Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,245,903	(T)5→4	coding (1474/1698 nt)	treA ←	periplasmic trehalase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,245,899	0	T	.	100.0%	136.1 / NA	33	coding (1478/1698 nt)	treA	periplasmic trehalase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (13/20);  total (13/20)

TTGCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGACCCACTGTAACGGTGCCCAG  >  NC_000913/1245766‑1246021                                                                                                                                      |                                                                                                                           ttGCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCttttct                                                                                                                       >  1:296864/1‑137 (MQ=255) ttGCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCttttct                                                                                                                       >  2:774388/1‑137 (MQ=255)  tGCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCttttctc                                                                                                                      <  1:1028985/139‑4 (MQ=255)  tGCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCttttctc                                                                                                                      <  1:577625/139‑4 (MQ=255)   gCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCttttctcc                                                                                                                     >  2:882663/1‑135 (MQ=255)         tCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCa                                                                                                              >  1:979343/1‑139 (MQ=255)              cAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGgt                                                                                                         <  2:450797/139‑1 (MQ=255)              cAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGgt                                                                                                         <  1:1110895/139‑1 (MQ=255)                      aTCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGaa                                                                                                 <  2:10062/139‑1 (MQ=255)                            cATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCttttctc                                                                                                                      <  2:306315/113‑4 (MQ=255)                            cATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCttttctc                                                                                                                      >  1:306315/1‑110 (MQ=255)                               tttCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCttttctc                                                                                                                      >  2:964748/1‑107 (MQ=255)                               tttCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCttttctc                                                                                                                      <  1:964748/110‑4 (MQ=255)                                        cACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGcc                                                                               <  1:308076/139‑1 (MQ=255)                                          cGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAg                                                                             >  2:1125102/1‑139 (MQ=255)                                                 ggTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGt                                                                      <  1:774388/139‑1 (MQ=255)                                                  gTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTc                                                                     <  1:989748/139‑1 (MQ=255)                                                       gCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATCGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCg                                                                >  2:706755/1‑139 (MQ=255)                                                            aGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCttttctc                                                                                                                      >  2:787804/1‑78 (MQ=255)                                                            aGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCttttctc                                                                                                                      <  1:787804/81‑4 (MQ=255)                                                            aGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCAcc                                                           >  2:43719/1‑139 (MQ=255)                                                            aGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCAcc                                                           >  2:91429/1‑139 (MQ=255)                                                             gCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCttttctc                                                                                                                      >  1:58827/1‑77 (MQ=255)                                                             gCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCttttctc                                                                                                                      <  2:58827/80‑4 (MQ=255)                                                                      tAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGcc                                                 <  1:1125102/139‑1 (MQ=255)                                                                          ggATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTa                                             <  1:829372/139‑1 (MQ=255)                                                                            atatTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGt                                           >  1:35763/1‑139 (MQ=255)                                                                             tatTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGc                                                                            <  1:579827/105‑1 (MQ=255)                                                                             tatTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGc                                                                            >  2:579827/1‑105 (MQ=255)                                                                                tCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCttttctc                                                                                                                      >  1:595330/1‑58 (MQ=255)                                                                                tCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCttttctc                                                                                                                      <  2:595330/61‑4 (MQ=255)                                                                                tCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTg                                       >  1:39883/1‑139 (MQ=255)                                                                                tCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTg                                       >  1:110957/1‑139 (MQ=255)                                                                                       cgccgcCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCttttctc                                                                                                                      <  2:1116626/54‑4 (MQ=255)                                                                                       cgccgcCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCttttctc                                                                                                                      >  1:1116626/1‑51 (MQ=255)                                                                                        gccgccCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCtt                               <  1:882663/139‑1 (MQ=255)                                                                                            ccccccGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGt                           >  2:521438/1‑139 (MQ=255)                                                                                              ccccGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTcg                         <  1:486577/139‑1 (MQ=255)                                                                                              ccccGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTcg                         <  1:521438/139‑1 (MQ=255)                                                                                              ccccGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTcg                         >  1:743738/1‑139 (MQ=255)                                                                                                ccGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTcgcg                       <  2:22441/139‑1 (MQ=255)                                                                                                 cGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGa                      <  1:91429/139‑1 (MQ=255)                                                                                                   ttCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGAcc                    <  2:110957/139‑1 (MQ=255)                                                                                                   ttCCGGTGGTGCTGACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGAcc                    <  1:43719/139‑1 (MQ=255)                                                                                                              cTGACATCATATTTTTCCACCAGC‑TTTACTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCg                                               >  2:670467/1‑101 (MQ=255)                                                                                                              cTGACATCAGATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCg                                               <  1:670467/101‑1 (MQ=255)                                                                                                                gACATCATATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGACCCACTGTAACGGTg       <  1:618670/139‑1 (MQ=255)                                                                                                                     catATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGcc                                                 <  2:1078877/92‑1 (MQ=255)                                                                                                                     catATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGcc                                                 >  1:1078877/1‑92 (MQ=255)                                                                                                                     catATTTTTCCACCAGC‑TTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGACCCACTGTAACGGTGCCCAg  <  2:296864/139‑1 (MQ=255)                                                                                                                                      |                                                                                                                           TTGCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGACCCACTGTAACGGTGCCCAG  >  NC_000913/1245766‑1246021

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑