Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,519,917	A→T	15.4%	intergenic (‑188/‑38)	PP_4852 ← / → PP_4853	AraC family transcriptional regulator/DMT superfamily permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,519,917	0	A	T	15.4%	82.8 / 9.2	39	intergenic (‑188/‑38)	PP_4852/PP_4853	AraC family transcriptional regulator/DMT superfamily permease
Reads supporting (aligned to +/- strand):  ref base A (16/17);  new base T (3/3);  total (19/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.24e-01

CTTGTAGACAGACACTCGATAATACAGGCCTATCGAGGACCTGCCTTGCAGGCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCTGGGCCGGCAACACCGTGGTCACCAAGATGTCCGCCGGTGCCATCCACCCTGCGGAGATCGGCTTCTACCGCTGG  >  NC_002947/5519773‑5520065                                                                                                                                                 |                                                                                                                                                     cTTGTAGACAGACACTCGATAATACAGGCCTATCGAGGACCTGCCTTGCAGGCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAagcag                                                                                                                                                  <  1:22037/149‑1 (MQ=255)       gacagacaCTCGATAATACAGGCCTATCGAGGACCTGCCTTGCAGGCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCTTTGCAGccctt                                                                                                                                             <  1:246843/148‑3 (MQ=255)       gacagacaCTCGATAATACAGGCCTATCGAGGACCTGCCTTGCAGGCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAag                                                                                                                                                     <  6:204214/140‑1 (MQ=255)       gacagacaCTCGATAATACAGGCCTATCGAGGACCTGCCTTGCAGGCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAag                                                                                                                                                     >  5:204214/1‑140 (MQ=255)              acTCGATAATACAGGCCTATCGAGGACCTGCCTTGCAGGCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGcc                                                                                                                                     >  1:271741/1‑149 (MQ=255)                tCGATAATACAGGCCTATCGAGGACCTGCCTTGCAGGCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGGAGGAGCGGGGTCCCCCGCGAAGGGCTGCAAAGCAGCCCCCTTCCCGcccc                                                                                                                                   >  4:333695/1‑149 (MQ=39)                  gATAATACAGGCCTATCGAGGACCTGCCTTGCAGGCCTTCGCGGGCTCCCCGCACCCACAGGATCTGCGCCAGCCTCCAGGCCGGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCCGCCCCATTCCCCCCCCCa                                                                                                                                 >  2:324103/1‑149 (MQ=38)                            gCCTATCGAGGACCTGCCTTGCAGGCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTAccc                                                                                                                       >  7:14837/1‑149 (MQ=255)                                   gAGGACCTGCCTTGCAGGCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCtgctgc                                                                                                                 <  3:52542/148‑1 (MQ=255)                                   gAGGACCTGCCTTGCAGGCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCtgctgc                                                                                                                 <  3:139247/148‑1 (MQ=255)                                   gAGGACCTGCCTTGCAGGCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCa                                                                                                                <  2:271741/149‑1 (MQ=255)                                     ggACCTGCCTTGCAGGCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATg                                                                                                              <  1:12405/149‑1 (MQ=255)                                            ccTTGCAGGCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTAc                                                                                                        <  1:121736/148‑1 (MQ=255)                                            ccTTGCAGGCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTAc                                                                                                        <  8:14837/148‑1 (MQ=255)                                            ccTTGCAGGCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTAc                                                                                                        <  7:292966/148‑1 (MQ=255)                                                 cAGGCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCCCCCGCGACGGGCTGCACAGCAGGCCCATTCCAGCCCCCAGCGGGTCCCCTGCGGCATGACGTACCTGTTc                                                                                                  >  3:302493/1‑149 (MQ=255)                                                  aGGCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTcc                                                                                                 >  4:236601/1‑149 (MQ=255)                                                   ggCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTccc                                                                                                <  7:197221/149‑1 (MQ=255)                                                   ggCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTccc                                                                                                <  1:137317/149‑1 (MQ=255)                                                    gCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTcccc                                                                                               <  4:52383/149‑1 (MQ=255)                                                       ttCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAAc                                                                                                           <  2:84912/134‑1 (MQ=255)                                                       ttCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAAc                                                                                                           >  1:84912/1‑134 (MQ=255)                                                                       tCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCt                                                                            >  8:29904/1‑149 (MQ=255)                                                                                     cgcCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCTGGGCCGGCAACAcc                                                              >  3:305029/1‑149 (MQ=255)                                                                                      gcCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCACCCCCCAGCGAGTACCCGGCTGCATGAACAACCAGTTCCCCCTCACCCCCCTCCTCATCTGGGCCGGCAACACCg                                                             >  4:11847/1‑149 (MQ=38)                                                                                        cAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCTGGGCCGGCAACACCGTg                                                           <  3:236601/149‑1 (MQ=255)                                                                                                aGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCTGGGCCGGCAACACCGTGGTCACCaa                                                   <  1:324103/149‑1 (MQ=255)                                                                                                     tgtgTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCCGCGAGTACCCTGCTGCCTGAACTACCAGGTCCCCCGCACCGCCCTCCTCATCTGGGCCGGCAACACCGTg                                                           >  6:248414/1‑136 (MQ=37)                                                                                                     tgtgTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCTGGGCCGGCAACACCGTg                                                           <  5:248414/136‑1 (MQ=255)                                                                                                             ccccGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCTGGGCCGGCAACACCGTGGTCACCAAGATGTCCGCCGGt                                      <  4:302493/149‑1 (MQ=255)                                                                                                              cccGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCTGGGCCGGCAACACCGTGGTCACCAAGATGTCCGCCGGTg                                     >  5:190453/1‑149 (MQ=255)                                                                                                                cGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCTGGGCCGGCAACACCGTGGTCACCAAGATGTCCGCCGGTGc                                    >  8:347039/1‑148 (MQ=255)                                                                                                                   aGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCCGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCTGGGCCGGCCACACCGGGGTCACCAAGATGGACGCCGGTGCCGTc                                >  4:197807/1‑149 (MQ=39)                                                                                                                       gCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCTGGGCCGGCAACACCGTGGTCACCAAGATGTCCGCCGGTGCCATCCAcc                            >  8:275852/1‑149 (MQ=255)                                                                                                                                     gAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCTGGGCCGGCAACACCGTGGTCACCAAGATGTCCGCCGGTGCCATCCACCCTGCGGAGATCGGc              <  7:188282/149‑1 (MQ=255)                                                                                                                                       ggggCTGCTTTGCAGCCCCATTCCCGCCCCCAGCGAGTACCCGGCGGCATGAACTACCTGTTCCCCCGCCCCGCCCTCCGCATCTGGGCCGGCAACCCCGGGGTCCGCCAGATGTCCGCCGGTGCCATCCACCCTGCGGAGATCGGCtt            >  2:175328/2‑149 (MQ=255)                                                                                                                                       ggggCTGCTTTGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCTGGGCCGGCAACACCGTGGTCACCAAGATGTCCGCCGGTGCCATCCACCCTGCGgagagatcgg             >  1:103403/2‑142 (MQ=255)                                                                                                                                       ggggCTGCTTTGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCTGGGCCGGCAACACCGTGGTCACCAAGATGTCCGCCGGTGCCATCCACCCTGCGga                     <  2:103403/139‑1 (MQ=255)                                                                                                                                        gggCTGCTTTGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCTGGGCCGGCAACACCGTGGTCACCAAGATGTCCGCCGGTGCCATCCACCCTGc                        <  4:352197/136‑1 (MQ=255)                                                                                                                                        gggCTGCTTTGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCTGGGCCGGCAACACCGTGGTCACCAAGATGTCCGCCGGTGCCATCCACCCTGC‑GAGATCggaag            >  3:352197/1‑144 (MQ=255)                                                                                                                                            tGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCTGGGCCGGCAACACCGTGGTCACCAAGATGTCCGCCGGTGCCATCCACCCTGCGGAGATCGGCTTCTAcc       >  7:10252/1‑149 (MQ=255)                                                                                                                                              cAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCTGGGCCGGCAACACCGTGGTCACCAAGATGTCCGCCGGTGCCATCCACCCTGCGGAGATCGGCTTCTACCGc     <  7:347039/149‑1 (MQ=255)                                                                                                                                                 agcagcCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCTGGGCCGGCAACACCGTGGTCACCAAGATGTCCGCCGGTGCCATCCACCCTGCGGAGATCGGCTTCTACCGCTgg  >  8:179009/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                                     CTTGTAGACAGACACTCGATAATACAGGCCTATCGAGGACCTGCCTTGCAGGCCTTCGCGGGCTCCCCGCTCCCACAGGATCTGCGCCAGCCTCCAGGCCTGTGTATCCCCCGTAGGAGCGGGTTCACCCGCGAAGGGCTGCAAAGCAGCCCCATTCCAGCCCCCAGCGAGTACCCTGCTGCATGAACTACCTGTTCCCCCTCACCGCCATCCTCATCTGGGCCGGCAACACCGTGGTCACCAAGATGTCCGCCGGTGCCATCCACCCTGCGGAGATCGGCTTCTACCGCTGG  >  NC_002947/5519773‑5520065

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: ‑