Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,942,370	A→G	13.2%	intergenic (+48/‑157)	betX → / → yjcH	choline/betaine/carnitine ABC transporter substrate‑binding protein BetX/inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,942,370	0	A	G	13.2%	85.6 / 6.5	39	intergenic (+48/‑157)	betX/yjcH	choline/betaine/carnitine ABC transporter substrate‑binding protein BetX/inner membrane protein
Reads supporting (aligned to +/- strand):  ref base A (19/13);  new base G (3/2);  total (22/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.60e-01

ATGCTGGCGATCCAGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAGGGTGTGGGTTCCATCCCGTATCTGTGCTGCTAGGA  >  NC_002947/1942227‑1942518                                                                                                                                                |                                                                                                                                                      aTGCTGGCGATCCAGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACggg                                                                                                                                                   <  5:252871/148‑1 (MQ=255)     tGGCGATCCAGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCgg                                                                                                                                              >  6:358583/1‑149 (MQ=255)       gCGATCCAGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGt                                                                                                                                            >  1:49509/1‑149 (MQ=255)        cGATCCAGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGtt                                                                                                                                           >  3:195347/1‑149 (MQ=255)        cGATCCAGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGtt                                                                                                                                           <  5:358583/149‑1 (MQ=255)          aTCCAGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGTTTa                                                                                                                                         <  6:70837/149‑1 (MQ=255)              aGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACgg                                                                                                                                                    <  4:245722/134‑1 (MQ=255)              aGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACgg                                                                                                                                                    >  3:245722/1‑134 (MQ=255)                    gggCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCACCCGTAGGAGCGGGTTTA‑cc                                                                                                                                      >  8:64003/1‑141 (MQ=38)                    gggCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCACCCGTAGGAGCGGGTTTA‑cc                                                                                                                                      <  7:64003/141‑1 (MQ=38)                      gCCAAGCCTGAAGCGGCCGCCATGGACTGGGTCGCCAAGTACCCTGATGGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGTTTA‑CCcg                                                                                                                                    <  6:68841/141‑1 (MQ=255)                      gCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGTTAA‑CCcg                                                                                                                                    >  5:68841/1‑141 (MQ=255)                        cAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCACCCGTAGGAGCGGGTTTA‑ccc                                                                                                                                     >  4:150302/1‑138 (MQ=38)                        cAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCACCCGTAGGAGCGGGTTTA‑ccc                                                                                                                                     <  3:150302/138‑1 (MQ=38)                               taaGCGGCGGCAATGGAGTGGGGCGCAATGAACCGTTTTGGTGTTATGGAGTGGATTGGCAATTAAAAGCCTTCCCGGGCAAATTTTTTTTCTTCGGGGGTAAACCCGCTCCTAGGGGTGGGGTTTTA‑CCCGCGAACGGGTCATCACt                                                                                                                    <  6:283137/147‑1 (MQ=255)                                   cGGCCGCCAAGGACGGGGTCGCCAAGCACCCTGATCGTGTCAAGGAGTGGACTGCCAAGTAAAAGCCTTCCAGGGCAAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGtt                                                                                                               <  5:133802/149‑1 (MQ=255)                                            aGGACTGGGGCGCCAAGCACCTTGATCGTGTGAAGGAGTGGACTGGCAATTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGAAAACCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCg                                                                                                      <  2:49509/149‑1 (MQ=255)                                                                ccTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCt                                                                                   >  1:96418/1‑148 (MQ=255)                                                                                    gACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTg                                                              >  2:246051/1‑149 (MQ=255)                                                                                       tGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCg                                                           >  1:317658/1‑149 (MQ=255)                                                                                           aaGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCTTCTGGTTGGCGTCCa                                                       >  7:278877/1‑149 (MQ=255)                                                                                           aaGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCa                                                       >  3:303588/1‑149 (MQ=255)                                                                                                          aGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGCTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATaaa                                          >  3:183383/1‑147 (MQ=255)                                                                                                             gCCATTGTTGTTTCTTCGGGGTTAAACCCGCTCCTCCGGGTGGGGTTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAg                                     <  2:317658/149‑1 (MQ=255)                                                                                                              ccAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAgg                                    <  2:96418/149‑1 (MQ=255)                                                                                                                    ttttttCTTCGCTGTTAACCCCGCTCCTCGGGGTGGGGTTTAA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAGGGtgtg                               <  8:51155/145‑1 (MQ=255)                                                                                                                      gttTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAGGGtgtg                               >  7:51155/1‑146 (MQ=255)                                                                                                                      gttTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAGGGTGTGGGt                            >  4:174903/1‑149 (MQ=255)                                                                                                                       tttCTTCGCGGGTAAACCCGCTCCTACGGGTGCGTGTTTA‑CCCGCGAACGAGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAGGGTGTGGGt                            <  4:195347/148‑1 (MQ=255)                                                                                                                       tttCTTCGCGGGTAAACCCGCTCCGACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGTCTTAGGTCGTCTGGTTGGCGGCCATCGGCAGCATAAAGTAAGGGTGTggggt                           >  3:175156/1‑147 (MQ=255)                                                                                                                                gggTAAACCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGAATAAAGTAAGGGAGTGGGTTCCAtgacg                   >  8:273968/1‑144 (MQ=255)                                                                                                                                 ggTAAACCCGCTCCTACGGGTGCGGGTTTANCCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGAGTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAGGgt                                  >  1:33082/1‑133 (MQ=255)                                                                                                                                 ggTAAACCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAGGgt                                  <  2:33082/132‑1 (MQ=255)                                                                                                                                 ggTAAACCCGCACCCGTAGGAGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAGGTAAGGGTGTGGGTTCCATCCCGt                  >  8:242829/1‑148 (MQ=38)                                                                                                                                      aCCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAGGGTGTGGGTTCCATCCCGTATCtgt            >  1:356214/1‑149 (MQ=255)                                                                                                                                       cccGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAGGGTGTGGGTTCCATCCCGTATCtgtg           >  2:57379/1‑149 (MQ=255)                                                                                                                                        ccGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAGGGTGTGGGTTCCATCCCGTATCTGtgc          <  3:174903/149‑1 (MQ=255)                                                                                                                                              cTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAGGGTGTGGGTTCCATCCCGTATCTGtgctgc       >  7:187265/1‑146 (MQ=255)                                                                                                                                              cTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAGGGTGTGGGTTCCATCCCGTATCTGTGCTGCTa     <  8:187265/148‑1 (MQ=255)                                                                                                                                                aCGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAAGCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAGGGTGTGGGTTCCATCCCGTATCTGTGCTGCTAGGa  >  1:258626/1‑149 (MQ=255)                                                                                                                                                |                                                                                                                                                      ATGCTGGCGATCCAGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAGGGTGTGGGTTCCATCCCGTATCTGTGCTGCTAGGA  >  NC_002947/1942227‑1942518

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: ‑