Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,942,369	T→C	13.0%	intergenic (+47/‑158)	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	1,942,369	0	T	C	13.0%	86.6 / 6.0	39	intergenic (+47/‑158)	betX/yjcH	choline/betaine/carnitine ABC transporter substrate‑binding protein BetX/inner membrane protein
Reads supporting (aligned to +/- strand):  ref base T (18/15);  new base C (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 = 3.17e-01

ATGCTGGCGATCCAGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAGGGTGTGGGTTCCATCCCGTATCTGTGCTGCTA  >  NC_002947/1942227‑1942515                                                                                                                                               |                                                                                                                                                    aTGCTGGCGATCCAGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACggg                                                                                                                                                <  5:252871/148‑1 (MQ=255)     tGGCGATCCAGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCgg                                                                                                                                           >  6:358583/1‑149 (MQ=255)       gCGATCCAGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGt                                                                                                                                         >  1:49509/1‑149 (MQ=255)        cGATCCAGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGtt                                                                                                                                        <  5:358583/149‑1 (MQ=255)        cGATCCAGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGtt                                                                                                                                        >  3:195347/1‑149 (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                                                                                                                                  <  3:150302/138‑1 (MQ=38)                        cAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCACCCGTAGGAGCGGGTTTA‑ccc                                                                                                                                  >  4:150302/1‑138 (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)                                                                                                                                               |                                                                                                                                                    ATGCTGGCGATCCAGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAGGGTGTGGGTTCCATCCCGTATCTGTGCTGCTA  >  NC_002947/1942227‑1942515

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: ‑