Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	850,389	T→C	intergenic (‑292/‑61)	rhtA ← / → ompX	threonine and homoserine efflux system/outer membrane protein X

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	850,389	0	T	C	100.0%	136.4 / NA	39	intergenic (‑292/‑61)	rhtA/ompX	threonine and homoserine efflux system/outer membrane protein X
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (20/19);  total (20/19)

AATGACAGGGAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTTCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGTAGCTGCGAC  >  NC_000913/850257‑850523                                                                                                                                     |                                                                                                                                       aatgaCAGGGAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCAtt                                                                                                                                  <  2:174792/139‑1 (MQ=255)  atgaCAGGGAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTa                                                                                                                                 <  1:1205323/139‑1 (MQ=255)       aGGGAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAAtttt                                                                                                                            >  1:1021944/1‑139 (MQ=255)           aaaaCATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTCACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGat                                                                                                                        <  2:149515/139‑1 (MQ=255)                  gCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGTCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTa                                                                                                                 <  2:210392/139‑1 (MQ=255)                             aCGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAATCGTTAGGAc                                                                                                      >  1:1323013/1‑139 (MQ=255)                             aCGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGAc                                                                                                      <  2:1021944/139‑1 (MQ=255)                                  gTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTAtt                                                                                                 >  2:1273043/1‑139 (MQ=255)                                          aaaaaGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATcac                                                                                         <  1:1241959/139‑1 (MQ=255)                                                                  aTAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATc                                                                                           <  1:1091829/113‑1 (MQ=255)                                                                  aTAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATc                                                                                           >  2:1091829/1‑113 (MQ=255)                                                                      cGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCAt                                                                                                                                   >  1:1231773/1‑69 (MQ=255)                                                                      cGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCAt                                                                                                                                   <  2:1231773/69‑1 (MQ=255)                                                                        gtgtATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATg                                                           <  2:250837/139‑1 (MQ=255)                                                                           tATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                            >  1:974324/1‑103 (MQ=255)                                                                           tATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                            <  2:974324/103‑1 (MQ=255)                                                                                   cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCAc                                                >  2:426888/1‑139 (MQ=255)                                                                                   cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCAc                                                >  2:1325228/1‑139 (MQ=255)                                                                                     ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGat                                                                                                                        <  2:1223208/65‑1 (MQ=255)                                                                                     ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGat                                                                                                                        >  1:1223208/1‑65 (MQ=255)                                                                                     ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                            >  2:984020/1‑93 (MQ=255)                                                                                     ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                            <  1:984020/93‑1 (MQ=255)                                                                                     ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                            <  1:496201/93‑1 (MQ=255)                                                                                     ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                            >  2:496201/1‑93 (MQ=255)                                                                                     ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCa                                                 >  1:605108/1‑136 (MQ=255)                                                                                     ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCa                                                 <  2:605108/136‑1 (MQ=255)                                                                                     ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTg                                              >  2:1048726/1‑139 (MQ=255)                                                                                     ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTg                                              >  2:139411/1‑139 (MQ=255)                                                                                                    tGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCt                               >  2:176297/1‑139 (MQ=255)                                                                                                           ttAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCg                        >  1:348712/1‑139 (MQ=255)                                                                                                               aCATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAgg                    <  1:498334/139‑1 (MQ=255)                                                                                                                   cacaAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACt                >  1:1303882/1‑139 (MQ=255)                                                                                                                        aTCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTAtt                                                                                                 >  2:1022819/1‑53 (MQ=255)                                                                                                                        aTCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTAtt                                                                                                 <  1:1022819/53‑1 (MQ=255)                                                                                                                        aTCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGt           >  2:1076779/1‑139 (MQ=255)                                                                                                                          cgcgAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                            <  2:396554/56‑1 (MQ=255)                                                                                                                          cgcgAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                            >  1:396554/1‑56 (MQ=255)                                                                                                                              aaGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGTAGCTGc     <  1:1048726/139‑1 (MQ=255)                                                                                                                                 agTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGTAGCTGCGAc  <  1:176297/139‑1 (MQ=255)                                                                                                                                     |                                                                                                                                       AATGACAGGGAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTTCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGTAGCTGCGAC  >  NC_000913/850257‑850523

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑