Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,400,959	A→C	intergenic (‑839/‑81)	lrhA ← / → alaA	transcriptional regulator LrhA/alanine transaminase AlaA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,400,959	0	A	C	100.0%	128.0 / NA	35	intergenic (‑839/‑81)	lrhA/alaA	transcriptional regulator LrhA/alanine transaminase AlaA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (23/12);  total (23/12)

AATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGCAAAAAAGGTCAAGATTCATGTCCCCCATTGAAAAATCCAGCAAATTAGAGAATGTCTGTTATGACATC  >  NZ_CP009273/2400823‑2401090                                                                                                                                         |                                                                                                                                    aaTTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAcca                                                                                                                                   <  1:239885/139‑1 (MQ=255)  aTTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAccac                                                                                                                                  <  2:559276/139‑1 (MQ=255)  aTTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAccac                                                                                                                                  <  2:451276/139‑1 (MQ=255)                  aTTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTa                                                                                                                   >  2:160045/1‑138 (MQ=255)                   ttCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACa                                                                                                                 <  1:30555/139‑1 (MQ=255)                                  tGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTgg                                                                                                                          >  2:794818/1‑115 (MQ=255)                                  tGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTgg                                                                                                                          <  1:794818/115‑1 (MQ=255)                                    cATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACtt                                                                                                >  1:141190/1‑139 (MQ=255)                                    cATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACtt                                                                                                >  2:47792/1‑139 (MQ=255)                                        tAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCa                                                                                             <  1:160045/138‑1 (MQ=255)                                         aaaGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACg                                                                                           >  1:793953/1‑139 (MQ=255)                                                    acCTCATTATTTTGTTATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTcc                                                                                                                             <  1:661978/94‑1 (MQ=255)                                                    acCTCATTATTTTGTTATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTcc                                                                                                                             >  2:661978/1‑94 (MQ=255)                                                      cTCATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGc                                                                               >  2:762097/1‑138 (MQ=255)                                                      cTCATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGc                                                                               >  2:395298/1‑138 (MQ=255)                                                         attattTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGa                                                                                    >  1:492673/1‑130 (MQ=255)                                                         attattTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGa                                                                                    <  2:492673/130‑1 (MQ=255)                                                                tGTCATTATTAAGTTATTAACAGCACAATCTAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGTGCAGTACATTGTTCTAAGCTGACTTCCACGGCAGTGATTGGCGATAACCGCa                                                                     >  1:367893/1‑138 (MQ=255)                                                                    attattAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAg                                                                                                       >  1:402959/1‑100 (MQ=255)                                                                    attattAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAg                                                                                                       <  2:402959/100‑1 (MQ=255)                                                                           aGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGCAAAAAAGGTCaa                                                          <  1:47792/138‑1 (MQ=255)                                                                                ttaACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTcc                                                                                              >  2:791201/1‑97 (MQ=255)                                                                                ttaACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTcc                                                                                              <  1:791201/97‑1 (MQ=255)                                                                                ttaACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGCAAAAAAGGTCAAGATTCa                                                    >  1:115291/1‑139 (MQ=255)                                                                                  aaCAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGCAAAAAAGGTCAAGATTCATg                                                  >  2:649501/1‑139 (MQ=255)                                                                                       cacaATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGCAAAAAAGGTCAAGATTCATGTcccc                                             >  2:269794/1‑139 (MQ=255)                                                                                       cacaATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGCAAAAAAGGTCAAGATTCATGTcccc                                             >  2:181977/1‑139 (MQ=255)                                                                                       cacaATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGCAAAAAAGGTCAAGATTCATGTcccc                                             >  1:680975/1‑139 (MQ=255)                                                                                                      cccTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGCAAAAAAGGTCAAGATTCATGTCCCCCATTGAAAAATCCAg                              <  1:395298/139‑1 (MQ=255)                                                                                                      cccTCTGGCAAAATCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGCAAAAAAGGTCAAGATTCATGTCCCCCATTGAAAAATCCAg                              >  2:541567/1‑139 (MQ=255)                                                                                                                  aTCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCt                                                                                                     >  2:675912/1‑56 (MQ=255)                                                                                                                  aTCTTATTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCt                                                                                                     <  1:675912/56‑1 (MQ=255)                                                                                                                       aTTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGa                                                                                    <  1:74970/68‑1 (MQ=255)                                                                                                                       aTTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGa                                                                                    >  2:74970/1‑68 (MQ=255)                                                                                                                       aTTCTGCAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGCAAAAAAGGTCAAGATTCATGTCCCCCATTGAAAAATCCAGCAAATTAGAGAATGt               <  1:269794/137‑1 (MQ=255)                                                                                                                             cAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGCAAAAAAGGTCAAGATTCATGTCCCCCATTGAAAAATCCAGCAAATTAGAGAATGTCTGTTAt        >  1:3211/1‑138 (MQ=255)                                                                                                                             cAGACCTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGCAAAAAAGGTCAAGATTCATGTCCCCCATTGAAAAATCCAGCAAATTAGAGAATGTCTGTTAt        >  1:545634/1‑138 (MQ=255)                                                                                                                                  cTTCAAACCACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGCAAAAAAGGTCAAGATTCATGTCCCCCATTGAAAAATCCAGCAAATTAGAGAATGTCTGTTATGACATc  >  1:755897/1‑139 (MQ=255)                                                                                                                                         |                                                                                                                                    AATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGCAAAAAAGGTCAAGATTCATGTCCCCCATTGAAAAATCCAGCAAATTAGAGAATGTCTGTTATGACATC  >  NZ_CP009273/2400823‑2401090

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑