Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,312,566	T→C	R142R (AGA→AGG)	alsR ←	d‑allose‑inducible als operon transcriptional repressor, autorepressor, repressor of rpiR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,312,566	0	T	C	100.0%	188.5 / NA	50	R142R (AGA→AGG)	alsR	d‑allose‑inducible als operon transcriptional repressor, autorepressor, repressor of rpiR
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (26/24);  total (26/24)

TGTAACAACGAAGCGGACATCATCATGATGTGAGCATCAGGATAGGCCTGACAGCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGTCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCA  >  NC_000913/4312432‑4312689                                                                                                                                       |                                                                                                                            tGTAACAACGAAGCGGACATCATCATGATGTGAGCATCAGGATAGGCCTGACAGCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTgg                                                                                                                         >  1:208904/1‑139 (MQ=255)         cGAAGCGGACATCATCATGATGTGAGCATCAGGATAGGCCTGACAGCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCt                                                                                                                      >  2:1180330/1‑134 (MQ=255)         cGAAGCGGACATCATCATGATGTGAGCATCAGGATAGGCCTGACAGCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCt                                                                                                                      <  1:1180330/134‑1 (MQ=255)         cGAAGCGGACATCATCATGATGTGAGCATCAGGATAGGCCTGACAGCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAg                                                                                                                 >  1:201854/1‑139 (MQ=255)           aaGCGGACATCATCATGATGTGAGCATCAGGATAGGCCTGACAGCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGaa                                                                                                               >  2:148529/1‑139 (MQ=255)                   atcatcatGATGTGAGCATCAGGATAGGCCTGACAGCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAgcggg                                                                                                       <  2:1086185/139‑1 (MQ=255)                        catGATGTGAGCATCAGGATAGGCCTGACAGCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCGGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCa                                                                                                  <  1:718261/139‑1 (MQ=255)                             tgtgAGCATCAGGATAGGCCTGACAGCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTg                                                                                             <  2:201854/139‑1 (MQ=255)                               tgAGCATCAGGATAGGCCTGACAGCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGa                                                                                           >  2:652707/1‑139 (MQ=255)                                  gCATCAGGATAGGCCTGACAGCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACgg                                                                                               <  2:450878/132‑1 (MQ=255)                                  gCATCAGGATAGGCCTGACAGCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACgg                                                                                               >  1:450878/1‑132 (MQ=255)                                  gCATCAGGATAGGCCTGACAGCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGAtct                                                                                        >  2:1119140/1‑139 (MQ=255)                                       aGGATAGGCCTGACAGCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCtcatca                                                                                   <  1:652707/139‑1 (MQ=255)                                                cTGACAGCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACg                                                                          <  2:100278/139‑1 (MQ=255)                                                   aCAGCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCtcat                                                                                     <  2:992889/125‑1 (MQ=255)                                                   aCAGCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCtcat                                                                                     >  1:992889/1‑125 (MQ=255)                                                   aCAGCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATc                                                                       >  2:589934/1‑139 (MQ=255)                                                      gCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGAc                                                                    <  1:768898/139‑1 (MQ=255)                                                      gCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGAc                                                                    <  1:967596/139‑1 (MQ=255)                                                                 tGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCAt                                                         >  1:269148/1‑139 (MQ=255)                                                                             tgtgCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGt                                                                                              <  1:739064/90‑1 (MQ=255)                                                                             tgtgCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGt                                                                                              >  2:739064/1‑90 (MQ=255)                                                                                gCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGt                                                                                              >  2:1072618/1‑87 (MQ=255)                                                                                gCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGt                                                                                              <  1:1072618/87‑1 (MQ=255)                                                                                 cTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTg                                         <  2:269148/139‑1 (MQ=255)                                                                                    tACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAAt                                                      <  1:807964/123‑1 (MQ=255)                                                                                    tACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAAt                                                      >  2:807964/1‑123 (MQ=255)                                                                                         cAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTaaa                                 >  2:606660/1‑139 (MQ=255)                                                                                           gCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCa                                                                                                  <  2:698191/72‑1 (MQ=255)                                                                                           gCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCa                                                                                                  >  1:698191/1‑72 (MQ=255)                                                                                           gCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATa                               <  1:669353/139‑1 (MQ=255)                                                                                            cacaGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACg                                                                                                >  1:865109/1‑73 (MQ=255)                                                                                            cacaGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACg                                                                                                <  2:865109/73‑1 (MQ=255)                                                                                              caGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCa                                                                                                  <  1:1119504/69‑1 (MQ=255)                                                                                              caGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCa                                                                                                  >  2:1119504/1‑69 (MQ=255)                                                                                              caGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCt                            >  1:1061662/1‑139 (MQ=255)                                                                                                 aTAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCg                                                >  2:1027103/1‑116 (MQ=255)                                                                                                 aTAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCg                                                <  1:1027103/116‑1 (MQ=255)                                                                                                 aTAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTAt                         <  1:148529/139‑1 (MQ=255)                                                                                                 aTAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTAt                         >  1:785413/1‑139 (MQ=255)                                                                                                 aTAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTAt                         >  2:1106840/1‑139 (MQ=255)                                                                                                 aTAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTAt                         <  2:674323/139‑1 (MQ=255)                                                                                                  tAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTAtt                        <  1:1106840/139‑1 (MQ=255)                                                                                                      aTTTGATCCTCCGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTcacc                    >  1:572392/1‑139 (MQ=255)                                                                                                               tccGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCtcatca                                                                                   >  2:7224/1‑67 (MQ=255)                                                                                                               tccGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCtcatca                                                                                   <  1:7224/67‑1 (MQ=255)                                                                                                               tccGGCACCGTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTgc           >  1:1040775/1‑139 (MQ=255)                                                                                                                        gTACAAATCCCGCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTtca  >  1:634294/1‑139 (MQ=255)                                                                                                                                   gCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGAcc                                                               >  1:37351/1‑67 (MQ=255)                                                                                                                                   gCTGCCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGAcc                                                               <  2:37351/67‑1 (MQ=255)                                                                                                                                       |                                                                                                                            TGTAACAACGAAGCGGACATCATCATGATGTGAGCATCAGGATAGGCCTGACAGCGTACGCCAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGTCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCA  >  NC_000913/4312432‑4312689

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑