Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,774,371	G→A	intergenic (+177/‑53)	mtlA → / → mtlD	mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,774,371	0	G	A	100.0%	143.2 / NA	45	intergenic (+177/‑53)	mtlA/mtlD	mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (23/22);  total (23/22)

CCTGATGCGCTACGCTTATCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGGAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTAAACTGCTGGCAGACGCGGGTATCCAA  >  NC_000913/3774237‑3774501                                                                                                                                       |                                                                                                                                   ccTGATGCGCTACGCTTATCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAaaaa                                                                                                                                >  2:826079/1‑139 (MQ=255)    gATGCGCTACGCTTATCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGcc                                                                                                                             >  2:628226/1‑139 (MQ=255)      tGCGCTACGCTTATCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTc                                                                                                                           >  2:877502/1‑139 (MQ=255)           tACGCTTATCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCAcccc                                                                                                                      >  2:1072988/1‑139 (MQ=255)               cTTATCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGcc                                                                                                                  >  2:1529520/1‑139 (MQ=255)                ttATCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGccc                                                                                                                 <  1:1529520/139‑1 (MQ=255)                  aTCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGAGAGGAAAAAGCCTCACCCCAGCCctc                                                                                                               >  2:377369/1‑139 (MQ=255)                   tCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCctct                                                                                                              <  1:377542/139‑1 (MQ=255)                        ccTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGt                                                                                                         <  2:1419051/139‑1 (MQ=255)                          tACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTaa                                                                                                       <  1:628226/139‑1 (MQ=255)                           aCAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTaaa                                                                                                      <  1:1072988/139‑1 (MQ=255)                                 tGCATCACAATTTGTTGCATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAACATCAtt                                                                                                >  1:1516473/1‑139 (MQ=255)                                 tGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACAtt                                                                                                >  1:238646/1‑139 (MQ=255)                                 tGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCAC‑GAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCctct                                                                                                              >  2:1279764/1‑124 (MQ=255)                                 tGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCAC‑GAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCctct                                                                                                              <  1:1279764/124‑1 (MQ=255)                                   cATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATtga                                                                                              <  1:877502/139‑1 (MQ=255)                                     tCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATtgatg                                                                                            <  2:705021/139‑1 (MQ=255)                                     tCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATtgatg                                                                                            <  1:52197/139‑1 (MQ=255)                                           tttGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGtt                                                                                      <  1:826079/139‑1 (MQ=255)                                              gttgAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAAt                                                                                   <  2:238646/139‑1 (MQ=255)                                                tgAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATAc                                                                                 >  2:125158/1‑139 (MQ=255)                                                    tttGCACGTTCTTGTACGGCGGATAAGGTGTTTACGCCGCATCCGGCGCTGCGCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAATCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATTCTagg                                                                             <  1:377369/139‑3 (MQ=255)                                                                       cGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGgcg                                                          <  2:1508797/139‑1 (MQ=255)                                                                         gATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGTTGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCa                                                        >  2:610786/1‑139 (MQ=255)                                                                         gATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCa                                                        >  2:388990/1‑139 (MQ=255)                                                                                           cATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGgc                                                           <  1:906497/118‑1 (MQ=255)                                                                                           cATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGgc                                                           >  2:906497/1‑118 (MQ=255)                                                                                                     tGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGgc                                                           >  1:124896/1‑108 (MQ=255)                                                                                                     tGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGgc                                                           <  2:124896/108‑1 (MQ=255)                                                                                                       ccccTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGTTGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTaaa                          <  1:610786/139‑1 (MQ=255)                                                                                                                  aCGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTGAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTAAACTGCTGGCAGa               >  1:942529/1‑139 (MQ=255)                                                                                                                      agagGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATtgatg                                                                                            >  1:897450/1‑58 (MQ=255)                                                                                                                      agagGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATtgatg                                                                                            <  2:897450/58‑1 (MQ=255)                                                                                                                      agagGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTAAACTGCTGGCAGAcgcg           >  2:746733/1‑139 (MQ=255)                                                                                                                      agagGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTAAACTGCTGGCAGAcgcg           >  2:974013/1‑139 (MQ=255)                                                                                                                       gagGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCtt                                    <  2:684238/113‑1 (MQ=255)                                                                                                                       gagGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCtt                                    >  1:684238/1‑113 (MQ=255)                                                                                                                       gagGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTAAACTGCTGGCAGACGCgg          >  2:1158126/1‑139 (MQ=255)                                                                                                                         gggTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGt                                                                                       >  2:154187/1‑60 (MQ=255)                                                                                                                         gggTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGt                                                                                       <  1:154187/60‑1 (MQ=255)                                                                                                                         gggTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGgc                                                           >  2:1419438/1‑88 (MQ=255)                                                                                                                         gggTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGgc                                                           <  1:1419438/88‑1 (MQ=255)                                                                                                                         gggTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTAAACTGCTGGCAGACGCGGGt        >  2:352468/1‑139 (MQ=255)                                                                                                                               gggTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTAAACTGCTGGCAGACGCGGGTATCCaa  <  1:352468/139‑1 (MQ=255)                                                                                                                                    aGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTAAACTGCTGGCAGAcgc            <  2:1148463/124‑1 (MQ=255)                                                                                                                                       |                                                                                                                                   CCTGATGCGCTACGCTTATCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGGAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTAAACTGCTGGCAGACGCGGGTATCCAA  >  NC_000913/3774237‑3774501

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑