Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,995,074	T→A	8.5%	intergenic (+146/+31)	PP_5251 → / ← PP_5252	transporter/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,995,074	0	T	A	8.5%	138.0 / 4.9	47	intergenic (+146/+31)	PP_5251/PP_5252	transporter/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (21/22);  new base A (2/2);  total (23/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.66e-01

ATGCCGGCCCTTACGGCCCATTCGCGGGTGAACCCGCTCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACGAACAGCCCAGCGCACCCCAGAAGCCCTGGAAGTCATTTACCGGCACGCTCGAATGCCGCGCCTTTTCGTGGCTGTGCGCATGCACACCACAAGGCC  >  NC_002947/5994928‑5995217                                                                                                                                                   |                                                                                                                                                aTGCCGGCCCTTACGGCCCATTCGCGGGTGAACCCGCTCCAACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCAGGTTTACCCGCGAAAGGGCCGGCACTGACGACACAAGAAAGGGACCCGTTAtt                                                                                                                                              >  1:813836/1‑150 (MQ=38)  tGCCGGCCCTTACGGCCCATTCGCGGGTGAACCCGCTCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTg                                                                                                                                             <  2:511387/150‑1 (MQ=255)  tGCCGGCCCTTACGGCCCATTCGCGGGTGAACCCGCTCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTg                                                                                                                                             <  1:830603/150‑1 (MQ=255)       gCCCTTACGGCCCATTCGCGGGTGATCCCGTTTTTACATAGATCTGCGTTAGACACACACCGGACGTTGGAAACATGCCGTTGTAGGAGCGGGTTTACCCGCGAAATGGCCGTCACTTAAGACATATGAAAGGTGCCAGTTATTGGcccc                                                                                                                                        <  2:813836/150‑1 (MQ=25)               ggCCCATTCGCGGGTGAACCCGCTCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTc                                                                                                                                >  2:515702/1‑150 (MQ=255)                   cATTCGCGGGTGAACCCGCTCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACAt                                                                                                                            >  1:341144/1‑150 (MQ=255)                     ttCGCGGGTGAACCCGCTCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCAGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACAtca                                                                                                                          >  1:414843/1‑150 (MQ=255)                      tCGCGGGTGAACCCGCTCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACAtcag                                                                                                                         >  2:582208/1‑150 (MQ=255)                        gcgGGTGAACCCGCTCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTg                                                                                                                                             <  2:822628/128‑1 (MQ=255)                        gcgGGTGAACCCGCTCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTg                                                                                                                                             >  1:822628/1‑128 (MQ=255)                                 cccGCTCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCGGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGa                                                                                                              >  1:473010/1‑150 (MQ=255)                                 cccGCTCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAATAACTGGcccctttct                                                                                                                                   <  1:749347/129‑6 (MQ=37)                                 cccGCTCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAATAACTGGcccctttct                                                                                                                                   >  2:749347/1‑124 (MQ=37)                                  ccGCTCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTa                                                                                                                                                <  1:749067/115‑1 (MQ=255)                                  ccGCTCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTa                                                                                                                                                >  2:749067/1‑115 (MQ=255)                                  ccGCTCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGaa                                                                                                             >  2:140300/1‑150 (MQ=255)                                  ccGCTCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGaa                                                                                                             >  2:620385/1‑150 (MQ=255)                                   ctcTCCGACACGGGTCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGaaa                                                                                                            <  2:234570/148‑1 (MQ=255)                                    gCTCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAg                                                                                                           <  1:709191/150‑1 (MQ=255)                                    gCTCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAg                                                                                                           <  2:828358/150‑1 (MQ=255)                                      tCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCg                                                                                                         <  1:228144/150‑1 (MQ=255)                                         tACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAg                                                                                                      <  2:89187/150‑1 (MQ=255)                                            acaGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGccccc                                                                                                                                       <  1:478070/114‑1 (MQ=255)                                            acaGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCAc                                                                                                   >  1:502446/1‑150 (MQ=255)                                            acaGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTAGccccc                                                                                                                                       >  2:478070/1‑114 (MQ=255)                                                aTCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGTAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACgggc                                                                                               <  1:590523/150‑4 (MQ=255)                                                   tGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACGAACAGc                                                                                            >  2:172638/1‑150 (MQ=255)                                                         aGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGTGTAGAAAGCGAAGCACGAACAGCCCAgcg                                                                                      <  1:582208/150‑1 (MQ=255)                                                           acacacacCGGACGTTGGAAACAGGCCGTTGTAGGCGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTGCGCTTAGAAAGCGAAGCACGAACAGCCCACCGCa                                                                                    >  1:158223/1‑150 (MQ=255)                                                             acacacCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACGAACAGCCCAGCGCAcc                                                                                  >  1:21795/1‑150 (MQ=255)                                                                cacCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACGaa                                                                                                <  2:202300/133‑1 (MQ=255)                                                                cacCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACGaa                                                                                                >  1:202300/1‑133 (MQ=255)                                                                                cAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACGAACAGCCCAGCGCACCCCAGAAGCCCTTGAAGTCa                                                               <  2:212982/150‑1 (MQ=255)                                                                                   gCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACGAACAGCCCAGCGCACCCCAGAAGccc                                                                        <  2:98008/138‑1 (MQ=255)                                                                                   gCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACGAACAGCCCAGCGCACCCCAGAAGccc                                                                        >  1:98008/1‑138 (MQ=255)                                                                                               gCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAATAACTGGcccct                                                                                                                                       >  2:619339/1‑62 (MQ=21)                                                                                               gCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAATAACTGGcccct                                                                                                                                       <  1:619339/63‑2 (MQ=21)                                                                                                  ggTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACGAACAGCCCAGCGCACCCCAGAAGCCCTGGAAGTCATTTACCGGCACGCTCGaa                                             <  1:172638/150‑1 (MQ=255)                                                                                                                    ccGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACGAACAGCCCAGCGCACCCCAGAAGCCCTGGAAGTCATTTACCGGCACGCTCGAATGCCGCGCCTTTTCGTgg                           >  1:143539/1‑150 (MQ=255)                                                                                                                              aGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACGAACAGCCCAGCGCACCCCAGAAGCCCTGGAAGTCATTTACCGGCACGCTCGAATGCCGCGCCTTTTCGTGGCTGTGCGCAt                 <  1:69995/150‑1 (MQ=255)                                                                                                                                acacAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACGAACAGCCCAGCGCACCCCAGCACCCCTGGAAGTCATTTCCCGGCACGCTCGAATGCCGCGCCTTTTCGTGGCTGTGCGCATGc               <  2:341144/150‑1 (MQ=255)                                                                                                                                acacAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACGAACAGCCCAGCGCACCCCAGAAGCCCTGGAAGTCATTTACCGGCACGCTCGAATGCCGCGCCTTTTCGTGGCTGTGCGCATGc               >  2:761043/1‑150 (MQ=255)                                                                                                                                    aaGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACGAACAGCCCAGCGCACCCCAGAAGCCCTGGAAGTCATTTACCGGCACGCTCGAATGCCGCGCCTTTTCGTGGCTGTGCGCATGCacac           <  2:473010/150‑1 (MQ=255)                                                                                                                                      gAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACGAACAGCCCAGCGCACCCCAGAAGCCCTGGAAGTCATTTACCGGCACGCTCGAATGCCGCGCCTTTTCGTGGCTGTGCGCATGCAcacca         <  1:515702/150‑1 (MQ=255)                                                                                                                                             gCCAGTTATTGGCCACCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACGAACAGCCCAGCGCACCCCAGAAGCCCTGGAAGTCATTTACCGGCACGCTCGAATGCCGCGCCTTTTCGTGGCTGTGCGCATGCACACCACAAGGcc  >  2:480585/1‑150 (MQ=255)                                                                                                                                                aGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACGAACAGCCCAGCGCACCCCAGAAGCCCTGGAAGTCATTTACCGGCACGCTCGAATGCCGCGCCTTTTCGTgg                           <  2:558735/122‑1 (MQ=255)                                                                                                                                                aGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACGAACAGCCCAGCGCACCCCAGAAGCCCTGGAAGTCATTTACCGGCACGCTCGAATGCCGCGCCTTTTCGTgg                           >  1:558735/1‑122 (MQ=255)                                                                                                                                                   |                                                                                                                                                ATGCCGGCCCTTACGGCCCATTCGCGGGTGAACCCGCTCCTACACAGATCTGCGGTAGACACACACCGGACGTTGGAAACAGGCCGTTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCACTGAAGACACAAGAAAGGGGCCAGTTATTGGCCCCCGTTCGTCACATCAGCTCAGCTTAGAAAGCGAAGCACGAACAGCCCAGCGCACCCCAGAAGCCCTGGAAGTCATTTACCGGCACGCTCGAATGCCGCGCCTTTTCGTGGCTGTGCGCATGCACACCACAAGGCC  >  NC_002947/5994928‑5995217

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: ‑