Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,264,290:1	+T	10.2%	intergenic (‑44/+40)	zinU ← / ← PP_4640	P‑loop guanosine triphosphatase‑dependent zinc chaperone/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,264,290	1	.	T	10.2%	178.0 / 16.7	49	intergenic (‑44/+40)	zinU/PP_4640	P‑loop guanosine triphosphatase‑dependent zinc chaperone/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (21/23);  new base T (2/3);  total (23/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.46e-01

GATCACGGCGAGCTTCAGGCCATGCTCGGCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGACGTTCGCGGAAGAATGCCTCGTAGCTCATCACCGGCTTGTCCGGATGCGTTTTCTG  >  NC_002947/5264142‑5264431                                                                                                                                                      |                                                                                                                                               gATCACGGCGAGCTTCAGGCCATGCTCGGCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAACTACTCCTGAATCTGAAAATGACTGTGGGAGcc                                                                                                                                                 >  8:278835/1‑149 (MQ=255)  aTCACGGCGAGCTTCAGGCCATGCTCGGCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑g                                                                                                                                               <  5:253705/149‑1 (MQ=255)  aTCACGGCGAGCTTCAGGCCATGCTCGGCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑g                                                                                                                                               >  4:67124/1‑149 (MQ=255)         cGAGCTTCAGGCCATGCTCGGCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTAccc                                                                                                                                        <  6:251577/149‑1 (MQ=255)         cGAGCTTCAGGCCATGCTCGGCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTAccc                                                                                                                                        <  3:67124/149‑1 (MQ=255)          gAGCTTCAGGCCATGCTCGGCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCa                                                                                                                                       <  8:31679/149‑1 (MQ=255)           aGCTTCAGGCCATGCTCGGCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAg                                                                                                                                      <  1:208956/149‑1 (MQ=255)                cAGGCCATGCTCGGCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTc                                                                                                                                  <  2:39620/148‑1 (MQ=255)                  ggCCATGCTCGGCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGTCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCCTGGGTAACC‑GGCTCCca                                                                                                                               <  8:65610/149‑1 (MQ=255)                  ggCCATGCTCGGCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTccc                                                                                                                                >  3:257641/1‑148 (MQ=255)                     cATGCTCGGCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAg                                                                                                                            >  5:217844/1‑149 (MQ=255)                     cATGCTCGGCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAg                                                                                                                            <  1:206500/149‑1 (MQ=255)                      aTGCTCGGCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAgg                                                                                                                           >  4:114837/1‑149 (MQ=255)                            ggCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTac‑a                                                                                                                    >  6:198538/1‑149 (MQ=255)                            ggCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGAACCTAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACTCAAAATACTCCGGAATCTGAAAATGACTTTGGGCGAC‑GGTTACCCAGGCTCCCACAGGTTTac‑a                                                                                                                    >  6:237345/1‑149 (MQ=255)                               cTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACg                                                                                                                  >  3:183301/1‑148 (MQ=255)                                  gAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAAc                                                                                                               <  3:114837/148‑1 (MQ=255)                                    gCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGc                                                                                                            <  5:198538/149‑1 (MQ=255)                                     cATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCCTGGGTAACC‑GGCTCCCACAgtc                                                                                                                          >  8:285276/1‑133 (MQ=39)                                     cATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCCTGGGTAACC‑GGCTCCCACAgtc                                                                                                                          >  4:83531/1‑133 (MQ=39)                                     cATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCCTGGGTAACC‑GGCTCCCACAgtc                                                                                                                          <  7:285276/135‑3 (MQ=39)                                     cATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCCTGGGTAACC‑GGCTCCCACAgtc                                                                                                                          <  3:83531/135‑3 (MQ=39)                                      aTGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAg                                                                                                          >  7:234450/1‑149 (MQ=255)                                               aGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAg                                                                                                 <  6:271834/149‑1 (MQ=255)                                               aGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAg                                                                                                 <  8:234450/149‑1 (MQ=255)                                                gCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGc                                                                                                <  3:59909/149‑1 (MQ=255)                                                             gCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGa                                                                                   >  3:96016/1‑149 (MQ=255)                                                              ccGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGa                                                                                   <  4:183301/148‑1 (MQ=255)                                                              ccGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGa                                                                                   <  6:217844/148‑1 (MQ=255)                                                              ccGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGAc                                                                                  <  7:281951/149‑1 (MQ=255)                                                                    tcGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCa                                                                            <  5:211073/148‑1 (MQ=255)                                                                           aGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAAc                                                                     <  4:257641/149‑1 (MQ=255)                                                                             ccTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGt                                                                   >  5:202309/1‑149 (MQ=255)                                                                               tgtgAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGc                                                                 >  4:128200/1‑149 (MQ=255)                                                                               tgtgAGGACGGTTAAGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCTCAGGCTCAACAGAACTTGGGCCCGGACTTGCCACCGTAACGTGc                                                                 >  4:234114/1‑149 (MQ=255)                                                                                     gACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCt                                                            >  6:102123/1‑148 (MQ=255)                                                                                       ctgTTACGTGAATGTGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGATCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGAc                                                         <  3:37269/147‑1 (MQ=255)                                                                                             cGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTACCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCTGACTTGCCACCGTAACGTGCTTCCTGACGTTcgc                                                   <  4:96585/149‑1 (MQ=255)                                                                                                 aaTGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGACGTTCGCgg                                                 >  2:257031/1‑147 (MQ=255)                                                                                                  aTGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGACGTTCGCGgaag                                              <  5:102123/149‑1 (MQ=255)                                                                                                             cACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGACGTTCGCGGAAGAATGCCTCGTa                                   <  1:11941/149‑1 (MQ=255)                                                                                                                  aaaaTACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGACGTTCGCGGAAGAATGCCTCGTAGCtca                              >  5:188049/1‑149 (MQ=255)                                                                                                                       aCTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGACGTTCGCGGAAGAATGCCTCGTAGCTCATCAcc                         >  6:253503/1‑149 (MQ=255)                                                                                                                         tCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGACGTTCGCGGAAGAATGCCTCGTAGCTCATCACCgg                       >  7:229361/1‑149 (MQ=255)                                                                                                                              aaTCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGACGTTCGCGGAAGAATGCCTCGTAGCTCATCACCGGCTTGt                  >  3:103108/1‑149 (MQ=255)                                                                                                                                tCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGACGTTCGCGGAAGAATGCCTCGTAGCTCATCACCGGCTTGTcc                >  4:97124/1‑149 (MQ=255)                                                                                                                                tCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGACGTTCGCGGAAGAATGCCTCGTAGCTCATCACCGGCTTGTcc                >  6:64208/1‑149 (MQ=255)                                                                                                                                tCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGACGTTCGCGGAAGAATGCCTCGTAGCTCATCACCGGCTTGTcc                >  3:230806/1‑149 (MQ=255)                                                                                                                                    aaaaTGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGACGTTCGCGGAAGAATGCCTCGTAGCTCATCACCGGCTTGTCCGGa             <  3:128200/148‑1 (MQ=255)                                                                                                                                     aaaTGACTGTGGGAGCC‑GTTTACCCAGGCTTGCTCAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGACGTTCGCGGAAGAATGCCTCGTAGCTCATCACCGGCTTGTCCGGATg           <  4:230806/149‑1 (MQ=255)                                                                                                                                              tgGGAGCC‑GGTTACCCAGGCTCCCACAGGTGTAC‑ACGAACCGCACGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGACGTTCGCGGAAGAATGCCTCGTAGCTCATCACCGGCTTGTCCGGATGCGTTTTCTg  <  5:226215/149‑1 (MQ=255)                                                                                                                                                ggAGCC‑GGTTACCCAGGCTCCCACAGGTTTACGACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGACGTTCGCGGAAGAATGCCTCGTAGCTCATCACCGGCTTGTCCGGATGCGTTTTCTg  >  1:192786/1‑148 (MQ=255)                                                                                                                                                      |                                                                                                                                               GATCACGGCGAGCTTCAGGCCATGCTCGGCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGACGTTCGCGGAAGAATGCCTCGTAGCTCATCACCGGCTTGTCCGGATGCGTTTTCTG  >  NC_002947/5264142‑5264431

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑