Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,958,496	G→A	intergenic (‑364/+24)	torY ← / ← cutC	TMAO reductase III (TorYZ), cytochrome c‑type subunit/copper homeostasis protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,958,496	0	G	A	100.0%	203.1 / NA	64	intergenic (‑364/+24)	torY/cutC	TMAO reductase III (TorYZ), cytochrome c‑type subunit/copper homeostasis protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (35/29);  total (35/29)

TATTTTTAGCACAACGCTATGCGCACTGTCACCCGCTCAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGGGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGATATAACGCGAATACTCGTCCGCGTGTTCATCTGATGACATGGACAATCC  >  NC_000913/1958360‑1958630                                                                                                                                         |                                                                                                                                       tatTTTTAGCACAACGCTATGCGCACTGTCACCCGCTCAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCACTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGc                                                                                                                                      >  2:493172/1‑139 (MQ=255)                    tGCGCACTGTCACCCGCTCAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTaaa                                                                                                                   >  2:664850/1‑139 (MQ=255)                       gcACTGTCACCCGCTCAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAAt                                                                                                                >  1:869322/1‑139 (MQ=255)                         aCTGTCACCCGCTCAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCa                                                                                                              >  1:249363/1‑139 (MQ=255)                           tGTCACCCGCTCAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCAtt                                                                                                            >  1:1189184/1‑139 (MQ=255)                           tGTCACCCGCTCAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCAtt                                                                                                            >  2:173399/1‑139 (MQ=255)                                cccGCTCAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGcc                                                                                                       <  2:1189184/139‑1 (MQ=255)                                      cAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATgg                                                                                                 <  2:249363/139‑1 (MQ=255)                                                         ttcgttTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCtttca                                                                              >  2:1094903/1‑139 (MQ=255)                                                             ttttttATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAAc                                                                                                                         <  2:936509/92‑1 (MQ=255)                                                             ttttttATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAAc                                                                                                                         >  1:936509/1‑92 (MQ=255)                                                                tttATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGc                                                                       <  1:854342/139‑1 (MQ=255)                                                                        gTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGa                                                                                       <  2:912833/115‑1 (MQ=255)                                                                        gTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGa                                                                                       >  1:912833/1‑115 (MQ=255)                                                                        gTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAAccgccg                                                               >  2:1202885/1‑139 (MQ=255)                                                                        gTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAAccgccg                                                               <  1:739116/139‑1 (MQ=255)                                                                        gTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAAccgccg                                                               >  1:894030/1‑139 (MQ=255)                                                                        gTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAAccgccg                                                               >  1:1054525/1‑139 (MQ=255)                                                                         ttCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCaa                                                                                          >  1:1052134/1‑111 (MQ=255)                                                                         ttCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCaa                                                                                          <  2:1052134/111‑1 (MQ=255)                                                                         ttCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACcgccgc                                                              >  2:788349/1‑139 (MQ=255)                                                                         ttCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACcgccgc                                                              >  2:227755/1‑139 (MQ=255)                                                                          tCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCgccgcc                                                             <  1:664850/139‑1 (MQ=255)                                                                            aGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGGTTCCTTTCATTTCAGCAACCGCCGcccc                                                           <  2:869322/139‑1 (MQ=255)                                                                            aGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGcccc                                                           <  1:493172/139‑1 (MQ=255)                                                                            aGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGcccc                                                           <  1:173399/139‑1 (MQ=255)                                                                                   aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAAc                                                                                                                         >  1:1088257/1‑70 (MQ=255)                                                                                   aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAAc                                                                                                                         <  2:1088257/70‑1 (MQ=255)                                                                                   aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGAt                                                                                                   >  1:1138329/1‑92 (MQ=255)                                                                                   aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGAt                                                                                                   <  2:1138329/92‑1 (MQ=255)                                                                                   aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCg                                                                                               >  1:77528/1‑96 (MQ=255)                                                                                   aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCg                                                                                               <  2:77528/96‑1 (MQ=255)                                                                                   aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGc                                                                       <  2:972990/120‑1 (MQ=255)                                                                                   aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGc                                                                       >  1:972990/1‑120 (MQ=255)                                                                                   aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAATCGCCGCCCCGTCTACg                                                    >  1:46858/1‑139 (MQ=255)                                                                                   aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACg                                                    >  2:707484/1‑139 (MQ=255)                                                                                   aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACg                                                    >  2:180719/1‑139 (MQ=255)                                                                                        aGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCgccgcc                                                             >  1:476424/1‑125 (MQ=255)                                                                                        aGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCgccgcc                                                             <  2:476424/125‑1 (MQ=255)                                                                                            cccTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGATATAAcgc                                           <  1:1094903/139‑1 (MQ=255)                                                                                                          cAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGatat                                                <  2:627834/120‑1 (MQ=255)                                                                                                          cAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGatat                                                >  1:627834/1‑120 (MQ=255)                                                                                                           aGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCg                                                                                               >  2:645406/1‑72 (MQ=255)                                                                                                           aGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCg                                                                                               <  1:645406/72‑1 (MQ=255)                                                                                                           aGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCtt                                                                                 >  2:108896/1‑86 (MQ=255)                                                                                                           aGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCtt                                                                                 >  1:355045/1‑86 (MQ=255)                                                                                                           aGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCtt                                                                                 <  1:108896/86‑1 (MQ=255)                                                                                                           aGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCtt                                                                                 <  2:355045/86‑1 (MQ=255)                                                                                                           aGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCgccgcc                                                             >  2:700077/1‑106 (MQ=255)                                                                                                           aGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCgccgcc                                                             <  1:700077/106‑1 (MQ=255)                                                                                                           aGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCAATTGGCCTGATAGGGTTCAATGGTTCCTTTCATTTCAGCAACCGCCGCCCCGCCTACGATATAACGCGAATACTCGTCcgcg                            >  1:916227/1‑139 (MQ=255)                                                                                                               gCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGATATAACGCGAATACTCGTCCGCGTGtt                        <  2:894030/139‑1 (MQ=255)                                                                                                                  tGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCaa                                                                                          <  2:269559/70‑1 (MQ=255)                                                                                                                  tGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCaa                                                                                          >  1:269559/1‑70 (MQ=255)                                                                                                                         agcaagcaTCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCgccgcc                                                             >  1:6260/1‑92 (MQ=255)                                                                                                                         agcaagcaTCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCgccgcc                                                             <  2:6260/92‑1 (MQ=255)                                                                                                                         agcaagcaTCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGATATAACGCGAATACTCGTCCGCGTGTTCATCtgatga              >  2:318704/1‑139 (MQ=255)                                                                                                                         agcaagcaTCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCACTTCAGCAACCGCCGCCCCGTCTACGATATAACGCGAATACTCGTCCGCGTGTTCATCtgatga              >  2:734220/1‑139 (MQ=255)                                                                                                                             agcaTCATATTGAGCGACATGATGCAACGGTaaaa                                                                                                                  >  2:282781/1‑35 (MQ=255)                                                                                                                             agcaTCATATTGAGCGACATGATGCAACGGTaaaa                                                                                                                  <  1:282781/35‑1 (MQ=255)                                                                                                                               catcatATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGATATAACGCGAATACTCGTCCGCGTGTTCATCTGATGACATGGa        <  1:734220/139‑1 (MQ=255)                                                                                                                                    tatTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGATATAACGCGAATACTCGTCCGCGTGTTCATCTGATGACATGGACAATc   >  2:661146/1‑139 (MQ=255)                                                                                                                                     atTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATTATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGATATAACGCGAATACTCGTCCGCGTGTTCATCTGATGACATGGACAATcc  <  1:227755/139‑1 (MQ=255)                                                                                                                                      ttGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGATATAACGCGAATACTCGTCCGCGTGTTCATCTGATGACATGGa        <  1:669333/132‑1 (MQ=255)                                                                                                                                         |                                                                                                                                       TATTTTTAGCACAACGCTATGCGCACTGTCACCCGCTCAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGGGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGATATAACGCGAATACTCGTCCGCGTGTTCATCTGATGACATGGACAATCC  >  NC_000913/1958360‑1958630

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑