Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,655,692	Δ1 bp	7.5%	intergenic (‑96/+56)	epd ← / ← tktA	D‑erythrose 4‑phosphate dehydrogenase/transketolase A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,655,692	0	T	.	7.5%	157.5 / 7.4	53	intergenic (‑96/+56)	epd/tktA	D‑erythrose 4‑phosphate dehydrogenase/transketolase A
Reads supporting (aligned to +/- strand):  ref base T (24/24);  new base . (2/2);  total (26/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.96e-01

CCGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCGGCGCCGACTCACCG  >  NC_002947/5655547‑5655841                                                                                                                                                   |                                                                                                                                                      ccGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGT‑GGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCtgtg                                                                                                                                                  <  1:785531/150‑1 (MQ=255)  cGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCtgtg                                                                                                                                                  <  2:1070618/150‑1 (MQ=255)         gCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAGAGGTTGCATGAAACC‑CTGTGGGAGCgg                                                                                                                                           <  2:1175750/150‑1 (MQ=37)                       gTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAAt                                                                                                                             <  1:856944/150‑1 (MQ=255)                             cTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGc                                                                                                                       <  2:1096341/150‑1 (MQ=255)                              tttGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAgg                                                                                                                        >  2:903095/1‑148 (MQ=255)                              tttGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAgg                                                                                                                        <  1:903095/148‑1 (MQ=255)                                     ggACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCtgt                                                                                                                                                   <  1:1182242/114‑1 (MQ=255)                                     ggACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCtgt                                                                                                                                                   >  2:1182242/1‑114 (MQ=255)                                              ggCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATc                                                                                                      <  1:949311/150‑1 (MQ=255)                                               gCATTCGGGGCTCACGAGACAGTTCAATTGTTGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCt                                                                                                     >  1:1245516/1‑150 (MQ=255)                                                 aTTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCCCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCttt                                                                                                   <  2:996917/150‑1 (MQ=255)                                                    cGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTaaa                                                                                                <  2:1205162/150‑1 (MQ=255)                                                     ggggCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAGAGGTTGCATGAAACC‑CTGTgg                                                                                                                                                 <  2:209355/100‑1 (MQ=21)                                                     ggggCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAGAGGTTGCATGAAACC‑CTGTgg                                                                                                                                                 >  1:209355/1‑100 (MQ=21)                                                       ggCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCgg                                                                                                                                           <  2:978346/104‑1 (MQ=255)                                                       ggCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCgg                                                                                                                                           >  1:978346/1‑104 (MQ=255)                                                        gCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTaa                                                                                                 >  2:650307/1‑145 (MQ=255)                                                        gCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTaa                                                                                                 <  1:650307/145‑1 (MQ=255)                                                          tCACGAGACAGTTCAATTGTCGTCAGTCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTgg                                                                                                                                                 <  2:1417519/95‑1 (MQ=255)                                                          tCACGAGACAGTTCAATTGTCGTCAGTCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTgg                                                                                                                                                 >  1:1417519/1‑95 (MQ=255)                                                              gagaCAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGc                                                                                                                       >  2:328045/1‑117 (MQ=255)                                                              gagaCAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCAACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGc                                                                                                                       <  1:328045/117‑1 (MQ=255)                                                                     ttCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGct                                                                               >  1:495879/1‑150 (MQ=255)                                                                        aaTTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCtt                                                                            <  2:495879/150‑1 (MQ=255)                                                                                     cTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGGTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAg                                                               >  2:1280400/1‑150 (MQ=255)                                                                                                 cGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAg                                                   <  2:225107/150‑1 (MQ=255)                                                                                                        gCATTCGCGGGCAAGCCCGCTCCCACAG‑GGGTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCCCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCATTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGCGTGAAg                                            >  1:505105/1‑150 (MQ=255)                                                                                                                  gCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCtt                                  >  1:1252133/1‑150 (MQ=255)                                                                                                                   caggCCCGCGCCCACAG‑GGTTTCATGCAATCTCTGTGTGAGCGGCCTTGTCTGCGAAGGAAGGCGACACCGCCCGCAGATCTTTAAATCATTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTc                                 <  2:505105/147‑1 (MQ=255)                                                                                                                      gCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGATACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGaa                              >  2:1099730/1‑150 (MQ=255)                                                                                                                        ccGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACa                            >  1:216924/1‑150 (MQ=255)                                                                                                                            tCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAg                                                               >  1:133565/1‑111 (MQ=255)                                                                                                                            tCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAg                                                               <  2:133565/111‑1 (MQ=255)                                                                                                                            tCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGc                        >  1:841907/1‑150 (MQ=255)                                                                                                                             cccACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCccgcaggctgacgacaattgaactgtctcgtgagccccgaatgccccaccgtccctacaaagttgcactcaacggttatggc                             <  1:352223‑M2/144‑83 (MQ=255)                                                                                                                             cccACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCccgcaggctgacgacaattgaactgtctcgtgagccccgaatgccccaccgtccctacaaagttgcactcaacggttatggc                             >  2:352223‑M2/1‑62 (MQ=255)                                                                                                                              ccACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCccgcaggctgacgacaattgaactgtctcgtgagccccgaatgccccaccgtccctacaaagttgcactcaacggttatggccgtatcg                      <  1:1308853‑M2/150‑90 (MQ=255)                                                                                                                               cacaG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAggg                                                 >  2:1280296/1‑122 (MQ=255)                                                                                                                               cacaG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAggg                                                 <  1:1280296/122‑1 (MQ=255)                                                                                                                               cacaG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGa                     >  1:42466/1‑150 (MQ=255)                                                                                                                               cacaG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGa                     >  1:925271/1‑150 (MQ=255)                                                                                                                                gcagaggTTGCATGAAACC‑CTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGaa                    >  2:973554/6‑150 (MQ=38)                                                                                                                                acaG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAg                                                               <  1:1029764/107‑1 (MQ=255)                                                                                                                                acaG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAg                                                               >  2:1029764/1‑107 (MQ=255)                                                                                                                                acaG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGc                        <  1:349064/146‑1 (MQ=255)                                                                                                                                acaG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGc                        >  2:349064/1‑146 (MQ=255)                                                                                                                                         tCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCGgcgc            <  2:1419118/150‑1 (MQ=255)                                                                                                                                           aTGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTAcc                                                                  <  2:482593/94‑1 (MQ=255)                                                                                                                                           aTGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTAcc                                                                  >  1:482593/1‑94 (MQ=255)                                                                                                                                            tGCAACGTCTGTGTTAGCGGTCTTGTCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCGGCGCCGa         >  2:19621/1‑150 (MQ=255)                                                                                                                                             gCAACCTCTGTGGGAGCGGGCTTGCCGGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTtc                                                        <  1:319485/102‑1 (MQ=255)                                                                                                                                             gCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTtc                                                        >  2:319485/1‑102 (MQ=255)                                                                                                                                                   tctGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCGGCGCCGACTCACCg  >  2:2803/1‑150 (MQ=255)                                                                                                                                                   |                                                                                                                                                      CCGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCGGCGCCGACTCACCG  >  NC_002947/5655547‑5655841

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑