCAGGCACTTGAGGAACAGGAGGACCATTGAGCTTGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGc                                                                                                                                       <  5:223872/147‑1 (MQ=255)             tttCTTCAGGCACTTGAGGAACAGGAGGACCATTGAGCTTGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTg                                                                                                                                  <  1:340536/149‑1 (MQ=255)                    aGGCACTTGAGGAACAGGAGGACCATTGAGCTTGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACGAACCGTTGACGGTTTGCTTTGGCACCTGCAACTg                                                                                                                            >  1:232845/1‑148 (MQ=255)                    aGGCACTTGAGGAACAGGAGGACCATTGAGCTTGTCTATTCAGCCCATGATGCGAAGAAATATCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTg                                                                                                                            >  8:275901/1‑148 (MQ=255)                     ggCACTTGAGGAACAGGAGGACCATTGAGCTTGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGaa                                                                                                                          <  3:205426/149‑1 (MQ=255)                     ggCACTTGAGGAACAGGAGGACCATTGAGCTTGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGaa                                                                                                                          <  7:166711/149‑1 (MQ=255)                            gAGGAACAGGAGGACCATTGAGCTTGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCAGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACg                                                                                                                    >  2:110424/1‑148 (MQ=255)                              ggAACAGGAGGACCATTGAGCTTGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCaa                                                                                                                 >  2:144094/1‑149 (MQ=255)                                   aggaggACCATTGAGCTTGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGa                                                                                                             >  3:222445/1‑148 (MQ=255)                                     gaggaCCATTGAGCTTGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGAACCTGCAACTGAATACACGCAACAGAA‑tt                                                                                                         >  5:309353/1‑149 (MQ=255)                                         aCCATTGAGCTTGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTtgt                                                                                                      <  1:112296/148‑1 (MQ=255)                                                 gCTTGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGa                                                                                                                                                     <  7:134996/94‑1 (MQ=255)                                                 gCTTGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGa                                                                                                                                                     >  8:134996/1‑94 (MQ=255)                                                  cTTGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGa                                                                                            <  5:285069/149‑1 (MQ=255)                                                   ttGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCgg                                                                                               >  4:222062/1‑145 (MQ=255)                                                   ttGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCgg                                                                                               <  3:222062/145‑1 (MQ=255)                                                   ttGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGaa                                                                                           >  3:53935/1‑149 (MQ=255)                                                   ttGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGaa                                                                                           >  3:58344/1‑149 (MQ=255)                                                      tCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTa                                                                                        <  1:210882/149‑1 (MQ=255)                                                                          aagaaATTTCCAATTAGCCGCCAACCAACATATTCTTGCCAGCGACCACCTTGGCCGACAAAACGTTGACGGTTTGCTTTTGCACCTGAAACTGAAGACACGCAACAGAA‑TTTTTCTGTCgg                                                                                               >  2:311249/1‑122 (MQ=255)                                                                               aTTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATg                                                               <  4:222445/149‑1 (MQ=255)                                                                                   cccATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATccgccg                                                                              >  1:171282/1‑130 (MQ=255)                                                                                   cccATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATccgccg                                                                              <  2:171282/130‑1 (MQ=255)                                                                                   cccATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATgag                                                             >  1:316511/1‑147 (MQ=255)                                                                                    ccATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAATTTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAgaa                                                           <  1:245343/149‑1 (MQ=255)                                                                                    ccATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAgaa                                                           <  4:53935/148‑1 (MQ=255)                                                                                    ccATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAgaa                                                           <  4:58344/148‑1 (MQ=255)                                                                                    acATTAGCCTCCAACCCCCCTATTCTTTCCAGCGAGCACCTTTGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAgaa                                                           <  6:309353/147‑1 (MQ=255)                                                                                     cATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAgaag                                                          >  8:163699/1‑148 (MQ=255)                                                                                           ccgccAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACGAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAGAAGGAAGAgg                                                   <  2:232845/149‑1 (MQ=255)                                                                                           ccgccAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTa                                                                  <  5:31616/134‑1 (MQ=255)                                                                                           ccgccAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTa                                                                  >  6:31616/1‑134 (MQ=255)                                                                                                     cccTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAGAAGGAaga                                                     <  5:8492/137‑1 (MQ=255)                                                                                                     cccTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAGAAGGAaga                                                     >  6:8492/1‑137 (MQ=255)                                                                                                      ccTATTCTTTCCAGCGAGAACATTGGACGACAAAGCGTTGACGGTTTGCTTTGGCAAATGCAACTGAAGACAGGAAACAGAA‑TTTGTATGTCGTGGAATTACTATACTCAGAAAGAGTCTTTAATGACTAGGTAGTCGGAGAAGCTc                                          >  6:87812/1‑147 (MQ=255)                                                                                                          ttCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAGAAGGAAGAGGGACAAGCTCccgcc                                     <  1:144094/148‑1 (MQ=255)                                                                                                                   gCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAGAAGGAAGAGGGACAAGCTCCCGCCGCCGCGGCaa                           >  1:95634/1‑149 (MQ=255)                                                                                                                            ttGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAGAAGGAAGAGGGACAAGCTCCCGCCGCCGCGGCAACTAGCCCAg                  >  8:229300/1‑149 (MQ=255)                                                                                                                                aaagcAAACCGTCAACGGTTTGCTTTGGCACCTGCAACTGAAGCCACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAGAAGGTAGAGGGACAAGCTCCCGCCGCCGCGGCAACTAGCCCAGCgg               >  3:239391/5‑148 (MQ=255)                                                                                                                                aaagcAAACCGTCAACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAGAAGGAAGAGGGACAAGCTCCcgccgccgc                                >  5:321078/5‑131 (MQ=255)                                                                                                                                aaagcAAACCGTCAACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAGAAGGAAGAGGGACAAGCTCCcgccgccgc                                <  6:321078/127‑1 (MQ=255)                                                                                                                                aaagcAAACCGTCAACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAGAAGGAAGAGGGACAAGCTCCCGCCGCCGCGGCAACTAGCCCAGCGGa              >  6:130706/5‑149 (MQ=255)                                                                                                                                 cGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAGAAGGAAGAGGGACAAGCTCCCGCCGCCGCGGCAACTAGCCCAGCGGAc             >  2:150190/1‑149 (MQ=255)                                                                                                                                   gcAAACCGTCAACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAGAAGGAAGAGGGACAAGCTCCCGCCGCCGCGGCAACTAGCCCAGCGGACt            >  5:29763/2‑148 (MQ=255)                                                                                                                                     aaaCCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAGAAGGAAGAGGGACAAGCTCCCGCCGCCGCGGCAACTAGCCCAGCGGACTta          >  2:116832/1‑148 (MQ=255)                                                                                                                                        ccGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAGAAGGAAGAGGGACAAGCTCCCGCCGCCGCGGCAACTAGCCCAGCGGACTTATACa      >  2:265027/1‑149 (MQ=255)                                                                                                                                             gACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAGAAGGAAGAGGGACAAGCTCCCGCCGCCGCGGCAACTAGCCCAGCGGACTTATACATCa   >  2:132439/1‑147 (MQ=255)                                                                                                                                             gACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAGAAGGAAGAGGGACAAGCTCCCGCCGCCGCGGCAACTAGCCCAGCGGACTTATACATCa   <  1:132439/147‑1 (MQ=255)                                                                                                                                             gACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAGAAGGAAGAGGGACAAGCTCCCGCCGCCGCGGCAACTAGCCCAGCGGACTTATACATCAc  >  4:57870/1‑148 (MQ=255)                                                                                                                                             |                                                                                                                                                     GCCTTGCTGTTGTTTCTTCAGGCACTTGAGGAACAGGAGGACCATTGAGCTTGTCTATTCAGCCCATGATGCGAAGAAATTTCCCATTAGCCGCCAACCCCCCTATTCTTGCCAGCGAGCACCTTGGCCGACAAACCGTTGACGGTTTGCTTTGGCACCTGCAACTGAAGACACGCAACAGAA‑TTTGTCTGTCGGGGAATTACTATCCGCCGAAAGCGTCTTTAATGAGAAGGAAGAGGGACAAGCTCCCGCCGCCGCGGCAACTAGCCCAGCGGACTTATACATCAC  >  NC_002947/4357607‑4357894

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: ‑