Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,358,354	A→G	T88T (ACT→ACC)	cadA ←	lysine decarboxylase, acid‑inducible

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,358,354	0	A	G	100.0%	157.2 / NA	44	T88T (ACT→ACC)	cadA	lysine decarboxylase, acid‑inducible
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (23/21);  total (23/21)

CAGTGCTTTAGTCAGCGGAGGCAGAATAGTGTTGATATATTCGTCAGTGGTCTGCTTGATCTTATTAGCAATATCTTCAGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGAGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACGCGCATTGTTTTCGATCAGTTTTAATAAGTCGTCA  >  NC_000913/4358210‑4358501                                                                                                                                                 |                                                                                                                                                    cAGTGCTTTAGTCAGCGGAGGCAGAATAGTGTTGATATATTCGTCAGTGGTCTGCTTGATCTTATTAGCAATATCTTCAGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGa                                                                                                                                                >  2:504873/1‑150 (MQ=255)  aGTGCTTTAGTCAGCGGAGGCAGAATAGTGTTGATATATTCGTCAGTGGTCTGCTTGATCTTATTAGCAATATCTTCAGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAAt                                                                                                                                              >  2:360293/1‑151 (MQ=255)  aGTGCTTTAGTCAGCGGAGGCAGAATAGTGTTGATATATTCGTCAGTGGTCTGCTTGATCTTATTAGCAATATCTTCAGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAAt                                                                                                                                              <  2:678173/151‑1 (MQ=255)     gCTTTAGTCAGCGGAGGCAGAATCGTGTTGATATATTCGTCAGCGGTCTGCTTGATCTTATTAGCAATATCTTCTGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGACATTCAGGCTTACATCGAGGGTGGAATACg                                                                                                                                           >  1:50527/1‑151 (MQ=255)      cTTTAGTCAGCGGAGGCAGAATAGTGTTGATATATTCGTCAGTGGTCTGCTTGATCTTATTAGCAATATCTTCAGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGt                                                                                                                                          >  1:584443/1‑151 (MQ=255)        ttAGTCAGCGGAGGCAGAATAGTGTTGATATATTCGTCAGTGGTCTGCTTGATCTTATTAGCAATATCTTCAGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGt                                                                                                                                          <  2:737866/149‑1 (MQ=255)           gTCAGCGGAGGCAGAATAGTGTTGATATATTCGTCAGTGGTCTGCTTGATCTTATTAGCAATATCTTCAGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTAtt                                                                                                                                       >  1:392646/1‑149 (MQ=255)           gTCAGCGGAGGCAGAATAGTGTTGATATATTCGTCAGTGGTCTGCTTGATCTTATTAGCAATATCTTCAGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTAtt                                                                                                                                       >  2:385593/1‑149 (MQ=255)             cAGCGGAGGCAGAATAGTGTTGATATATTCGTCAGTGGTCTGCTTGATCTTATTAGCAATATCTTCAGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCg                                                                                                                                   <  1:504962/151‑1 (MQ=255)                  gaagCAGAATAGTGTTGATATATTCGTCAGTGGTCTGCTTGATCTTATTAGCAATATCTTCAGCAGCCCCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAAc                                                                                                                                <  2:772490/146‑1 (MQ=255)                        gAATAGTGTTGATATATTCGTCAGTGGTCTGCTTGATCTTATTAGCAATATCTTCAGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACaa                                                                                                                        <  1:87890/151‑1 (MQ=255)                                       atTCGTCAGTGGTCTGCTTGATCTTATTAGCAATATCTTCAGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGt                                                                                                          <  1:112584/150‑1 (MQ=255)                                             cAGTGGTCTGCTTGATCTTATTAGCAATATCTTCAGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCAtttt                                                                                                   <  2:178839/151‑1 (MQ=255)                                                 ggTCTGCTTGATCTTATTAGCAATATCTTCAGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCt                                                                                                <  2:177016/150‑1 (MQ=255)                                                 ggTCTGCTTGATCTTATTAGCAATATCTTCAGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCt                                                                                                <  1:621135/150‑1 (MQ=255)                                                          gATCTTATTAGCAATATCTTCAGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGGTCATTTTGTACATttct                                                                                         >  1:644822/1‑148 (MQ=255)                                                               tattaGCAATATCTTCAGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGc                                                                                     <  1:93177/147‑1 (MQ=255)                                                                attaGCAATATCTTCAGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAg                                                                                 <  1:349333/150‑1 (MQ=255)                                                                             tCAGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATtata                                                                     <  2:527642/149‑1 (MQ=255)                                                                                  agcaCCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATcc                                                              <  2:623819/151‑1 (MQ=255)                                                                                    caCCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATccc                                                             >  2:444335/1‑150 (MQ=255)                                                                                     aCCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATccc                                                             >  2:123860/1‑149 (MQ=255)                                                                                        cAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTAGCACAGCTCGAGGTTATATTTATCCCAGTc                                                         >  1:718047/1‑150 (MQ=255)                                                                                         aGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCa                                                        >  1:763062/1‑150 (MQ=255)                                                                                                  tCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAAcg                                               <  1:430714/150‑1 (MQ=255)                                                                                                    aaaGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAAcgccg                                            >  1:276119/1‑151 (MQ=255)                                                                                                             aaTCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGAc                                     <  2:700834/149‑1 (MQ=255)                                                                                                               tCTGTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACgcgc                                 >  2:427052/1‑151 (MQ=255)                                                                                                                  gTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTTATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACGCGCAt                               >  1:70419/1‑150 (MQ=255)                                                                                                                  gTAAACGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACGCGCa                                <  2:393446/149‑1 (MQ=255)                                                                                                                    aaaCGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACGCGCATTGt                            <  1:271189/151‑1 (MQ=255)                                                                                                                      aCGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACGCGCATTGttt                          >  2:36273/1‑151 (MQ=255)                                                                                                                       cGCAGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACGCGCATTGtttt                         >  2:41082/1‑151 (MQ=255)                                                                                                                          aGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACGCGCATTGTTTTCg                       >  2:747865/1‑150 (MQ=255)                                                                                                                          aGGTCATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACGCGCATTGTTTTCg                       >  2:472414/1‑150 (MQ=255)                                                                                                                              cATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACGCGCATTGTTTTCGATc                    >  1:752914/1‑149 (MQ=255)                                                                                                                              cATTCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACGCGCATTGTTTTCGATCa                   <  1:153642/150‑1 (MQ=255)                                                                                                                                 tCAGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACGCGCATTGTTTTCGATCAGtt                <  1:677853/150‑1 (MQ=255)                                                                                                                                   aGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACGCGCATTGTTTTCGATCAGtttt              >  1:155820/1‑150 (MQ=255)                                                                                                                                   aGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACGCGCATTGTTTTCGATCAGtttt              >  2:328627/1‑150 (MQ=255)                                                                                                                                   aGGCTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACGCGCATTGTTTTCGATCAGTTTta             <  2:534924/151‑1 (MQ=255)                                                                                                                                      cTTACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACGCGCATTGTTTTCGATCAGTTTtaat           >  2:458341/1‑150 (MQ=255)                                                                                                                                       ttACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACGCGCATTGTTTTCGATCAGTTTtaat           >  1:532782/1‑149 (MQ=255)                                                                                                                                        tACATCGAGGGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACGCGCATTGTTTTCGATCAGTTTtaataa         <  1:297296/150‑1 (MQ=255)                                                                                                                                              gaggGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACGCGCATTGTTTTCGATCAGTTTTAATAAGTCGTCa  <  2:655302/151‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                    CAGTGCTTTAGTCAGCGGAGGCAGAATAGTGTTGATATATTCGTCAGTGGTCTGCTTGATCTTATTAGCAATATCTTCAGCAGCACCCAGCGCATATTCAAAGAAGCTAATCTGTAAACGCAGGTCATTCAGGCTTACATCGAGAGTGGAATACGTATTAGCGAACGCGTACAACGGCAGGTTCTCGTTCATTTTGCTAATTTCTTCGCACAGCTCGAGATTATATTTATCCCAGTCAAAAATAACGCCGCACAGACGCGCATTGTTTTCGATCAGTTTTAATAAGTCGTCA  >  NC_000913/4358210‑4358501

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑