Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,955,598	C→A	H90N (CAC→AAC)	ilvA →	threonine deaminase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,955,598	0	C	A	100.0%	178.5 / NA	51	H90N (CAC→AAC)	ilvA	threonine deaminase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (36/15);  total (36/15)

CATTCTGGTGAAGCGCGAAGATCGCCAGCCAGTGCACAGCTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACCACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACATCAAAGTCGACGCGGTGCGCGGCTTCGGCGGCGAAGTGCTGCTCCACGGCGCG  >  NC_000913/3955471‑3955729                                                                                                                                |                                                                                                                                    cATTCTGGTGAAGCGCGAAGATCGCCAGCCAGTGCACAGCTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCg                                                                                                                         >  1:604835/1‑140 (MQ=255)    tCTGGTGAAGCGCGAAGATCGCCAGCCAGTGCACAGCTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTcg                                                                                                                      >  2:1439973/1‑140 (MQ=255)        gTGAAGCGCGAAGATCGCCAGCCAGTGCACAGCTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGtt                                                                                                                  <  1:491757/140‑1 (MQ=255)         tGAAGCGCGAAGATCGCCAGCCAGTGCACAGCTTTAAGCTACGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGttt                                                                                                                 >  2:665933/1‑140 (MQ=255)             gcgcGAAGATCGCCAGCCAGTGCACAGCTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTttctt                                                                                                             >  1:411555/1‑140 (MQ=255)             gcgcGAAGATCGCCAGCCAGTGCACAGCTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTttctt                                                                                                             >  1:1459169/1‑140 (MQ=255)                cgAAGATCGCCAGCCAGTGCACAGCTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTg                                                                                                          >  1:1485427/1‑140 (MQ=255)                  aaGATCGCCAGCCAGTGCACAGCTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTgcg                                                                                                        >  1:1714750/1‑140 (MQ=255)                   aGATCGCCAGCCAGTGCACAGCTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTgcgc                                                                                                       <  1:293161/140‑1 (MQ=255)                      tCGCCAGCCAGTGCACAGCTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGt                                                                                                    <  2:1026188/140‑1 (MQ=255)                       cGCCAGCCAGTGCACAGCTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGtt                                                                                                   <  1:1439973/140‑1 (MQ=255)                               agTGCACAGCTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGa                                                                                           <  1:1455869/140‑1 (MQ=255)                                 tGCACAGCTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAg                                                                                         >  1:778420/1‑140 (MQ=255)                                 tGCACAGCTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAg                                                                                         >  2:496044/1‑140 (MQ=255)                                 tGCACAGCTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAg                                                                                         >  2:1401543/1‑140 (MQ=255)                                  gCACAGCTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAgg                                                                                        <  1:539515/140‑1 (MQ=255)                                      aGCTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCt                                                                                    <  2:1621018/140‑1 (MQ=255)                                      aGCTTTAAGCTACGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCt                                                                                    <  1:665933/140‑1 (MQ=255)                                        cTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGa                                                                                  >  2:1017998/1‑140 (MQ=255)                                        cTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGa                                                                                  >  1:1835432/1‑140 (MQ=255)                                           tAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTg                                                                                   >  2:160519/1‑136 (MQ=255)                                           tAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTg                                                                                   <  1:160519/136‑1 (MQ=255)                                           tAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCg                                                                               >  1:1057344/1‑140 (MQ=255)                                           tAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCg                                                                               >  2:1518016/1‑140 (MQ=255)                                                  cgcgGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGcc                                                                        >  2:2025929/1‑140 (MQ=255)                                                  cgcgGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGcc                                                                        >  1:580265/1‑140 (MQ=255)                                                  cgcgGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGcc                                                                        >  1:1613187/1‑140 (MQ=255)                                                  cgcgGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGcc                                                                        >  2:309597/1‑140 (MQ=255)                                                  cgcgGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGcc                                                                        >  1:1313961/1‑140 (MQ=255)                                                  cgcgGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGcc                                                                        >  2:1775930/1‑140 (MQ=255)                                                  cgcgGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGcc                                                                        >  2:107611/1‑140 (MQ=255)                                                       cgcATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAaccg                                                                   >  1:1396225/1‑140 (MQ=255)                                                          aTACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGTTTAGGCGTGAAGGCCCTGATCGTTATGCAAaccgcca                                                                <  2:1814325/140‑1 (MQ=255)                                                               ccATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAaccgccaccgcc                                                           <  1:1518016/140‑1 (MQ=255)                                                                 atgatgGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGa                                                         >  1:107864/1‑140 (MQ=255)                                                                   gatgGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACa                                                       <  1:309597/140‑1 (MQ=255)                                                                   gatgGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACa                                                       <  2:1628164/140‑1 (MQ=255)                                                                      ggCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACATCa                                                    >  1:1947254/1‑140 (MQ=255)                                                                        cGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACATCaaa                                                  >  2:356034/1‑140 (MQ=255)                                                                        cGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACATCaaa                                                  >  2:1485270/1‑140 (MQ=255)                                                                          ggCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACATCAAAGt                                                >  1:1287648/1‑140 (MQ=255)                                                                            cgtGACGGAAGAACAGAAAGCGCACGGCGTAATCACTGCTTCTGCGGGTAACAACGCGGAGGGCGCCGCGTTTTCTCCTGCGCGGTTAGGGGTGAAGGCCGTGATCGTTGTGCCACCCGCCGCCGCCGACATCAAAGTCg                                              <  2:1075646/138‑1 (MQ=255)                                                                               gACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGTCAACCGCCACCGCCGACATCAAAGTCGAcg                                           <  2:604835/140‑1 (MQ=255)                                                                                       aaCAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACATCAAAGTCGACGCGGTgcgc                                   >  1:803112/1‑140 (MQ=255)                                                                                                cgcACGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACATCAAAGTCGACGCGGTGCGCGGCTTcggc                          >  1:639359/1‑140 (MQ=255)                                                                                                    cGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACATCAAAGTCGACGCGGTGCGCGGCTTCGgcggcg                      <  2:1313961/140‑1 (MQ=255)                                                                                                    cGGCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCATGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACATCAAAGTCGACGCGGTGCGCGGCTTCGgcggcg                      <  1:1361897/140‑1 (MQ=255)                                                                                                     ggCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACATCAAAGTCGACGCGGTGCGCGGCTTCGGCGGCGa                     <  2:778420/140‑1 (MQ=255)                                                                                                      gCGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACATCAAAGTCGACGCGGTGCGCGGCTTCGGCGGCGaa                    >  1:456893/1‑140 (MQ=255)                                                                                                       cGTGATCACTGCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACATCAAAGTCGACGCGGTGCGCGGCTTCGGCGGCGAAg                   <  2:107864/140‑1 (MQ=255)                                                                                                                 gCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACATCAAAGTCGACGCGGTGCGCGGCTTCGGCGGCGAAGTGCTGCTCCa         >  2:1001839/1‑140 (MQ=255)                                                                                                                 gCTTCTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACATCAAAGTCGACGCGGTGCGCGGCTTCGGCGGCGAAGTGCTGCTCCa         >  1:1366968/1‑140 (MQ=255)                                                                                                                     cTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACATCAAAGTCGACGCGGTGCGCGGCTTCGGCGGCGAAGTGCTGCTCCACGgc     >  2:1121169/1‑140 (MQ=255)                                                                                                                     cTGCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACATCAAAGTCGACGCGGTGCGCGGCTTCGGCGGCGAAGTGCTGCTCCACGgc     >  1:826891/1‑140 (MQ=255)                                                                                                                       gCGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACATCAAAGTCGACGCGGTGCGCGGCTTCGGCGGCGAAGTGCTGCTCCACGgcgc   <  1:1090273/140‑1 (MQ=255)                                                                                                                        cGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACATCAAAGTCGACGCGGTGCGCGGCTTCGGCGGCGAAGTGCTGCTCCACGGcgcg  >  1:134708/1‑140 (MQ=255)                                                                                                                        cGGGTAACAACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGCCCCTGATCGTTATGCCAACCGCCACCGCCGACATCAAAGTCGACGCGGTGCGCGGCTTCGGCGGCGAAGTGCTGCTCCACGGcgcg  <  1:1401543/140‑1 (MQ=255)                                                                                                                                |                                                                                                                                    CATTCTGGTGAAGCGCGAAGATCGCCAGCCAGTGCACAGCTTTAAGCTGCGCGGCGCATACGCCATGATGGCGGGCCTGACGGAAGAACAGAAAGCGCACGGCGTGATCACTGCTTCTGCGGGTAACCACGCGCAGGGCGTCGCGTTTTCTTCTGCGCGGTTAGGCGTGAAGGCCCTGATCGTTATGCCAACCGCCACCGCCGACATCAAAGTCGACGCGGTGCGCGGCTTCGGCGGCGAAGTGCTGCTCCACGGCGCG  >  NC_000913/3955471‑3955729

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑