Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,597,846	(T)5→4	intergenic (‑286/‑138)	livK ← / → panM	leucine transporter subunit/PanD autocleavage accelerator, panothenate synthesis

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,597,842	0	T	.	100.0%	312.1 / NA	67	intergenic (‑282/‑142)	livK/panM	leucine transporter subunit/PanD autocleavage accelerator, panothenate synthesis
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (31/36);  total (31/36)

TTATTGATAGATAAACAGAAAAAAGTGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACATTTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATAAAAAAGAGAAAGCCTCCGATTA  >  NC_000913/3597744‑3597934                                                                                                   |                                                                                             ttATTGATAGATAAACAGAAAAAAGTGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACAtt                                                                                             >  2:458015/1‑100 (MQ=255)    ttGATAGATAAACAGAAAAAAGTGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACAttttc                                                                                          <  2:810135/100‑2 (MQ=255)      gatagataAACAGAAAAAAGTGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACAttttcat                                                                                        <  2:1488196/100‑4 (MQ=255)      gatagataAACAGAAAAAAGTGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACAttttcat                                                                                        >  2:457911/1‑97 (MQ=255)      gatagataAACAGAAAAAAGTGCCTTTGTCAGCATAAAATAACGGCACAAAGGACGGAATAATTCACTATCATTCAGGGGATTATGCTGGACAtttt                                                                                           >  2:1424789/1‑97 (MQ=255)         agataAACAGAAAAAAGTGCCTTTGTCAGCATAAAATAACTGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATtct                                                                                    <  2:24765/100‑1 (MQ=255)           ataAACAGAAAAAAGTGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTctct                                                                                  >  1:1522954/1‑100 (MQ=255)            taAACAGAAAAAAGTGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTa                                                                                 >  1:1801849/1‑100 (MQ=255)            taAACAGAAAAAAGTGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTa                                                                                 >  1:1631544/1‑100 (MQ=255)             aaaCAGAAAAAAGTGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTaa                                                                                >  1:1465015/1‑100 (MQ=255)              aaCAGAAAAAAGTGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAAt                                                                               >  2:463026/1‑100 (MQ=255)              aaCAGAAAAAAGTGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAAt                                                                               >  1:583802/1‑100 (MQ=255)                cAGAAAAAAGTGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGt                                                                             >  2:745105/1‑100 (MQ=255)                  gAAAAAAGTGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGttt                                                                           >  1:869163/1‑100 (MQ=255)                   aaaaaaGTGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGtttt                                                                          >  2:538531/1‑100 (MQ=255)                     aaaaGTGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTaa                                                                        <  2:588460/100‑1 (MQ=255)                          tGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTg                                                                   <  1:1330910/100‑1 (MQ=255)                          tGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTg                                                                   <  2:1765846/100‑1 (MQ=255)                          tGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTg                                                                   <  2:499654/100‑1 (MQ=255)                          tGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTg                                                                   <  2:489535/100‑1 (MQ=255)                           gCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGt                                                                  >  2:627183/1‑100 (MQ=255)                           gCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGt                                                                  >  2:236382/1‑100 (MQ=255)                             cTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTaa                                                                >  2:1694490/1‑100 (MQ=255)                              tatGTCAGCATAAAACAACGGCAAAAAGGTCTGAATAATTCACTATCATTTAGGGGAATACGCTGGACA‑TTTTCAATCTCTTATGTTTTAATCTTATAat                                                               <  1:1083105/98‑1 (MQ=255)                                  tCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAattatt                                                           >  2:1250998/1‑100 (MQ=255)                                   cAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTg                                                          <  2:995614/100‑1 (MQ=255)                                    aGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGc                                                         >  2:1299625/1‑100 (MQ=255)                                     gCATAAAATAACTGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCt                                                        <  2:503959/100‑1 (MQ=255)                                      cATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTg                                                       <  2:1256411/100‑1 (MQ=255)                                       aTAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGt                                                      <  2:1087128/100‑1 (MQ=255)                                        tAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGtt                                                     <  1:1687119/100‑1 (MQ=255)                                              aaCGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTaaaaaa                                               <  2:497702/100‑1 (MQ=255)                                              aaCGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTaaaaaa                                               >  1:1465141/1‑100 (MQ=255)                                               aCGGCACAAATGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAAGGTCTTAATTTTGTAATTATTGCTGTTAAAAAAt                                              <  1:1193796/100‑1 (MQ=255)                                               aCGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAAt                                              <  1:1817354/100‑1 (MQ=255)                                                cGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAAtt                                             <  2:1066021/100‑1 (MQ=255)                                                cGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAAtt                                             <  1:447509/100‑1 (MQ=255)                                                 ggCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTa                                            >  1:949012/1‑100 (MQ=255)                                                 ggCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTa                                            >  1:1317963/1‑100 (MQ=255)                                                 ggCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTAAAGTTAAAAAATTa                                            >  2:1475352/1‑100 (MQ=255)                                                  gCACAAAGGGCGGAATAATTCACTATCATTTAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAAt                                              <  1:891487/97‑1 (MQ=255)                                                  gCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTaa                                           >  2:1501342/1‑100 (MQ=255)                                                   cacaAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAAt                                          >  1:1026978/1‑100 (MQ=255)                                                   cacaAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAAt                                          <  1:961958/100‑1 (MQ=255)                                                    acaAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAAt                                          <  1:53111/99‑1 (MQ=255)                                                      aaaGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCAc                                       <  1:1170114/100‑1 (MQ=255)                                                       aaGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCAcc                                      <  2:1249249/100‑1 (MQ=255)                                                          ggCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGc                                   >  1:1385413/1‑100 (MQ=255)                                                          ggCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGc                                   <  1:745101/100‑1 (MQ=255)                                                          ggCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAACTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGc                                   >  1:1003382/1‑100 (MQ=255)                                                                ataatTCACTATCATTCAGGTGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGTTGTTAAAAAATTAATCAACTGCCAAAAg                             <  1:632984/100‑1 (MQ=255)                                                                   atTCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGaaa                          <  2:1505117/100‑1 (MQ=255)                                                                    ttCACTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAAt                         <  2:344218/100‑1 (MQ=255)                                                                       aCTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATaaa                      <  1:986419/100‑1 (MQ=255)                                                                        cTATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATaaaa                     >  2:1791603/1‑100 (MQ=255)                                                                         tATCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATaaaaa                    <  2:882172/100‑1 (MQ=255)                                                                          aTCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATaaaaaa                   >  2:832760/1‑100 (MQ=255)                                                                           ttattttggggATTATGTTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATAAAAAag                  <  2:1202664/93‑1 (MQ=255)                                                                           tCATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATAAAAAag                  <  1:464693/100‑1 (MQ=255)                                                                           tCATTCAGGGGATTACGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATAAAAAag                  <  2:1794691/100‑1 (MQ=255)                                                                            cATTCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATAAAAAaga                 <  2:1016527/100‑1 (MQ=255)                                                                               tCAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATAAAAAAGAGaa              <  2:869169/100‑1 (MQ=255)                                                                                cAGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATAAAAAAGAGaaa             <  1:458013/100‑1 (MQ=255)                                                                                 aGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTACTCACCTGCCAAAAGAAATAAAAAAGAGAAAg            >  1:1225438/1‑100 (MQ=255)                                                                                 aGGGGATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATAAAAAAGAGAAAg            >  1:764533/1‑100 (MQ=255)                                                                                  gtggATTCTGCTGGATA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATAAATAAgaga               >  1:38850/3‑96 (MQ=255)                                                                                  ggggATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATAAAAAAGAGAAAGc           >  1:195617/1‑100 (MQ=255)                                                                                   gggATTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATAAAAAAGAGAAAGcc          <  2:523075/100‑1 (MQ=255)                                                                                      aTTATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATAAAAAAGAGAAAGCCTcc       <  2:1522965/100‑1 (MQ=255)                                                                                       ttATGCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATAAAAAAGAGAAAGCCTCCg      >  2:1468915/1‑100 (MQ=255)                                                                                         aTGCTGGACA‑TTTTCATTCTATAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATAAAAAAGAGAAAGCCTCCGAt    >  1:1108283/1‑100 (MQ=255)                                                                                           gCTGGACA‑TTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATAAAAAAGAGAAAGCCTCCGATTa  >  1:684175/1‑100 (MQ=255)                                                                                                   |                                                                                             TTATTGATAGATAAACAGAAAAAAGTGCCTTTGTCAGCATAAAATAACGGCACAAAGGGCGGAATAATTCACTATCATTCAGGGGATTATGCTGGACATTTTTCATTCTCTAATGTTTTAATTTTGTAATTATTGCTGTTAAAAAATTAATCACCTGCCAAAAGAAATAAAAAAGAGAAAGCCTCCGATTA  >  NC_000913/3597744‑3597934

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑