Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,897,770	A→G	12.9%	intergenic (‑170/+64)	PP_5172 ← / ← PP_5173	hypothetical protein/RND family transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,897,770	0	A	G	12.9%	138.8 / 10.1	56	intergenic (‑170/+64)	PP_5172/PP_5173	hypothetical protein/RND family transporter
Reads supporting (aligned to +/- strand):  ref base A (25/23);  new base G (3/4);  total (29/27)
Fisher's exact test for biased strand distribution p-value = 7.05e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.42e-01

GGGCGCCGGGCAGAGGTTTGAAGGGGTTTTGCGCCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAGGAACAGCAGCGTCAGCAAGGTCGCCA  >  NC_002947/5897621‑5897916                                                                                                                                                      |                                                                                                                                                    gggCGCCGGGCAGAGGTTTGAAGGGGTTTTGCGCCTGGCTTGA‑GGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACACGCGAATa                                                                                                                                                     >  1:123746/1‑149 (MQ=255)    cgcCGGGCAGAGGTTTGAAGGGGTTTTGCGCCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACAATTTAAGAGAACACGCCTCTGGTAGGAGAGGGTTTACCCCCGAATACg                                                                                                                                                   >  7:290265/1‑149 (MQ=255)      ccGGGCAGAGGTTTGAAGGGGTTTTGCGCCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACggt                                                                                                                                                 <  5:96127/149‑1 (MQ=255)       cGGGCAGAGGTTTGAAGGGGTTTTGCGCCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACggtg                                                                                                                                                >  5:131058/1‑149 (MQ=255)          gCAGAGGTTTGAAGGGGTTTTGCGCCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTc                                                                                                                                             >  6:136505/1‑149 (MQ=255)           cAGAGGTTTGAAGGGGTTTTGCGCCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATGCgatggtg                                                                                                                                             >  6:230816/1‑147 (MQ=255)            agagGTTTGAAGGGGTTTTGCGCCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGa                                                                                                                                           <  6:131058/149‑1 (MQ=255)              agGTTTGAAGGGGTTTTGCGCCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATg                                                                                                                                         >  6:254146/1‑149 (MQ=255)                gTTTGAAGGGGTTTTGCGCCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCa                                                                                                                                       >  1:6515/1‑149 (MQ=255)                 tttGAAGGGGTTTTGCGCCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCAc                                                                                                                                      <  2:83790/149‑1 (MQ=255)                                cgcCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATGCGATGGTGCATCGACCACCGTATT‑CGCgg                                                                                                                       <  5:230816/148‑1 (MQ=25)                                cgcCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCgg                                                                                                                       <  2:6515/148‑1 (MQ=255)                                cgcCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCCCTGGTAGGAGCGGGTTTACCCGCGAATGCGATGGTGCATCGACCACCGTATT‑CGCgg                                                                                                                       <  4:137271/148‑1 (MQ=25)                                     ggCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATGCGATGGTGCATCGACCACCGTATT‑CGCGGGTAAAc                                                                                                                 >  5:321048/1‑149 (MQ=25)                                             ggCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTAAACGCGAATACGGTGGTCGATGAACCATCGCATT‑AGCGGGGAAACCCGGTcc                                                                                                          >  3:40940/1‑148 (MQ=255)                                              gCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTTACCGCGAATTCGGTGGTCGATTCACCATAGCATTACCCGGTTAAAccggtccga                                                                                                         >  1:292634/1‑142 (MQ=255)                                               cAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATGCGATGGTGCATCGACCACCGTATT‑CGCGGGTAAACCCGCTCCTAc                                                                                                       <  6:321048/149‑1 (MQ=21)                                               cAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTAc                                                                                                       >  1:26964/1‑149 (MQ=255)                                                    gtagtGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATGCga                                                                                                                                                  <  5:284230/102‑2 (MQ=255)                                                    gtagtGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATGCga                                                                                                                                                  >  6:284230/1‑101 (MQ=255)                                                      attGAGGTTGGAATATTATTAAAAATATTGTTTAATAATTTTTATATAACTATTTAAGTGAACACGCCTTTGGTAGGAGCGGGTTTACCCGGTAATACGGTGGTGGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAgggg                                                                                                 <  8:148586/146‑1 (MQ=25)                                                       gttaGGCGGTATTATTCTTAAAAATACTTTTTAATAATTTTTATATAACCATTTAAGATAACACGCCTGTGGTAGGAGGGGGTTTACCCGCTAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGcc                                                                                               <  2:111221/146‑1 (MQ=37)                                                          aGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGAt                                                                                                                                          <  2:19943/104‑1 (MQ=255)                                                          aGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGAt                                                                                                                                          >  1:19943/1‑104 (MQ=255)                                                          aGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCat                                                                                             <  7:11247/148‑1 (MQ=255)                                                                  ttattCTTAAAATTATTTTTTACTAATTTTTTTATACCCATTTAAGCGAACACGCCTCTGGTTTGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATGGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCt                                                                                     <  8:290265/148‑1 (MQ=37)                                                                       cTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGc                                                                               >  8:34218/1‑149 (MQ=255)                                                                        ttAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCg                                                                              <  2:26964/149‑1 (MQ=255)                                                                        ttAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCg                                                                              >  2:278178/1‑149 (MQ=255)                                                                        ttAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGACTCTGGTAGGAGCGGGTTTACCATCGAATAAGGTGGTCGATTAACCATCGCATT‑CTAGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCg                                                                              >  3:203491/1‑149 (MQ=38)                                                                          aaaaaTACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGc                                                                               <  5:136505/146‑1 (MQ=255)                                                                            aaaTACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGtt                                                                          >  2:24637/1‑149 (MQ=255)                                                                                             ttttATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGGGTGTTTCTGCGGCTCGCGGATc                                                         >  3:230365/1‑149 (MQ=255)                                                                                                       ccATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTc                                                                                                           >  5:79983/1‑89 (MQ=255)                                                                                                       ccATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTc                                                                                                           <  6:79983/89‑1 (MQ=255)                                                                                                       ccATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAgg                                               >  5:332862/1‑149 (MQ=255)                                                                                                        cATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGc                                              >  8:235328/1‑149 (MQ=255)                                                                                                             aaGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACg                                          >  3:78196/1‑148 (MQ=255)                                                                                                                  aaCACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAgc                                    <  4:78196/149‑1 (MQ=255)                                                                                                                  aaCACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAgc                                    >  5:329678/1‑149 (MQ=255)                                                                                                                       gCCTCTGGTAGGAGGTGGTTTACCCGCTAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGTCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCgg                               <  1:44409/149‑1 (MQ=255)                                                                                                                       gCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGcc                                             >  2:59558/1‑135 (MQ=255)                                                                                                                       gCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGcc                                             <  1:59558/135‑1 (MQ=255)                                                                                                                         ctctGGTAGGAGGGGGTTTCCCCTCTAATACGGTGGTCGATGCACCATCGCATT‑CGCGGTAAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCg                                <  5:179126/146‑1 (MQ=255)                                                                                                                         ctctGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑AGCGGGTAAACCCCCTCCTACCAGGGGGCATATGGGCCTTCAGGCGTGGTTGTGCGGGTCGCGGCTCTTGTACCAGGCCACGTAAAGCGccc                                >  6:179126/1‑145 (MQ=37)                                                                                                                             ggTAGTCGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGAATT‑GGCGGTTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAGGa                          <  2:123746/148‑1 (MQ=255)                                                                                                                              gTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAGGaa                         <  6:329678/148‑1 (MQ=255)                                                                                                                               tAGCAGCGGGTTTACCCGCGAATACGGTGGCCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAGGAAca                       <  8:261439/149‑1 (MQ=255)                                                                                                                                    gCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAGGAACagcagc                  <  5:254146/149‑1 (MQ=255)                                                                                                                                        gTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAgcgc                                  <  6:192014/129‑1 (MQ=255)                                                                                                                                        gTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAgcgc                                  >  5:192014/1‑129 (MQ=255)                                                                                                                                        gTTAACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAGGAACAGCAGCGTCa              <  2:286229/149‑1 (MQ=255)                                                                                                                                              ccGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAGGAACAGCAGCGTCAGCAAgg        >  4:301352/1‑149 (MQ=255)                                                                                                                                              ccGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAGGAACAGCAGCGTCAGCAAgg        >  7:4865/1‑149 (MQ=255)                                                                                                                                               cgcgAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAGGAACAGCAGCGTCAGCAAGGt       >  6:1880/1‑149 (MQ=255)                                                                                                                                               cgcgAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAGGAACAGCAGCGTCAGCAAGGt       >  3:51681/1‑149 (MQ=255)                                                                                                                                                    aTACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAGGAACAGCAGCGTCAGCAAGGTCGCCa  <  7:19403/149‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                    GGGCGCCGGGCAGAGGTTTGAAGGGGTTTTGCGCCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATT‑CGCGGGTAAACCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAGGAACAGCAGCGTCAGCAAGGTCGCCA  >  NC_002947/5897621‑5897916

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: ‑