Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,511,485	G→A	8.9%	pseudogene (124/1851 nt)	PP_1325 ←	putative lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,511,485	0	G	A	8.9%	119.2 / 3.1	45	pseudogene (124/1851 nt)	PP_1325	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base G (19/22);  new base A (2/2);  total (21/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.58e-01

GGGCCGGCTTGAGCGTGTCCAGCGGGACCTGCTCGAGAATGCGTGCGGCGCGTGGGAAGTCCTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGCCAGCAGGGCGGCGAGGCAGAGGGCTGTGAGCAGCCGCAGGCAAGCGATCATGTAAAG  >  NC_002947/1511338‑1511614                                                                                                                                                     |                                                                                                                                  aggCCGGCTTGAGCGTGTCCAGCGGGACCTGCTCGAGAATGCGTGCGGCGCGTGGGAAGTCCTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGtt                                                                                                                                 >  2:587607/2‑150 (MQ=255)   gCCGGCTTGAGCGTGTCCAGCGGGACATACTCGAGAATGCGTGCGGCGCCATCGGAGTCCTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGc                                                                                                                               >  1:108284/1‑150 (MQ=255)    ccGGCTTGAGCGTGTCCAGCGGGACCTGCTCGAGAATGCGTGCGGCGCGTGGGAAGTCCTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCt                                                                                                                              >  1:85222/1‑150 (MQ=255)       gCTTGAGCGTGTCCAGCGGGACCTGCTCGAGAATGCGTGCGGCGCGTGGGAAGTCCTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGa                                                                                                                           >  1:651636/1‑150 (MQ=255)            aGCGTGTCCAGCGGGACCTGCTCGAGAATGCGTGCGGCGCGTGGGAAGTCCTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTg                                                                                                                      <  2:85222/150‑1 (MQ=255)            aGCGTGTCCAGCGGGACCTGCTCGAGAATGCGTGCGGCGCGTGGGAAGTCCTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTg                                                                                                                      <  2:597393/150‑1 (MQ=255)            aGCGTGTCCAGCGGGACCTGCTCGAGAATGCGTGCGGCGCGTGGGAAGTCCTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTg                                                                                                                      <  2:491443/150‑1 (MQ=255)                  tCCAGCGGGACCTGCTCGAGAATGCGTGCGGCGCGTGGGAAGTCCTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTcc                                                                                                                >  2:478686/1‑150 (MQ=255)                    cAGCGGGACCTGCTCGAGAATGCGTGCGGCGCGTGGGAAGTCCTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCgg                                                                                                              >  2:760326/1‑150 (MQ=255)                      gCGGGACCTGCTCGAGAATGCGTGCGGCGCGTGGGAAGTCCTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCgggg                                                                                                            >  1:737313/1‑150 (MQ=255)                           aCCTGCTCGAGAATGCGTGCGGCGCGTGGGAAGTCCTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGt                                                                                                       <  2:651636/150‑1 (MQ=255)                                 tCGAGAATGCGTGCGGCGCGTGGGAAGTCCTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAACTGCTCGaaaa                                                                                                                        <  1:25934/127‑4 (MQ=255)                                 tCGAGAATGCGTGCGGCGCGTGGGAAGTCCTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAACTGCTCGaaaa                                                                                                                        >  2:25934/1‑124 (MQ=255)                                        tgcgtgcgGCGCGTGGGAAGTCCTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCa                                                                                          <  1:760326/150‑1 (MQ=255)                                          cgtgcgGCGCGTGGGAAGTCCTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAgg                                                                                        <  2:108284/150‑1 (MQ=255)                                                    gTGGGAAGTCCTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAgg                                                                              <  1:127673/150‑1 (MQ=255)                                                          aGTCCTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGc                                                                        <  1:478686/150‑1 (MQ=255)                                                             ccTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAACTGCTCGaaaag                                                                                                                       <  2:78606/100‑5 (MQ=255)                                                             ccTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAACTGCTCGaaaag                                                                                                                       >  1:78606/1‑96 (MQ=255)                                                               ttCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGgcg                                                                   >  1:150091/1‑150 (MQ=255)                                                                           gCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCggg                                                                                                             <  1:167523/96‑1 (MQ=255)                                                                           gCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCggg                                                                                                             >  2:167523/1‑96 (MQ=255)                                                                            ccAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGt                                                                                                           <  2:67804/97‑1 (MQ=255)                                                                            ccAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGt                                                                                                           >  1:67804/1‑97 (MQ=255)                                                                            ccAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTT‑GAGTTAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGCcagca                                                      <  1:53939/150‑1 (MQ=255)                                                                                gTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGCCAGCAGggc                                                  <  2:295096/150‑1 (MQ=255)                                                                                         gcTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGCCAGCAGGGCGGCGAGGCa                                         >  2:672374/1‑150 (MQ=255)                                                                                            cAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGCCAGCAGGGCGGCGAGGCagag                                      <  2:150091/150‑1 (MQ=255)                                                                                                  cagcagCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGAGTGGTAGTTAGCACAGGCTGGACGAGTCCGTTCTGGCGCATGTTGCCAGCATGGCGGCGAGGCAGAGGGCtgt                                <  2:737313/150‑1 (MQ=255)                                                                                                   agcagcGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGCCAGCAGGGCGGCGAGGCAGAGGGCtgtg                               <  2:648700/150‑1 (MQ=255)                                                                                                    gcagcGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGCCAGCAGGGCGGCGAGGCAGAGGGCTGTGa                              <  1:587607/150‑1 (MQ=255)                                                                                                       gcgcGGCGTCTTCCGCAGACTTGCTGGAAGCGGCAGTTGCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGCCAGCAGGGCGGCGAGGCAGAGGGCTGTGagca                           >  1:285585/1‑150 (MQ=255)                                                                                                         gcggcgTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGCCAGCAGGGCGGCGAGGCAGAGGGCTGTGagcagc                         >  2:766578/1‑150 (MQ=255)                                                                                                               tCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTGCGGGGGGAGTGGGAGTTCGCCCAGGCTGGATGAGTGCGAGCTGGCGGAGGTTGCCAGCAGGGCGGCGAGGCGGAGGGCTGTGGGCAGCCGCAgg                   >  2:27875/1‑150 (MQ=255)                                                                                                                 ttCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGc                                                           >  1:193270/1‑108 (MQ=255)                                                                                                                 ttCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGc                                                           <  2:193270/108‑1 (MQ=255)                                                                                                                 ttCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGAGCGTGGTCGTTTGCTCAGGATGGATGCGGGCGAGTTGGGGGAGGCTGCCTATAGGGCGGCGAGGCGGAGGGCCGTGAGCAGCCGCAGGCa                 >  1:264919/1‑150 (MQ=255)                                                                                                                 ttCCGCAGACTTGCTGGAAGCGGCCTTTTAGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGAGCGCGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGCCAGCAGGGGGGCGAGGCAGAGGGCTGTGAGCAGACGCAGGCa                 >  1:759240/1‑150 (MQ=255)                                                                                                                   ccGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGCCAGCAGGGCGGCGAGGCAGAGGGCTGTGAGCAGCCGCAGGCAAg               <  1:672374/150‑1 (MQ=255)                                                                                                                       aGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGCCAGCAGGGCGGCGAGGCAGAGGGCTGTGAGCAGCCGCAGGCAAGCGAt           <  2:35056/150‑1 (MQ=255)                                                                                                                                ggAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGTGTTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGCCAGCAGGGCGGCGAGGCAGAGGGCTGTGAGCAGCCGCAGGCAAGCGATCATGTAAAg  <  2:285585/150‑1 (MQ=255)                                                                                                                                 gAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGCCAGCAGGGCGGCGAGGCagag                                      >  2:585318/1‑113 (MQ=255)                                                                                                                                 gAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGCCAGCAGGGCGGCGAGGCagag                                      <  1:585318/113‑1 (MQ=255)                                                                                                                                         cTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCTCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGCcagca                                                      >  1:65028/1‑89 (MQ=255)                                                                                                                                         cTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGCcagca                                                      <  2:65028/89‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                  GGGCCGGCTTGAGCGTGTCCAGCGGGACCTGCTCGAGAATGCGTGCGGCGCGTGGGAAGTCCTTCTGCTTGTAGGCCAGGTCGGCGGCGCTCAGGCGCAGCAGCGCGGCGTCTTCCGCAGACTTGCTGGAAGCGGCCTTTTCGAG‑CAGTTGCTCGATGCTGGCGTCCGGGGTGCGTGGTAGTTCGCCCAGGCTGGATGAGGGCGAGCTGGCGCAGGCTGCCAGCAGGGCGGCGAGGCAGAGGGCTGTGAGCAGCCGCAGGCAAGCGATCATGTAAAG  >  NC_002947/1511338‑1511614

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑