Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,088,540	A→T	12.9%	intergenic (+31/‑223)	pmbA → / → PP_0943	regulatory protease/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,088,540	0	A	T	12.9%	82.1 / 5.3	31	intergenic (+31/‑223)	pmbA/PP_0943	regulatory protease/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (14/13);  new base T (2/2);  total (16/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.87e-01

TGAAGGACATGTTCCAGCAGATTGTCGCGATCGGTAGCGATCTTGAAACCCGTAGCAATATTCATACGGGCTCGGTGTTGATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGCACTACACCTTTCCCTGCAAATCCGAAGACCCGGCCCTCGCGCCGGGTTTT  >  NC_002947/1088400‑1088679                                                                                                                                             |                                                                                                                                            tGAAGGACATGTTCCAGCAGATTGTCGCGATCGGTAGCGATCTTGAAACCCGTAGCAATATTCATCCGATCTTGGTGTTGATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTc                                                                                                                                    <  1:38893/150‑1 (MQ=255)                               tCGGTAGCGATCTTGAAACCCGTAGCAATATTCATACGGGCTCGGTGTTGATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTg                                                                                                      <  1:362414/150‑1 (MQ=255)                                   tAGCGATCTTGAAACCCGTAGCAATATTCATACGGGCTCGGTGTTGATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTTTACCCGcgaaag                                                                                                                                 >  2:542053/1‑114 (MQ=39)                                   tAGCGATCTTGAAACCCGTAGCAATATTCATACGGGCTCGGTGTTGATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTTTACCCGcgaaag                                                                                                                                 <  1:542053/119‑6 (MQ=39)                                           ttGAAACCCGTAGCAATATTCATACGGGCTCGGTGTTGATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGt                                                                                          >  1:29530/1‑150 (MQ=255)                                              aaaCCCGTAGCAATATTCATACGGGCTCGGTGTTGATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGt                                                                                       >  1:422049/1‑150 (MQ=255)                                                    gTAGCAATATTCATACGGGCTCGGTGTTGATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGc                                                                                 <  1:547350/150‑1 (MQ=255)                                                        cAATATTCATACGGGCTCGGTGTTGATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGCGGGt                                                                             <  2:164374/150‑1 (MQ=255)                                                          atatTCATACGGGCTCGGTGTTGATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTTTACCCGcgaaa                                                                                                                                  >  2:375346/1‑91 (MQ=38)                                                          atatTCATACGGGCTCGGTGTTGATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTTTACCCGcgaaa                                                                                                                                  <  1:375346/95‑5 (MQ=38)                                                                     ggCTCGGTGTTGATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGCGTTGGACACAGGCCGTTGTAGGAGCGGGTTCACCCGCGAagt                                                                <  2:1138/150‑2 (MQ=255)                                                                       cTCGGTGTTGATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGCGGGTTc                                                                           >  1:211701/1‑137 (MQ=255)                                                                       cTCGGTGTTGATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGCGGGTTc                                                                           <  2:211701/137‑1 (MQ=255)                                                                            tgtTGATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGa                                                         >  1:143381/1‑150 (MQ=255)                                                                                gATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGgtggtg                                                                                                                       >  1:159964/1‑84 (MQ=255)                                                                                gATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGgtggtg                                                                                                                       <  2:159964/84‑1 (MQ=255)                                                                                gATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTa                                                                                      >  1:452576/1‑117 (MQ=255)                                                                                gATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTa                                                                                      <  2:452576/117‑1 (MQ=255)                                                                                     aGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGCGGGTTCACCcgc                                                                     <  2:313981/129‑1 (MQ=255)                                                                                     aGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGCGGGTTCACCcgc                                                                     >  1:313981/1‑129 (MQ=255)                                                                                        ggATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGCACTacac                                             <  2:422049/150‑1 (MQ=255)                                                                                         gATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGCACTACAcc                                            >  2:533953/1‑150 (MQ=255)                                                                                             aCCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGCACTACACCTTTc                                        >  2:404604/1‑150 (MQ=255)                                                                                                gTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGCACTACACCTTTCCCt                                     >  2:453331/1‑150 (MQ=255)                                                                                                    cTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGCACTACACCTTTCCCTGCaa                                 >  2:268023/1‑150 (MQ=255)                                                                                                                 tttAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGCACTACACCTTTCCCTGCAAATCCGCAGACCCg                    >  2:523608/1‑150 (MQ=255)                                                                                                                      ccTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGCACTACACCTTTCCCTGCAAATCCGAAGACCCGGCCCt               <  1:533953/150‑1 (MQ=255)                                                                                                                        tGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGCACTACACCTTTCCCTGCAAATCCGAAGACCCGGcgcgag             >  1:412538/1‑145 (MQ=255)                                                                                                                                   tttCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGCACTACACCTTTCCCTGCAAATCCGAAGACCCg                    <  1:524899/132‑1 (MQ=255)                                                                                                                                   tttCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGCACTACACCTTTCCCTGCAAATCCGAAGACCCg                    >  2:524899/1‑132 (MQ=255)                                                                                                                                   tttCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGCACTACACCTTTCCCTGCAAATCCGAAGACCCGGCCCTCGCGCCGGGtttt  <  2:143381/150‑1 (MQ=255)                                                                                                                                             |                                                                                                                                            TGAAGGACATGTTCCAGCAGATTGTCGCGATCGGTAGCGATCTTGAAACCCGTAGCAATATTCATACGGGCTCGGTGTTGATCGAGCGGATGACCGTTGCTGGTAGCTGATCTTTAGCCTGCGCCGGCCCTTTCGCGGGTAAACCCGCTCCTACACGGTGGTGGACGTACATCGGGGTTGGACACAGGCCGTTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGCACTACACCTTTCCCTGCAAATCCGAAGACCCGGCCCTCGCGCCGGGTTTT  >  NC_002947/1088400‑1088679

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑