Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,264,296	C→A	10.4%	intergenic (‑50/+34)	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	5,264,296	0	C	A	10.4%	136.1 / 7.4	48	intergenic (‑50/+34)	zinU/PP_4640	P‑loop guanosine triphosphatase‑dependent zinc chaperone/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (21/22);  new base A (2/3);  total (23/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.89e-01

CGAGCTTCAGGCCATGCTCGGCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGACGTTCGCGGAAGAATGCCTCGTAGCTCATCACCGGCTTGTCCGGATGCGTTTTCTGCATGTGTT  >  NC_002947/5264150‑5264439                                                                                                                                                    |                                                                                                                                                 cGAGCTTCAGGCCATGCTCGGCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTAccc                                                                                                                                                <  3:67124/149‑1 (MQ=255) cGAGCTTCAGGCCATGCTCGGCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTAccc                                                                                                                                                <  6:251577/149‑1 (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                                                                                                                                  <  7:285276/135‑3 (MQ=39)                             cATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCCTGGGTAACC‑GGCTCCCACAgtc                                                                                                                                  <  3:83531/135‑3 (MQ=39)                             cATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCCTGGGTAACC‑GGCTCCCACAgtc                                                                                                                                  >  4:83531/1‑133 (MQ=39)                              aTGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAg                                                                                                                  >  7:234450/1‑149 (MQ=255)                                       aGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAg                                                                                                         <  8:234450/149‑1 (MQ=255)                                       aGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAg                                                                                                         <  6:271834/149‑1 (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)                                                                                                                                               ggTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGACGTTCGCGGAAGAATGCCTCGTAGCTCATCACCGGCTTGTCCGGATGCGTTTTCTGCATGTGtt  <  5:64208/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                 CGAGCTTCAGGCCATGCTCGGCCTTGAGCATGTACTTGAGCAAGGTGGTCTTGCCGGCACCGAGGAAGCCTGTGAGGACGGTTACGGGAATGGGCATCTGCACGCAAAATACTCCTGAATCTGAAAATGACTGTGGGAGCC‑GGTTACCCAGGCTCCCACAGGTTTAC‑ACGAACCGCAGGCTCAACAGCACTTGGGCCCGGACTTGCCACCGTAACGTGCTTCCTGACGTTCGCGGAAGAATGCCTCGTAGCTCATCACCGGCTTGTCCGGATGCGTTTTCTGCATGTGTT  >  NC_002947/5264150‑5264439

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: ‑