Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,821,960	C→T	13.7%	T80M (ACG→ATG)	PP_2475 →	TetR family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,821,960	0	C	T	13.7%	68.6 / 2.6	29	T80M (ACG→ATG)	PP_2475	TetR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (13/12);  new base T (2/2);  total (15/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACGAGATTTTGCAGGCCGCTAACGTGCCGAAAGGCTCGTTTTACCATTATTTTAAGTCCAAAGAGCAGTACGGCCAGTCGTTGCTTGAGGATTACTTTCGCAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCTGCGACGACCAGAAGTGCCTGGTGGTGAAGCTGAGCGCAGAGGTAGCTGATCTTTCGGAGCCCATGCGCCTCACGCTGCGCGATGG  >  NC_002947/2821812‑2822104                                                                                                                                                     |                                                                                                                                                 aaCGAGATTTTGCAGGCCGCTAACGTGCAGAAAGGCTCGTTTTAGCATTTTTTTAAGACCAAAGAGCAGTAGGACCAGACGTTGCTAGAGGATTACTTTCGGCATTATTTGGCTAGCAAGGATGAGCGTATTGCGGTCACGGGCAacac                                                                                                                                                  >  6:236699/1‑149 (MQ=255)           tGCAGGCCGCTAACGTGCCGAAAGGCTCGTTTTACCATTATTTTAAGTCCAAAGAGCAGTACGGCCAGTCGTTGCTTGAGGATTACTTTCGCAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGa                                                                                                                                         <  1:18866/148‑1 (MQ=255)                  cGCTAACGTGCCGAAAGGCTCGTTTTACCATTATTTTAAGTCCAAAGAGCAGTACGGCCAGTCGTTGCTTGAGGATTACTTTCGCAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGa                                                                                                                                 >  4:27097/1‑149 (MQ=255)                       tcGTGCCGAAAGGCTCGTTTTACCATTATTTTAAGTCCAAAGAGCAGTACGGCCAGTCGTTGCTTGAGGATTACTATCGCATTTATTTGGCGATCATGGATGATCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATggg                                                                                                                             <  5:236699/147‑1 (MQ=255)                            ccGAAAGGCTCGTTTTACCATTATTTTAAGTCCAAAGAGCAGTACGGCCAGTCGTTGCTTGAGGATTACTTTCGCAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTg                                                                                                                       <  6:340959/149‑1 (MQ=255)                              gAAAGGCTCGTTTTACCATTATTTTAAGTCCAAAGAGCAGTACGGCCAGTCGTTGCTTGAGGATTACTTTCGCAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTgg                                                                                                                      >  2:255490/1‑148 (MQ=255)                                   gCTCGTTTTACCATTATTTTAAGTCCAAAGAGCAGTACGGCCAGTCGTTGCTTGAGGATTACTTTCGCAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAg                                                                                                                >  2:327967/1‑149 (MQ=255)                                     tCGTTTTACCATTATTTTAAGTCCAAAGAGCAGTACGGCCAGTCGTTGCTTGAGGATTACTTTCGCAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACATGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTg                                                                                                              >  7:39384/1‑149 (MQ=255)                                              cATTATTTTAAGTCCAAAGAGCAGTACGGCCAGTCGTTGCTTGAGGATTACTTTCGCAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTAtt                                                                                                                        >  1:5002/1‑130 (MQ=255)                                              cATTATTTTAAGTCCAAAGAGCAGTACGGCCAGTCGTTGCTTGAGGATTACTTTCGCAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTAtt                                                                                                                        <  2:5002/130‑1 (MQ=255)                                                              aaGAGCAGTACGGCCAGTCGTTGCTTGAGGATTACTTTCGCAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCt                                                                                       >  4:211748/1‑147 (MQ=255)                                                                gagCAGTACGGCCAGTCGTTGCTTGAGGATTACTTTCGCAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCTGcga                                                                                   <  3:103471/149‑1 (MQ=255)                                                                 agCAGTACGGCCAGTCGTTGCTTGAGGATTACTTTCGCAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCTGcgac                                                                                  <  3:211748/149‑1 (MQ=255)                                                                              gTCGTTGCTTGAGGATTACTTTCGCAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTa                                                                                                          >  5:114923/1‑112 (MQ=255)                                                                              gTCGTTGCTTGAGGATTACTTTCGCAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTa                                                                                                          <  6:114923/112‑1 (MQ=255)                                                                                      ttGAGGATTACTTTCGCAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCTGCGACGACCAGAAGTGCCTggtggt                                                              >  8:167140/1‑148 (MQ=255)                                                                                            aTTACTTTCGCAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCTGCGACGACCAGAAGTGCCTGGTGGTGAAGCt                                                        >  2:192142/1‑148 (MQ=255)                                                                                                 tttCGCAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCTGCGACGACCAGAAGTGCCTGGTGGTGAAGCTGAgcg                                                   >  8:106731/1‑148 (MQ=255)                                                                                                     gCAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCTGCGACGACCAGAAGTGCCTGGTGGTGAAGCTGAGCGCagag                                              <  3:27097/149‑1 (MQ=255)                                                                                                      cAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCTGCGACGACCAGaa                                                                          <  4:156547/120‑1 (MQ=255)                                                                                                       aaTTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCTGCGACGACCAGAAGTGCCTGGTGGTGAAGCTGAGCGCAGAgg                                             >  7:70133/1‑148 (MQ=255)                                                                                                       aaTTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCTGCGACGACCAGAAGTGCCTGGTGGTGAAGCTGAGCGCAGAGGt                                            <  5:96348/149‑1 (MQ=255)                                                                                                          tattTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCTGCGACGACCAGAAGTGCCTGGTGGTGAAGCTGAGCGCAGAGGTAGc                                         >  2:125271/1‑149 (MQ=255)                                                                                                           attTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCTGCGACGACCAGAAGTGCCTGGTGGTGAAGCTGAGCGCAGAGGTAGCt                                        >  5:165772/1‑149 (MQ=255)                                                                                                                  gAGCATGGATGAGCGTTTTGCCGTCACGGGCAACATGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCTGCGACGACCAGAAGTGCCTGGTGGTGAAGCTGAGCGCAGAGGTAGCTGATCttt                                 <  8:39384/149‑1 (MQ=255)                                                                                                                          aTGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCTGCGACGACCAGAAGTGCCTGGTGGTGAAGCTGAGCGCAGAGGTAGCTGATCTTTCGGAGccc                         <  1:327967/149‑1 (MQ=255)                                                                                                                              gCGTTTTGCCGTCACGGGCAACATGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCTGCGACGACCAGAAGTGCCTGGTGGTGAAGCTGAGCGCAGAGGTAGCTGATCTTTCGGAGCCCATgc                     >  3:166204/1‑149 (MQ=255)                                                                                                                                           aCGGGCAACATGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCTGCGACGACCAGAAGTGCCTGGTGGTGAAGCTGAGCGCAGAGGTAGCTGATCTTTCGGAGCCCATGCGCCTCACGCTgc         <  4:166204/148‑1 (MQ=255)                                                                                                                                             gggCAACACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCTGCGACGACCAGAAGTGCCTGGTGGTGAAGCTGAGCGCAGAGGTAGCTGATCTTTCGGAGCCCATGCGCCTCACGCTgcgc       >  2:50691/1‑148 (MQ=255)                                                                                                                                                 aaCACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCTGCGACGACCAGAAGTGCCTGGTGGTGAAGCTGAGCGCAGAGGTAGCTGATCTTTCGGAGCCCATGCGCCTCACGCTGCGCGATgg  <  7:167140/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                 AACGAGATTTTGCAGGCCGCTAACGTGCCGAAAGGCTCGTTTTACCATTATTTTAAGTCCAAAGAGCAGTACGGCCAGTCGTTGCTTGAGGATTACTTTCGCAATTATTTGGCGAGCATGGATGAGCGTTTTGCCGTCACGGGCAACACGGCTCGCGAGCGCCTGATGGGGTATTGGCAGAAGTGGCTAGACAGCTACTGCGAGCCCTGCGACGACCAGAAGTGCCTGGTGGTGAAGCTGAGCGCAGAGGTAGCTGATCTTTCGGAGCCCATGCGCCTCACGCTGCGCGATGG  >  NC_002947/2821812‑2822104

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑