Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,087,589	T→C	intergenic (‑239/‑75)	rhaD ← / → rhaS	rhamnulose‑1‑phosphate aldolase/HTH‑type transcriptional activator RhaS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,087,589	0	T	C	100.0%	181.1 / NA	49	intergenic (‑239/‑75)	rhaD/rhaS	rhamnulose‑1‑phosphate aldolase/HTH‑type transcriptional activator RhaS
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (22/27);  total (22/27)

TGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTTCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTTCCGTCTGGTAA  >  NZ_CP009273/4087456‑4087704                                                                                                                                      |                                                                                                                    tGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTc                                                                                                                >  1:199877/1‑139 (MQ=255)           gCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTa                                                                                                       <  2:95027/138‑1 (MQ=255)              aCCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGt                                                                                                   <  2:407367/139‑1 (MQ=255)               ccAGGGAAAGATGAACGTGATGATGTTCACAATTTGCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTa                                                                                                  <  1:130333/139‑1 (MQ=255)                cAGGGAAAGATGAACGTGATGATGTTCACAATTTGCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACG‑TTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAg                                                                                                <  2:463965/139‑1 (MQ=255)                  gggAAAGATGAACGTGATGATGTTCACAATTTGCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAg                                                                                                >  1:419028/1‑138 (MQ=255)                         aTGAACGTGATGATGTTCACAATTTGCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGAc                                                                                        <  2:383273/139‑1 (MQ=255)                         aTGAACGTGATGATGTTCACAATTTGCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGAc                                                                                        <  2:467331/139‑1 (MQ=255)                         aTGAACGTGATGATGTTCACAATTTGCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGAc                                                                                        <  2:524991/139‑1 (MQ=255)                          tGAACGTGATGATGTTCACAATTTGCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGAcc                                                                                       >  2:624022/1‑139 (MQ=255)                          tGAACGTGATGATGTTCACAATTTGCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGAAAGAACCTGAcc                                                                                       >  2:464128/1‑139 (MQ=255)                            aaCGTGATGATGTTCACAATTTGCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTa                                                                                                       <  1:346688/121‑1 (MQ=255)                            aaCGTGATGATGTTCACAATTTGCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCt                                                                                      <  2:493195/138‑1 (MQ=255)                            aaCGTGATGATGTTCACAATTTGCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTc                                                                                     <  1:389317/139‑1 (MQ=255)                            aaCGTGATGATGTTCACAATTTGCTGAATTGTGGGGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTa                                                                                                       >  2:346688/1‑121 (MQ=255)                                          cacaATTTGCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTc                                                                       >  1:292088/1‑139 (MQ=255)                                           acaATTTGCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCg                                                                      >  2:157513/1‑139 (MQ=255)                                             aaTTTGCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGcc                                                                    <  2:199877/139‑1 (MQ=255)                                                  gCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGtt                                                               >  2:487863/1‑139 (MQ=255)                                                  gCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGtt                                                               >  2:561037/1‑139 (MQ=255)                                                   cTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTg                                                              <  2:349428/139‑1 (MQ=255)                                                      aaTTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTgac                                                            <  2:400239/138‑1 (MQ=255)                                                      aaTTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTga                                                             <  2:441534/137‑1 (MQ=255)                                                                  gtgatgCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAAACTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGc                                               >  2:307061/1‑139 (MQ=255)                                                                     atgCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAAc                                                                                             <  2:448740/90‑1 (MQ=255)                                                                     atgCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAAc                                                                                             >  1:448740/1‑90 (MQ=255)                                                                     atgCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAg                                            >  2:321675/1‑139 (MQ=255)                                                                     atgCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGCAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAg                                            >  1:277580/1‑139 (MQ=255)                                                                        cTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTAt                                         >  1:126106/1‑139 (MQ=255)                                                                           aCCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATg                                        <  2:277580/137‑1 (MQ=255)                                                                           aCCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATg                                        <  1:545198/137‑1 (MQ=255)                                                                           aCCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGa                                       <  2:182417/138‑1 (MQ=255)                                                                           aCCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGAc                                      >  2:117707/1‑139 (MQ=255)                                                                            ccGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGAcc                                     <  2:126106/139‑1 (MQ=255)                                                                            ccGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGAcc                                     <  1:624022/139‑1 (MQ=255)                                                                            ccGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGAcc                                     <  1:321675/139‑1 (MQ=255)                                                                               cATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTga                                                             <  2:173088/112‑1 (MQ=255)                                                                               cATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTga                                                             >  1:173088/1‑112 (MQ=255)                                                                                                       tCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTgac                                                            >  2:159299/1‑89 (MQ=255)                                                                                                       tCTTGAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTgac                                                            <  1:159299/89‑1 (MQ=255)                                                                                                           gAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCaggag                                                 <  1:552437/96‑1 (MQ=255)                                                                                                           gAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCaggag                                                 >  2:552437/1‑96 (MQ=255)                                                                                                           gAAAAATCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTTCCGt         <  1:561037/136‑1 (MQ=255)                                                                                                             aaaaTCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTTCCGTCTgg     >  2:332690/1‑138 (MQ=255)                                                                                                               aaTCGACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTTCCGTCTGGTaa  >  1:353566/1‑139 (MQ=255)                                                                                                                   gACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGAcc                                     >  2:102923/1‑100 (MQ=255)                                                                                                                   gACGTTTTTTACGTGGTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGAcc                                     <  1:102923/100‑1 (MQ=255)                                                                                                                                  gTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACa                             >  1:39873/1‑93 (MQ=255)                                                                                                                                  gTTTCCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACa                             <  2:39873/93‑1 (MQ=255)                                                                                                                                      |                                                                                                                    TGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCTGAATTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCTTGAAAAATCGACGTTTTTTACGTGGTTTTCCGTCGAAAATTTAAGGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTTCCGTCTGGTAA  >  NZ_CP009273/4087456‑4087704

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑