Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,321,039	C→G	8.2%	intergenic (‑275/‑143)	PP_3791 ← / → PP_5629	site‑specific recombinase/protease/amidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,321,039	0	C	G	8.2%	141.9 / 4.2	49	intergenic (‑275/‑143)	PP_3791/PP_5629	site‑specific recombinase/protease/amidase
Reads supporting (aligned to +/- strand):  ref base C (23/22);  new base G (2/2);  total (25/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.04e-01

AGGAGCTCACTAAATGCCCCCGGCGGTCTGGAGTCAATTGCGTGTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCCTTCTATGAGCACCGCTAGCTGAACCTTGATGTCTGTTTGAAGCCGCCGTACGCTATCGGCATTCATGGAGGAATCTGGC  >  NC_002947/4320893‑4321179                                                                                                                                                   |                                                                                                                                              aggagCTCACTAAATGCCCCCGGCGGTCTGGAGTCAATTGCGTGTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCcagcag                                                                                                                                             <  2:6472/149‑1 (MQ=255) aggagCTCACTAAATGCCCCCGGCGGTCTGGAGTCAATTCCGTGTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCcagc                                                                                                                                               <  5:282667/147‑1 (MQ=255)        cACTAAATGCCCCCGGCGGTCTGGAGTCAATTGCGTGTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTa                                                                                                                                      >  2:255444/1‑149 (MQ=255)           tAAATGCCCCCGGCGGTCTGGAGTCAATTGCGTGTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTc                                                                                                                                   >  1:156475/1‑149 (MQ=255)             aaTGCCCCCGGCGGTCTGGTGTCAATTGCGTGTTATCTAAGTTTCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCATGCTTGCCGACACTTCACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGCATTCtt                                                                                                                                 <  2:265770/149‑1 (MQ=255)                 cccccGGCGGTCTGGAGTCAATTGCGTGTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAAtt                                                                                                                             >  7:254606/1‑149 (MQ=255)                  ccccGGCGGTCTGGAGTCAATTGCGTGTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAAtt                                                                                                                             >  2:229142/1‑148 (MQ=255)                         ggTCTGGAGTCAATTGCGTGTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATAtt                                                                                                                     <  8:86424/149‑1 (MQ=255)                         ggTCTGGAGTCAATTGCGTGTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATAtt                                                                                                                     <  2:268113/149‑1 (MQ=255)                           tCTGGAGTCAATTGCGTTTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAATCTTGCCGACACTTGAAAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGa                                                                                                                   <  6:170676/149‑1 (MQ=255)                           tCTGGAGTCAATTGCGTGTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCATGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTg                                                                                                                    >  7:67911/1‑148 (MQ=255)                             tGGAGTCAATTGCGTGTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCcagcag                                                                                                                                             >  6:146362/1‑121 (MQ=255)                             tGGAGTCAATTGCGTGTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCcagcag                                                                                                                                             <  5:146362/121‑1 (MQ=255)                               gAGTCAATTGCGTGTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATcc                                                                                                              <  2:156475/149‑1 (MQ=255)                               gAGTCAATTGCGTGTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATc                                                                                                               >  2:48114/1‑148 (MQ=255)                                 gTCAATTGCGTGTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCaa                                                                                                            <  7:31436/149‑1 (MQ=255)                                    aaTTGCGTGTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAatat                                                                                                         >  8:43382/1‑149 (MQ=255)                                      ttGCGTGTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATcg                                                                                                       >  6:319713/1‑149 (MQ=255)                                         cGTGTTATCTAAGATGCGTCATCTTCTCTTTCGCCCTCATATTCGTAGTCAATCAAGCTTGCCGACACTTGTCAAATTTCAAATTACCCTAAGGCCCTGGTGCCATCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATcgcg                                                                                                     <  5:232513/148‑1 (MQ=255)                                         cGTGTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGa                                                                                                    <  1:48114/149‑1 (MQ=255)                                            gtTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCg                                                                                                 >  8:173386/1‑149 (MQ=255)                                               aTCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGG‑ATTCAATATcgaaatta                                                                                                 <  3:59403/146‑7 (MQ=255)                                               aTCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGG‑ATTCAATATcgaaatta                                                                                                 >  4:59403/1‑140 (MQ=255)                                                tCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGa                                                                                              <  5:319713/148‑1 (MQ=255)                                                  tAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAAca                                                                                           >  5:283282/1‑149 (MQ=255)                                                    aGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGaa                                                                                             <  8:67911/145‑1 (MQ=255)                                                      aTGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCGAATATCGCGACCGGGAAcatcat                                                                                       >  4:322430/1‑149 (MQ=255)                                                         cGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCAtcct                                                                                    <  6:22166/149‑1 (MQ=255)                                                                ttCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCCTTc                                                                              >  1:130921/1‑148 (MQ=255)                                                                ttCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCCTTc                                                                              >  6:144628/1‑148 (MQ=255)                                                                   gCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCCTTCTAt                                                                           <  1:229142/148‑1 (MQ=255)                                                                    cTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATACAATATCGCGACCGGGAACATCATCCTCCCTTCTAt                                                                           >  7:49654/1‑147 (MQ=255)                                                                             tCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCCTTCTATGAGCACCGc                                                                  >  2:197773/1‑147 (MQ=255)                                                                                 aaTCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCTACCGGGACCATCATCCTCCCTGATATGAGCACCGCTAGCt                                                             >  8:224942/1‑148 (MQ=255)                                                                                      ttctaaattaaCCTTTCCGACACTTGACAAATTTAAAATTACCCTAAGGCCCTGGTGCCATCATCACATTATTCATAATTTCCTTATTTATCTCCAATATCGCGACCGGGAACATCATCCTCCCTTCTATGAGCACCGCTAGCTGAAcc                                                        <  1:255444/144‑1 (MQ=255)                                                                                      tAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCCTTCTATGAGCACCGCTAGCTGAACCt                                                       >  6:91551/1‑149 (MQ=255)                                                                                        gTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCCTTCTATGAGCACCGCTAGCTGAACCTTg                                                     <  8:254606/149‑1 (MQ=255)                                                                                         tcaatcaaGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCCTTCTATGAGCACCGCTAGCTGAACCTTGa                                                    <  5:91551/149‑1 (MQ=255)                                                                                          caatcaaGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCCTTCTATGAGCACCGCTAGCTGAACCTTGa                                                    <  7:43382/148‑1 (MQ=255)                                                                                          caatcaaGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCATTCTATGAGCACCGCTAGCTGAACCTGGAt                                                   >  4:171798/1‑149 (MQ=255)                                                                                           aatcaaGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCCTTCTATGAGCACCGCTAGCTGAACCTTGAt                                                   <  1:197773/148‑1 (MQ=255)                                                                                             tcaaGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCCTTCTATGAGCACCGCTAGCTGAACCTTGATGTc                                                >  1:143525/1‑149 (MQ=255)                                                                                                      ccGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCCTTCTATGAGCACCGCTAGCTGAACCTTGATGTCTGTTTGaa                                        <  7:173386/148‑1 (MQ=255)                                                                                                      ccGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCCTTCTATGAGCACCGCTAGCTGAACCTTGATGTCTGTTTGaa                                        <  3:183654/148‑1 (MQ=255)                                                                                                               gACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCCTTCTATGAGCACCGCTAGCTGAACCTTGATGTCTGTTTGAAGCCGCCGTAc                              >  1:149853/1‑149 (MQ=255)                                                                                                                aCAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCCATCTATGAGCACCGCTAGCTGAACCTTGATGTCTGTTTGAAGCCGCCGTAc                              <  4:216265/148‑1 (MQ=255)                                                                                                                     tttCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCCTTCTATGAGCACCGCTAGCTGAACCTTGATGTCTGTTTGAAGCCGCCGTACGCTATc                        >  2:18589/1‑149 (MQ=255)                                                                                                                       tCAAATTACCCTAAGGCCCTGGTGCCAGGAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACatcatc                                                                                      >  6:237061/1‑85 (MQ=255)                                                                                                                       tCAAATTACCCTAAGGCCCTGGTGCCAGGAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACatcatc                                                                                      >  6:232912/1‑85 (MQ=255)                                                                                                                       tCAAATTACCCTAAGGCCCTGGTGCCAGGAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACatcatc                                                                                      <  5:237061/85‑1 (MQ=255)                                                                                                                       tCAAATTACCCTAAGGCCCTGGTGCCAGGAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACatcatc                                                                                      <  5:232912/85‑1 (MQ=255)                                                                                                                                 cTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCCTTCTATGAGCACCGCTAGCTGAACCTTGATGTCTGTTTGAAGCCGCCGTACGCTATCGGCATTCATgga            <  2:246975/149‑1 (MQ=255)                                                                                                                                           ggTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCCTTCTATGAGCACCGCTAGCTGAACCTTGATGTCTGTTTGAAGCCGCCGTACGCTATCGGCATTCATGGAGGAATCTGGc  >  4:42707/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                              AGGAGCTCACTAAATGCCCCCGGCGGTCTGGAGTCAATTGCGTGTTATCTAAGATGCGTCAGCTTCGCTTTCGCCCTCATAATCGTAGTCAATCAAGCTTGCCGACACTTGACAAATTTCAAATTACCCTAAGGCCCTGGTGCCAGCAGCACAGTATTCTTAATTTCGATATTGA‑ATCCAATATCGCGACCGGGAACATCATCCTCCCTTCTATGAGCACCGCTAGCTGAACCTTGATGTCTGTTTGAAGCCGCCGTACGCTATCGGCATTCATGGAGGAATCTGGC  >  NC_002947/4320893‑4321179

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: ‑