Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,529,197	A→G	87.8%	S11P (TCA→CCA)	envZ ←	sensory histidine kinase in two‑component regulatory system with OmpR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,529,197	0	A	G	87.8%	94.6 / 5.8	41	S11P (TCA→CCA)	envZ	sensory histidine kinase in two‑component regulatory system with OmpR
Reads supporting (aligned to +/- strand):  ref base A (2/3);  new base G (20/16);  total (22/19)
Fisher's exact test for biased strand distribution p-value = 6.49e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.78e-01

ATCAACATACGCACTTCGTACGCGAGGACTTTATTAAACTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGAACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGCCCAGACCCCAGACGGTCTGAATGTAACGCGGATGCGCTGGATCTTCTTCCACCATGCGGCGCAGACGCGAAATCTGCACGTCGAT  >  CP009273/3529055‑3529343                                                                                                                                               |                                                                                                                                                   atcaACATACGCACTTCGTACGCGAGGACTTTATTAAACTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATGACGTACGGGACAATGGGCTTCg                                                                                                                                              >  2:198841/1‑149 (MQ=255)                  ctACGCGAGGACTTTATTCAACTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATc                                                                                                                             <  2:189061/148‑1 (MQ=255)                      gcgAGGACTTTATTAAACTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGGGCaa                                                                                                                               >  1:108712/1‑143 (MQ=255)                       cgAGGATTTTATTAAACTGCGGGAGGCTCGGGAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAAt                                                                                                                              <  1:130342/143‑1 (MQ=255)                        gAGGACTTTATTAAACTGCTGGAGGCTCGGCAACATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCa                                                                                                                       <  2:504140/149‑1 (MQ=255)                               ttattaAATCGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGAACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTa                                                                                                                <  2:261838/149‑1 (MQ=255)                                   taAACTGCTGGAGGCTCGGAAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCGGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCtt                                                                                                                  >  1:246466/1‑143 (MQ=255)                                    aaaCTGCTGGAGGCTCGGCAAAATCGCGAATTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGAGCAATCGCCTCATGCttt                                                                                                                 >  1:192887/1‑143 (MQ=255)                                    aaaCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCttt                                                                                                                 >  1:243734/1‑143 (MQ=255)                                     aaCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTa                                                                                                                <  1:464934/143‑1 (MQ=255)                                        tgctgGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTcc                                                                                                       >  2:600903/1‑149 (MQ=255)                                            ggAGGCTCGGCAAAATCGCGAAGTTCAGCACAACCAGATAAGTCGGCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGAACTTAGTGGCGAGAAGCGCAATAGCGTCAGGCTTTAGAGCAGt                                                                                                         >  1:296527/1‑143 (MQ=255)                                                gCTCAGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGAACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACaaa                                                                                               <  2:562506/149‑1 (MQ=255)                                                    ggCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTaac                                                                                                 >  1:22613/1‑141 (MQ=255)                                                     gCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCCCATGCTTTAGAGCCGTCCGGTACaa                                                                                                >  1:2698/1‑143 (MQ=255)                                                         aaTCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAACTGGACTCCGTGGCGAGACGCGCAATCACTCCATCCCTTACACACCTCCGGCACTAAGAc                                                                                            <  1:137735/143‑1 (MQ=255)                                                         aaTCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGGTTTAGAGCCGTCCGGAACAAAGAc                                                                                            >  1:489682/1‑143 (MQ=255)                                                           tCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGATCCGTCCGGTACAAAGACGTAGccca                                                                                    <  2:319927/149‑1 (MQ=255)                                                             gcgAAGTCCAGCACCACCAGATAATTCGGCACCAGGCTGGCGACCAGCAAAGTCACGATGAGCAACAACGTACGCGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGcccata                                                                                  <  2:186350/149‑3 (MQ=255)                                                                   ttCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAGGACGTGGcccgga                                                                                  >  1:510084/1‑143 (MQ=255)                                                                    tCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGcccagac                                                                                 <  1:278322/143‑1 (MQ=255)                                                                          ccaccaGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGGGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGcccagaccccaga                                                                           <  1:227643/143‑1 (MQ=255)                                                                              caGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGCCCAGACCCCAGACGGTCTGAAt                                                                 <  2:142355/149‑1 (MQ=255)                                                                                           aCCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGCCCAGACCCCAGCCGGTCTGAATGTAACGCGGATgc                                                    >  2:294341/1‑149 (MQ=255)                                                                                                 cTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGCCCAGACCCCAGACGGTCTGAATGTAACGCGGaacc                                                    >  1:194003/1‑140 (MQ=255)                                                                                                        aCAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGATTTGTGGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGCCCAGACCCCAGACGGTCTGAATGTAACGCGGATGCGCTGGATcttctt                                       <  2:332922/149‑1 (MQ=255)                                                                                                         cAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGCCCAGACCCCCGACGGTCTGAACGTAACGCGGGCGCGCTGGAtc                                            >  1:198479/1‑143 (MQ=255)                                                                                                                    cGATGAGCAATAACGTACGGGCAAATGGACCTCGGAGCGAGAAACGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGCCCAGACCCCAGACGGTCTGAATGTAACGCGGATGCGCTGGATCTTCTTCCACCATgcggc                           <  2:276277/149‑1 (MQ=255)                                                                                                                     gATGAGCAATAACGTACGGGCAAATGAACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGCCCAGACCCCAGACGGTCTGAATGTACCGCAGATGCGCTGGATCATCTTCCACCATgcggcg                          >  2:160549/1‑149 (MQ=255)                                                                                                                             aTAACGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGCCCAGACCCCAGACGGTCTGAATGTAACGCGGATGCGCTGGATCTTCTTCCACCATGCGGCGCAGAcgcg                  >  2:76500/1‑149 (MQ=255)                                                                                                                              gaaCGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGCCCAGACCCCAGACGGTCTGAATGTAACGCGGATGCGCTGGATCTTCTTCCACCATGCGGCGCAg                       >  1:379355/2‑143 (MQ=255)                                                                                                                                ccgatctggCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGCCCAGACCCCAGACGGTCTGAATGTAACGCGGATGCGCTGGATCTTCTTCCACCATGCGGCGCAGACGCGaaa               <  2:106422/142‑1 (MQ=255)                                                                                                                                aCGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGCCCAGACCCCAGACGGTCTGAATGTAACGCGGATGCGCTGGATCTTCTTCCACCATGCGGCGCAGACGCGaaa               <  2:217380/149‑1 (MQ=255)                                                                                                                                 cGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGCCCAGACCCCAGACGGTCTGAATGTAACGCGGATGCGCTGGATCTTCTTCCACCATGCCGGGCAgccc                    >  1:518320/1‑140 (MQ=255)                                                                                                                                 cGTACGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGCCCAGACCCCAGACGGTCCGCCTGTAACGCGGATGCGCTGGATCTTCTTCCACCATGCGGCGCAGACGCGAAAt              <  2:498346/149‑1 (MQ=255)                                                                                                                                     cGGGCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGCCCAGACCCCAGACGGTCTGAATGTAACGCGGATGCGCTGGATCTCCTTCCACCATGCGGAGCAGAAGCGAAAGCTGc          >  2:141588/1‑149 (MQ=255)                                                                                                                                      gggCAAATGGACTACGTGGCGCGAAGCGCAATCGCCTCATGCTTTAGGGCCGTCCGGTACAAAGACGTAGCCCAGACCCCAGACGGTCTGAATGTAACGCGGATGCGCTGGATCTTCTTCCACCATGCGGCGCAGACGCGaaa               <  1:543110/143‑1 (MQ=255)                                                                                                                                        gCAAATGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGGCCGGTACAAAGACGTAGCCCAGACCCCAGACGGTCTGAATGTAACGCGGATGCGCTGGATCTTCTTCCACCATGCGGCGCAGACGCGAAAtg             >  1:95346/1‑142 (MQ=255)                                                                                                                                            aTGGACTTCGTGGCGAGATGCGCAATCGCCTCAAGCTTTAGAGCCGTCCGGTACAAAGAAGTAGGCCAGACCCCAGCCGGTCTGAATGTAACGCAGATGCGCTGGATCTTCTTCCACCACGCGGCGCAGACGCGAAATCTGCa         >  1:71783/1‑143 (MQ=255)                                                                                                                                            aTGGACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGCCCAGACCCCAGACGGGCTGAATGTAACGCGGATGCGCTGGCTCTTCGTCCACCCTGCGGCGCAGACGCGAAATCTGcc         >  1:456830/1‑142 (MQ=255)                                                                                                                                             tGAACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGCCCAGACCCCAGACGGTCTGAATGTAACGCGGATGCGCTGGATCTTCTTCCACCATGCGGCGCAGACGCGAAATCTGCACGTCGAt  <  2:410116/149‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                   ATCAACATACGCACTTCGTACGCGAGGACTTTATTAAACTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTACGGGCAAATGAACTTCGTGGCGAGAAGCGCAATCGCCTCATGCTTTAGAGCCGTCCGGTACAAAGACGTAGCCCAGACCCCAGACGGTCTGAATGTAACGCGGATGCGCTGGATCTTCTTCCACCATGCGGCGCAGACGCGAAATCTGCACGTCGAT  >  CP009273/3529055‑3529343

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑