Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,942,366	T→A	12.9%	intergenic (+44/‑161)	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	1,942,366	0	T	A	12.9%	84.4 / 6.7	39	intergenic (+44/‑161)	betX/yjcH	choline/betaine/carnitine ABC transporter substrate‑binding protein BetX/inner membrane protein
Reads supporting (aligned to +/- strand):  ref base T (19/15);  new base A (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 = 2.28e-01

GATGCTGGCGATCCAGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAGGGTGTGGGTTCCATCCCGTATCTGTGC  >  NC_002947/1942226‑1942510                                                                                                                                             |                                                                                                                                                  gATGCTGGCGATCCAGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTc                                                                                                                                                  >  1:163406/1‑142 (MQ=255) gATGCTGGCGATCCAGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTc                                                                                                                                                  <  2:163406/142‑1 (MQ=255)  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                                                                                                                              <  7:64003/141‑1 (MQ=38)                     gggCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCACCCGTAGGAGCGGGTTTA‑cc                                                                                                                              >  8:64003/1‑141 (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)                                                                                                                                             |                                                                                                                                                  GATGCTGGCGATCCAGGAAGGGGCCAAGCCTGAAGCGGCCGCCAAGGACTGGGTCGCCAAGCACCCTGATCGTGTGAAGGAGTGGACTGGCAAGTAAAAGCCTTCCAGGGCCAATGTTGTTTCTTCGCGGGTAAACCCGCTCCTACGGGTGCGGGTTTA‑CCCGCGAACGGGTCATCACTTTGTTACGCAATCGGTAAAACACCGTTGCATCTAAGACTAAGGTCGTCTGGTTGGCGTCCATCGGCAGCATAAAGTAAGGGTGTGGGTTCCATCCCGTATCTGTGC  >  NC_002947/1942226‑1942510

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: ‑