Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,225,951	A→G	8.5%	S49S (TCT→TCC)	PP_3705 ←	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,225,951	0	A	G	8.5%	128.8 / 2.2	47	S49S (TCT→TCC)	PP_3705	membrane protein
Reads supporting (aligned to +/- strand):  ref base A (21/22);  new base G (2/2);  total (23/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.12e-01

ACGCATCCCAACCAGAATAATGGCAACAACTATTAAAGTAACCGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAGAATAGAGAGGCTTACGCACAATAAATATAATGAATACGACAGCAGGAACTATTACCCAAGTCAAAC  >  NC_002947/4225804‑4226099                                                                                                                                                     |                                                                                                                                                     aCGCATCCCAACCAGAATAATGGCAACAACTATTAAAGTAACCGTCAAGCGAAGCAGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAg                                                                                                                                                     <  6:99118/149‑1 (MQ=255)          aaCCAGAATAATGGCAACAACTATTAAAGTAACCGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTa                                                                                                                                            >  6:45071/1‑149 (MQ=255)          aaCCAGAATAATGGCAACAACTATTAAAGTAACCGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTa                                                                                                                                            <  1:19601/149‑1 (MQ=255)          aaCCAGAATAATGGCAACAACTATTAAAGTAACCGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTa                                                                                                                                            >  7:191469/1‑149 (MQ=255)           aCCAGAATAATGGCAACAACTATTAAAGTAACCGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTAc                                                                                                                                           >  1:255755/1‑149 (MQ=255)             cAGAATAATGGCAACAACTATTAAAGTAACCGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGa                                                                                                                                         <  7:75644/149‑1 (MQ=255)                    atGGCAACAACTATTAAAGTAACCGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCaaa                                                                                                                                  <  8:210602/149‑1 (MQ=255)                       gCAACAACTATTAAAGTAACCGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATa                                                                                                                                >  5:75348/1‑148 (MQ=255)                        caacaaCTATTAAAGTAACCGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACa                                                                                                                              <  7:235861/149‑1 (MQ=255)                        caacaaCTATTAAAGTAACCGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACa                                                                                                                              <  1:191934/149‑1 (MQ=255)                         aacaacTATTAAAGTAACCGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAg                                                                                                                             >  2:132291/1‑149 (MQ=255)                         aacaacTATTAAAGTAACCGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAg                                                                                                                             >  5:191646/1‑149 (MQ=255)                                 ttAAAGTAACCGTCAAGAGAAGCTGCCAATACTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAAtt                                                                                                                     >  1:29267/1‑149 (MQ=255)                                   aaaGTAACCGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGAcccc                                                                                                                                     >  7:137851/1‑131 (MQ=255)                                   aaaGTAACCGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGAcccc                                                                                                                                     <  8:137851/131‑1 (MQ=255)                                    aaGTAACCGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAGAATCAGCAAAGAAACCATTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAGGACGCCCCTACGACCCCAAATACAGCTACAATTgc                                                                                                                   >  1:66772/1‑149 (MQ=255)                                    aaGTAACCGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTgcg                                                                                                                  >  7:105495/1‑149 (MQ=255)                                      gTAACCGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAGGACGCCCCTACGACCCCAAATACAGCTACAATTgcggc                                                                                                                <  2:66772/149‑1 (MQ=255)                                         aCCGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGATAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGAGgcgc                                                                                                              <  5:223681/148‑1 (MQ=255)                                           cGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAg                                                                                                           <  5:45071/149‑1 (MQ=255)                                                 gagaAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAg                                                                                                           >  3:169445/1‑143 (MQ=255)                                                 gagaAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAg                                                                                                           <  4:169445/143‑1 (MQ=255)                                                 gagaAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAAc                                                                                                     >  3:81767/1‑149 (MQ=255)                                                  agaAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAAcc                                                                                                    <  4:62226/149‑1 (MQ=255)                                                       ttGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGa                                                                                                 >  4:36795/2‑147 (MQ=255)                                                         gCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGt                                                                                             >  8:86924/1‑149 (MQ=255)                                                           cAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGttt                                                                                           >  6:237202/1‑149 (MQ=255)                                                            aaTTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTg                                                                                          <  7:240863/149‑1 (MQ=255)                                                                   aGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCaa                                                                                    <  2:162121/148‑1 (MQ=255)                                                                         cTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGa                                                                             <  8:191469/149‑1 (MQ=255)                                                                            gag‑aTCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGAt                                                                            <  2:255755/147‑1 (MQ=255)                                                                                    gCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAGGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAg                                                                    >  2:190819/1‑148 (MQ=255)                                                                                     cAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAGaa                                                                  <  2:29267/149‑1 (MQ=255)                                                                                          aaaCCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAGAATagag                                                             <  6:75348/149‑1 (MQ=255)                                                                                           aaCCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAGGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAGAATagaga                                                            <  1:190819/149‑1 (MQ=255)                                                                                                ttGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAGAATAGAGAGGCt                                                        >  1:263632/1‑148 (MQ=255)                                                                                                        aaCTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAGAATAGAGAGGCTTACGCACaa                                               <  4:81767/149‑1 (MQ=255)                                                                                                             cACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAGAATAGAGAGGCTTACGCACaataaa                                           >  6:113426/1‑148 (MQ=255)                                                                                                                    cgcAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACTATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAGAATAGAGAGGCTTACGCACAATAAATATAATg                                    <  6:191646/148‑1 (MQ=255)                                                                                                                              ggAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAGAATAGAGAGGCTTACGCACAATAAATATAATGAATACGAcagc                         <  1:132291/149‑1 (MQ=255)                                                                                                                                       tAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAGAATAGAGAGGCTTACGCACAATAAATATAATGAATACGACAGCAGGAACt                  <  7:86924/147‑1 (MQ=255)                                                                                                                                            ggAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAGAATAGAGAGGCTTACGCACAATAAATATAATGAATACGGCAGCAGGAACTATTAcc            >  5:67260/1‑148 (MQ=255)                                                                                                                                                  acaAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAGAGTAGAGAGGCTTACGCACAATAAATATAATGAATACGACAGCAGGAACTATTAc             >  2:290460/1‑141 (MQ=255)                                                                                                                                                  acaAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAGAGTAGAGAGGCTTACGCACAATAAATATAATGAATACGACAGCAGGAACTATTAc             <  1:290460/141‑1 (MQ=255)                                                                                                                                                  acaAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAGAATAGAGAGGCTTACGCACAATAAATATAATGAATACGACAGCAGGAACTATTACCCAAGTc      >  5:286436/1‑148 (MQ=255)                                                                                                                                                  acaAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAGAATAGAGAGGCTTACGCACAATAAATATAATGAATACGACAGCAGGAACTATTACCCAAGTc      >  1:201342/1‑148 (MQ=255)                                                                                                                                                  acaAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAGAATAGAGAGGCTTACGCACAATAAATATAATGAATACGACAGCAGGAACTATTACCCAAGTc      >  4:213450/1‑148 (MQ=255)                                                                                                                                                    aaGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCcgcg                                                                              <  2:87599/74‑1 (MQ=255)                                                                                                                                                    aaGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCcgcg                                                                              >  1:87599/1‑74 (MQ=255)                                                                                                                                                    aaGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAGAATAGAGAGGCTTACGCACAATAAATATAATGAATACGACAGCAGGAACTATTACCCAAGTCaaa   >  3:102874/1‑149 (MQ=255)                                                                                                                                                     aGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAGAATAGAGAGGCTTACGCACAATAAATATAATGAATACGACAGCAGGAACTATTACCCAAGTCAAAc  >  4:159527/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                     ACGCATCCCAACCAGAATAATGGCAACAACTATTAAAGTAACCGTCAAGAGAAGCTGCCAATTCTGAGGCAGCTTGAG‑ATCAGCAAAGAAACCCTTGAAGTAAACTTCACCCTGCGCAAGGATAGGAGCGCTGTAAATGGAGACACAAGACGCCCCTACGACCCCAAATACAGCTACAATTGCGGCGCCAGTCGAACCAGATAGTTTGCGGCAAGCCGCGATAAACGCAGAATAGAGAGGCTTACGCACAATAAATATAATGAATACGACAGCAGGAACTATTACCCAAGTCAAAC  >  NC_002947/4225804‑4226099

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: ‑