Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,111,743	G→A	11.4%	H180Y (CAT→TAT)	PP_2726 ←	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,111,743	0	G	A	11.4%	90.0 / 3.0	35	H180Y (CAT→TAT)	PP_2726	membrane protein
Reads supporting (aligned to +/- strand):  ref base G (14/17);  new base A (2/2);  total (16/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.90e-01

ACGGTATCCAATGCAGGCGACCAGACCGTATGACCGCAACGTGAACACGCCAGGGTGTCATGAGGCTCATGGTAGGCCGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAAATACAAACTGAGATCGCCATCGGTTTCCAGAAGGCCCAGTCGAACCTGGCCCAGGTGCTCGACACCTTGCTGGCGTAGCTCCATGAACAGCTCATT  >  NC_002947/3111601‑3111890                                                                                                                                               |                                                                                                                                                    aCGGTATCCAATGCAGGCGACCAGACCGTATGACCGCAACGTGAACACGCCAGGGTGTCATGAGGCTCATGGTAGGCCGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGAc                                                                                                                                               <  5:146600/149‑1 (MQ=255)     tATCCAATGCAGGCGACCAGACCGTATGACCGCAACGTGAACACGCCAGGGTGTCATGAGGCTCATGGTAGGCCGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGgc                                                                                                                                           <  8:207327/149‑1 (MQ=255)         cAATGCAGGCGACCAGACCGTATGACCGCAACGTGAACACGCCAGGGTGTCATGAGGCTCATGGTAGGCCGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGgcagca                                                                                                                                       >  7:92231/1‑149 (MQ=255)         cAATGCAGGCGACCAGACCGTATGACCGCAACGTGAACACGCCAGGGTGTCATGAGGCTCATGGTAGGCCGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGgcagc                                                                                                                                        <  5:330962/148‑1 (MQ=255)                           cGTATGACCGCAACGTGAACACGCCAGGGTGTCATGAGGCTCATGGTAGGCCGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCgtg                                                                                                                     <  2:222386/149‑1 (MQ=255)                             tATGACCGCAACGTGAACACGCCAGGGTGTCATGAGGCTCATGGTAGGCCGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCgtgtg                                                                                                                   >  8:107552/1‑149 (MQ=255)                                    gCAACGTGAACACGCCAGGGTGTCATGAGGCTCATGGTAGGCCGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATACTCGACCGGCAGCACTGACAGGCCTGGGCgtgt                                                                                                                    <  1:125924/141‑1 (MQ=255)                                    gCAACGTGAACACGCCAGGGTGTCATGAGGCTCATGGTAGGCCGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATACTCGACCGGCAGCACTGACAGGCCTGGGCgtgt                                                                                                                    >  2:121224/1‑141 (MQ=255)                                    gCAACGTGAACACGCCAGGGTGTCATGAGGCTCATGGTAGGCCGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATACTCGACCGGCAGCACTGACAGGCCTGGGCgtgt                                                                                                                    >  2:125924/1‑141 (MQ=255)                                    gCAACGTGAACACGCCAGGGTGTCATGAGGCTCATGGTAGGCCGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATACTCGACCGGCAGCACTGACAGGCCTGGGCgtgt                                                                                                                    <  1:121224/141‑1 (MQ=255)                                       aCGTGAACACGCCAGGGTGTCATGAGGCTCATGGTAGGCCGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGAt                                                                                                         >  6:65243/1‑149 (MQ=255)                                          tGAACACGCCAGGGTGTCATGAGGCTCATGGTAGGCCGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGt                                                                                                      <  5:65243/149‑1 (MQ=255)                                            aaCACGCCAGGGTGTCATGAGGCTCATGGTAGGCCGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAg                                                                                                    <  7:107552/149‑1 (MQ=255)                                                 gCCAGTTTGTAATGAGGCTCATGGTAGGCCGGGAAACAACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGTCGATGCTCGCCCTGCAGCACTGACAGGCCTCGGCGTGAGACTTGCTGATCGTAGAAATa                                                                                               >  6:347188/1‑149 (MQ=255)                                                       gtgtCATGAGGCTCATGGTAGGCCGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGGGTCTTGCTGATCGTAGAAATACAAACt                                                                                         <  5:347188/149‑1 (MQ=255)                                                       gtgtCATGAGCCTCATGGTAGGCCGGGAAACCACAGCTCACGAAGCAATGCACCCCGCCTCCGGGCGGCGATGTGTACTCAGGGCGAAGCTCGACCGGCAGCACTGACAGGCCTAGGCGTGTGGATTGATGATCGTAGAAATACaaaa                                                                                          >  8:288878/1‑147 (MQ=255)                                                                 gCTCATGGTAGGCCGGGAAACCACAGCTCACGCAGCAATTCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCGCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAACTACAAACTGAGATCGCCa                                                                               <  5:118081/149‑1 (MQ=255)                                                                       ggTAGGCCGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGAACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAAATACAAACTGAGATCGCCATCGGtt                                                                         >  3:128655/1‑149 (MQ=255)                                                                            gCCGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCgtgt                                                                                                                    <  1:137231/101‑1 (MQ=255)                                                                            gCCGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCgtgt                                                                                                                    >  2:137231/1‑101 (MQ=255)                                                                              cGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAAATACAAACTGAGATCGCCATCGGTTTCCAg                                                                    >  6:97466/1‑147 (MQ=255)                                                                                    aCCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAAATACAAACTGAGATCGCCATCGGTTTCCAGAAGGcc                                                              >  5:116836/1‑147 (MQ=255)                                                                                              aCGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAAATACAAACTGAGATCGCCATCGGTTTCCAGAAGGCCCAGTCGAACCTg                                                  >  2:270056/1‑149 (MQ=255)                                                                                               cGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAAATACAAACTGAGATCGCCATCGGTTTCCAGAAGGCCCAGTCGAACCTgg                                                 <  1:270056/149‑1 (MQ=255)                                                                                                    caATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAAATACAAACTGAGATCGCCATCGGTTTCCAGAAGGCCCAGTCGAACCTGGCCCAg                                            <  5:97466/149‑1 (MQ=255)                                                                                                          aCCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAAATACAAACTGAGATCGCCATCGGTTCCCAGAAGGCCCAGTCGAACCTGGCCCAGGTGCTc                                      <  4:33796/149‑1 (MQ=255)                                                                                                          aCCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAAATAC‑AACTGAGATCGCCATCGGTTTCCAGAAGGCCCAGTCGAACCTGGCCCAGGTGCTCg                                     >  7:240064/1‑149 (MQ=255)                                                                                                                 cgcCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAAATACAAACTGAGATCGCCATCGGTTTCCAGAAGGCCCAGTCGAACCTGGCCCAGGTGCTCGACACCt                               <  7:288878/149‑1 (MQ=255)                                                                                                                       gcggcgATGTGTACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAAATACAAACTGAGATCGCCATCGGTTTCCAGAAGGCCCAGTCGAACCTGGCCCAGGTGCTCGACACCTTGCTgg                         <  6:330352/149‑1 (MQ=255)                                                                                                                                tgaaCTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAAATACAAACTGAGATCGCCATCGGTTTCCAGAAGGCCCAGTCGAACCTGGCCCAGGTGCTCGACACCTTGCTGGCGTAGCTc                 <  4:128655/145‑1 (MQ=255)                                                                                                                                       cGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAAATACAAACTGAGATCGCCATCGGTTTCCAGAAGGCCCAGTCGAACCTGGCCCAGGTGCTCGACACCTTGCTGGCGTAGCTCCATGAACa         <  7:182442/149‑1 (MQ=255)                                                                                                                                       cGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAAATACAAACTGAGATCGCCATCGGTTTCCAGAAGGCCCAGTCGAACCTGGCCCAGGTGCTCAACACCTTGCTGGCGTAGCTCCATGaa           <  6:116836/147‑1 (MQ=255)                                                                                                                                           cGATGCTCGATCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAAATACAAACTGAGATCGCCATCGGTTTCCAGAAGGCCCAGTCGAACCTGGCCCAGGTGCTCGACACCTTGCTGGCGTAGCTCCATGAACAGCt      >  6:58470/1‑148 (MQ=255)                                                                                                                                            gATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAAATACAAACTGAGATCGCCATCGGTTTCCAGAAGGCGCAGTCGAACCTGGCCCAGGTGCTCGACACCTTGCTGGCGTAGCTCCATGAACAGCTCa    >  8:94875/1‑149 (MQ=255)                                                                                                                                              tGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAAATACAAACTGAGATCGCCATCGGTTTCCAGAAGGCCCAGTCGAACCTGGCCCAGGTGCTCGACACCTTGCTGGCGTAGCTCCATGAACAGCTCAtt  >  2:325459/1‑149 (MQ=255)                                                                                                                                               gCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAAATACAAACTGAGATCGCCATCGGTTTCCAGAAGGCCCAGTCGAACCTGGCCCAGGTGCTCGACACCTTGCTGGCGTAGCTCCATGAACatttcacc  >  8:243587/1‑141 (MQ=255)                                                                                                                                               |                                                                                                                                                    ACGGTATCCAATGCAGGCGACCAGACCGTATGACCGCAACGTGAACACGCCAGGGTGTCATGAGGCTCATGGTAGGCCGGGAAACCACAGCTCACGCAGCAATGCACCCCGGCGCCGGGCGGCGATGTGTACTCCGGGCGATGCTCGACCGGCAGCACTGACAGGCCTGGGCGTGTGTCTTGCTGATCGTAGAAATACAAACTGAGATCGCCATCGGTTTCCAGAAGGCCCAGTCGAACCTGGCCCAGGTGCTCGACACCTTGCTGGCGTAGCTCCATGAACAGCTCATT  >  NC_002947/3111601‑3111890

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: ‑