Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,344,321	A→T	15.2%	intergenic (+52/‑104)	PP_3817 → / → PP_3818	polyamine ABC transporter ATP‑binding protein/phosphate‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,344,321	0	A	T	15.2%	116.6 / 14.3	53	intergenic (+52/‑104)	PP_3817/PP_3818	polyamine ABC transporter ATP‑binding protein/phosphate‑binding protein
Reads supporting (aligned to +/- strand):  ref base A (17/26);  new base T (3/5);  total (21/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.11e-02

GACAGCGTGAAGGTGCGTTGGGCAGTGGCAGACGCTTGCATTTATACCGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCACCCGGCATGCTCCGCCTGCTTGTCTTGCTGCTCACCCTGCT  >  NC_002947/4344177‑4344459                                                                                                                                                  |                                                                                                                                           gACAGCGTGAAGGTGCGTTGGGCAGTGGCAGACGCTTGCATTTATACCGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGa                                                                                                                                         >  5:285213/1‑148 (MQ=255) gACAGCGTGAAGGTGCGTTGGGCAGTGGCAGACGCTTGCATTTATACCGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGAt                                                                                                                                        >  8:83530/1‑149 (MQ=255)  aCAGCGTGAAGGTGCGTTGGGCAGTGGCAGACGCTTGCATTTATACCGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATc                                                                                                                                       <  6:163383/149‑1 (MQ=255)    aGCGTGAAGGTGCGTTGGGCAGTGGCAGACGCTTGCATTTATACCGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTg                                                                                                                                     <  4:261229/149‑1 (MQ=255)       gTGAAGGTGCGTTGGGCAGTGGCAGACGCTTGCATTTATACCGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTgg                                                                                                                                    >  3:234607/1‑147 (MQ=255)        tGAAGGTGCGTTGGGCAGTGGCAGACGCTTGCATTTATACCGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGTGTGCCGCGCGGGCGGTGCTCGATCTGGCAg                                                                                                                                 <  2:17353/149‑1 (MQ=37)                 gTTGGGCAGTGGCAGACGCTTGCATTTATACCGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGTGTGCCGCGCGGGCGGTGCTCGATCTGGCAgg                                                                                                                                >  8:223079/1‑141 (MQ=37)                 gTTGGGCAGTGGCAGACGCTTGCATTTATACCGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGTGTGCCGCGCGGGCGGTGCTCGATCTGGCAgg                                                                                                                                <  7:223079/141‑1 (MQ=37)                     ggccggggCCGACGCTTGCAGTAATACCGAAGGGGCCGACCCCGACCGGAGCCCCTCGGCCGGGGCGCATTACCGCCCTTGACCGCGG‑CCGCGCCTCCCAGAGCGAGCACCGCCCGCGCGGCACCCGCTCTGGCAGGCGCTGCACTAtt                                                                                                                    <  6:285600/143‑1 (MQ=255)                     ggCTGTGGAAGACGTTTTCATTTATACCTATTGGGCCGAGAGCGACCTGAGCAAGGCGGCGGGGGCTAATTAACGCTATTGTACGTTG‑CAGCGCCTGCCAGATCTAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTAtt                                                                                                                    <  2:184353/149‑1 (MQ=255)                        aGTGGCAGACGCTTGAATTAATCCCGAATGGGCCCAGAGCGACCTGACCAAGGCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCCCCCACCGCCCGCGCGGCACACGATCTGTCAGGCGCTGCACTATTGGa                                                                                                                 <  6:267257/149‑1 (MQ=255)                            gCAGACGCTTGCATTTATACCGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGTGTGCCGCGCGGGCGGTGCTCGATCTgg                                                                                                                                    <  1:3062/126‑1 (MQ=25)                             cAGACGCTTGCATTTATACCGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCg                                                                                                             >  5:160179/1‑148 (MQ=255)                                  gCTTGCATTTATACCGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGTGTGCCGCGCGGGCGGTGCTCGATCTGGCa                                                                                                                                  >  1:47831/1‑122 (MQ=25)                                  gCTTGCATTTATACCGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGTGTGCCGCGCGGGCGGTGCTCGATCTGGCa                                                                                                                                  <  2:47831/122‑1 (MQ=25)                                      gCATTTATACCGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCg                                                                                                    <  4:234607/148‑1 (MQ=255)                                       cATTTATACCGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGt                                                                                                   <  7:1430/148‑1 (MQ=255)                                           tataCCGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACAt                                                                                              >  3:252220/1‑149 (MQ=255)                                             taCCGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGCTG‑CAGCGCCTGCCAGACCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACAtt                                                                                             <  6:189046/148‑1 (MQ=255)                                               ccGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCTCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTatc                                                                                          <  7:267757/149‑1 (MQ=255)                                               ccGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTatc                                                                                          <  6:160179/149‑1 (MQ=255)                                                 gattGGGCCGAGCGCGACCTTAGCATGGGGGCGGGGGCGTTTTACGGCTTTTGT‑CGTTGCCCGCGCCTGCCTTATCGACCACCGCCCGGGCGCAACACTATTTGGCTGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTatcat                                                                                        <  4:164028/146‑1 (MQ=255)                                                 gAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCTAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTatcat                                                                                        <  4:252220/149‑1 (MQ=255)                                                  aaTCGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCAGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGGGCTGCACTATTGGCGGCGTACGCCCCGGGACATTatcat                                                                                        >  4:206108/1‑148 (MQ=255)                                                       gCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGc                                                                                   >  2:111907/1‑148 (MQ=255)                                                              gCGACCTGAGCAAGTCGGCCGGGGCGAATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCg                                                                           <  3:46227/149‑1 (MQ=255)                                                                        cAAGTCGGCCGGGGCGCATTAACTCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCg                                                                 <  7:217377/149‑1 (MQ=255)                                                                        cAAGGCGGCCGGGGCGCATTAACGCTCTTGTCCGTGG‑CAGCGCCGGCCAGATCGAGCACCGCCCGCGCGGCACACTATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCg                                                                 <  6:285213/149‑1 (MQ=255)                                                                           gTCGGCCGGGGCGCATTAACGCTCTTGAACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTatcat                                                                                        >  1:14202/1‑123 (MQ=255)                                                                            tCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCg                                                                 >  1:285746/1‑145 (MQ=255)                                                                            tCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCg                                                                 <  2:285746/145‑1 (MQ=255)                                                                            tCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCCCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGcc                                                              >  2:253528/1‑148 (MQ=255)                                                                               gCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCACATCGAGCACCGCCCGCGCGGCACACGATCAGGCAGGCGCTGCACTATTTGAGGCGTACGCCCCGTCACATTATAATACCGCCACTGTCGTAATCTGCCCGCCCAc                                                           >  4:146797/1‑148 (MQ=255)                                                                                     gcgcATTAACGCTCTTGACCGTTC‑CAGCGCCTCCAACATCGAGCCCCGCCCGCGCGCCACACCATCGGCCTGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGc                                                    <  1:302017/149‑1 (MQ=255)                                                                                               gCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCAc                                          >  5:277252/1‑149 (MQ=255)                                                                                                   ttGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCACCCgg                                      >  5:335470/1‑149 (MQ=255)                                                                                                   ttGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCACCCgg                                      >  2:58317/1‑149 (MQ=255)                                                                                                      tACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACCCGATCTGGCAGGCGCGGGACGATTGGAGGCGTACGCCCCGGGACATTATCATCCCGCCACGGTGGGAATCTGCCGGGCAACGCTATGCCCCAGGTCACCCGGcct                                   >  4:143986/1‑147 (MQ=255)                                                                                                        cGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCACCCGGCATGc                                 <  7:83530/149‑1 (MQ=255)                                                                                                          ttG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCACCCGGCATGCTc                               <  6:277252/149‑1 (MQ=255)                                                                                                                  gcCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCACCCGGCATGCTCCGCCTGc                        <  6:335470/149‑1 (MQ=255)                                                                                                                       ccAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCACCCGGCATGCTCCGCCTGc                        >  5:32801/1‑144 (MQ=255)                                                                                                                       ccAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACCGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCACCCGGCATGCTCCGCCTGc                        <  6:32801/144‑1 (MQ=255)                                                                                                                        cAGATCGTGTGCCGCGCGGGCGGTGCTCGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCACCCGGCATGCTCCGCCTGc                        >  7:202049/1‑143 (MQ=37)                                                                                                                        cAGATCGTGTGCCGCGCGGGCGGTGCTCGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCACCCGGCATGCTCCGCCTGc                        <  8:202049/143‑1 (MQ=37)                                                                                                                        cAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCACCCGGCATGCTCCGCCTGCTTGTCt                  >  6:208623/1‑149 (MQ=255)                                                                                                                            tCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCACCCGGCATGCTCCGCCTGCTTGTCTtgc               <  3:143986/148‑1 (MQ=255)                                                                                                                              gAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCACCCGGCATGCTCCGCCTGCTTGTCTtgctgc            <  5:208623/149‑1 (MQ=255)                                                                                                                               aGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCACCCGGCATGCTCCGCCTGCTTGTCTTgctgct           >  6:87564/1‑149 (MQ=255)                                                                                                                                      cccgcGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCACCCGGCATGCTCCGCCTGCTTGTCTTGCTGCTCACCCTg    <  5:87564/149‑1 (MQ=255)                                                                                                                                       ccgcGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCACCCGGCATGCTCCGCCTGCTTGTCTTGCTGCTCACCCTGc   <  1:58317/149‑1 (MQ=255)                                                                                                                                       ccgcGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCACCCGGCATGCTCCGCCTGCTTGTCTTGCTGCTCACCCTGc   <  3:146797/149‑1 (MQ=255)                                                                                                                                        ggcgcgGCACACGATCTGGCTGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCACCCGGCATGCTCCGCCTGCTTGTCTTGCTGCTCACCCTGCt  <  3:206108/148‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                           GACAGCGTGAAGGTGCGTTGGGCAGTGGCAGACGCTTGCATTTATACCGAATGGGCCGAGAGCGACCTGAGCAAGTCGGCCGGGGCGCATTAACGCTCTTGTACGTTG‑CAGCGCCTGCCAGATCGAGCACCGCCCGCGCGGCACACGATCTGGCAGGCGCTGCACTATTGGAGGCGTACGCCCCGTCACATTATCATCACGCCACTGTCGTAATCTGCCGGCCAACTCTATGCCACAGGTCACCCGGCATGCTCCGCCTGCTTGTCTTGCTGCTCACCCTGCT  >  NC_002947/4344177‑4344459

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑