Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,947,041	C→A	intergenic (+9/+87)	trpT → / ← hdfR	tRNA‑Trp/DNA‑binding transcriptional dual regulator HdfR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,947,041	0	C	A	100.0%	182.1 / NA	53	intergenic (+9/+87)	trpT/hdfR	tRNA‑Trp/DNA‑binding transcriptional dual regulator HdfR
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (25/28);  total (25/28)

CTGTCACGCAGGGGGTCGCGGGTTCGAGTCCCGTCCGTTCCGCCACCCTAATTAGGGGCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCATTCATATTAATACACTTCATCCAGCACGTTAATTTTCAAAAGATCGC  >  NC_000913/3946904‑3947168                                                                                                                                          |                                                                                                                                ctgTCACGCAGGGGGTCGCGGGTTCGAGTCCCGTCCGTTCCGCCACCCTAATTAGGGGCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACt                                                                                                                               >  1:471232/1‑140 (MQ=255)  tgTCACGCAGGGGGTCGCGGGTTCGAGTCCCGTCCGTTCCGCCACCCTAATTAGGGGCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACtt                                                                                                                              >  2:783323/1‑140 (MQ=255)      aCGCAGGGGGTCGCGGGTTCGAGTCCCGTCCGTTCCGCCACCCTAATTAGGGGCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCg                                                                                                                          >  2:210027/1‑140 (MQ=255)                tCGCGGGTTCGAGTCCCGTCCGTTCCGCCACCCTAATTAGGGGCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAgg                                                                                                                >  1:415055/1‑140 (MQ=255)                      gTTCGAGTCCCGTCCGTTCCGCCACCCTAATTAGGGGCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGAttttt                                                                                                          >  2:65084/1‑140 (MQ=255)                       ttCGAGTCCCGTCCGTTCCGCCACCCTAATTAGGGGCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGAtttttt                                                                                                         <  1:183102/140‑1 (MQ=255)                           aGTCCCGTCCGTTCCGCCACCCTAATTAGGGGCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTAt                                                                                                     <  2:28878/140‑1 (MQ=255)                           aGTCCCGTCCGTTCCGCCACCCTAATTAGGGGCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTAt                                                                                                     <  1:688553/140‑1 (MQ=255)                            gTCCCGTCCGTTCCGCCACCCTAATTAGGGGCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATc                                                                                                    <  2:248915/140‑1 (MQ=255)                            gTCCCGTCCGTTCCGCCACCCTAATTAGGGGCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATc                                                                                                    <  2:471232/140‑1 (MQ=255)                                  tccgtTCCGCCACCCTAATTAGGGGCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAAt                                                                                              >  2:783205/1‑140 (MQ=255)                                      ttCCGCCACCCTAATTAGGGGCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAAcc                                                                                          <  1:127786/140‑1 (MQ=255)                                          gCCACCCTAATTAGGGGCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCctct                                                                                      <  2:395206/140‑1 (MQ=255)                                               ccTAATTAGGGGCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGaa                                                                                 <  2:755996/140‑1 (MQ=255)                                                        gggCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCt                                                                        >  1:133718/1‑140 (MQ=255)                                                         ggCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCtt                                                                       >  1:448872/1‑140 (MQ=255)                                                          gCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTc                                                                      >  2:188608/1‑140 (MQ=255)                                                          gCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTc                                                                      <  1:210027/140‑1 (MQ=255)                                                          gCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTc                                                                      <  1:543589/140‑1 (MQ=255)                                                          gCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTc                                                                      <  2:684438/140‑1 (MQ=255)                                                            gTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTa                                                                    >  2:68617/1‑140 (MQ=255)                                                             tAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTAc                                                                   >  2:44118/1‑140 (MQ=255)                                                             tAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTAc                                                                   >  1:316572/1‑140 (MQ=255)                                                             tAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTAc                                                                   >  1:591826/1‑140 (MQ=255)                                                             tAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTAc                                                                   >  1:52338/1‑140 (MQ=255)                                                               gTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCg                                                                 <  1:188608/140‑1 (MQ=255)                                                               gTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCg                                                                 <  1:176387/140‑1 (MQ=255)                                                                   aaTTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCATCTACCGGCAt                                                             <  2:427288/140‑1 (MQ=255)                                                                        gTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTg                                                        >  2:693059/1‑140 (MQ=255)                                                                          agagCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCtt                                                                       <  2:439632/123‑1 (MQ=255)                                                                          agagCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCtt                                                                       >  1:439632/1‑123 (MQ=255)                                                                          agagCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTgcc                                                      >  2:590096/1‑140 (MQ=255)                                                                            agCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTgccag                                                    >  2:359211/1‑140 (MQ=255)                                                                             gCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTgccagc                                                   <  1:888426/140‑1 (MQ=255)                                                                               aCCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTgccagcca                                                 >  2:727681/1‑140 (MQ=255)                                                                                 cGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCAtt                                               <  1:68617/140‑1 (MQ=255)                                                                                 cGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCAtt                                               <  1:303941/140‑1 (MQ=255)                                                                                 cGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCAtt                                               <  1:44118/140‑1 (MQ=255)                                                                                 cGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCAtt                                               <  1:441507/140‑1 (MQ=255)                                                                                 cGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCAtt                                               <  2:52338/140‑1 (MQ=255)                                                                                 cGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCAtt                                               <  1:783205/140‑1 (MQ=255)                                                                                 cGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCAtt                                               <  1:828758/140‑1 (MQ=255)                                                                                  ggTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCATTc                                              >  1:35943/1‑140 (MQ=255)                                                                                   gTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGGAAGCTAAGGATTTTTTTTATCTGACATAACCCTCTCCGAAGTAAATCCTTCTACCGACATCCTTGCCAGCCATTCa                                             >  2:853918/1‑140 (MQ=255)                                                                                   gTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCATTCa                                             >  1:86497/1‑140 (MQ=255)                                                                                   gTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCATTCa                                             <  1:359211/140‑1 (MQ=255)                                                                                   gTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCATTCa                                             >  1:881775/1‑140 (MQ=255)                                                                                     ctcCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCATTCata                                           <  2:591826/140‑1 (MQ=255)                                                                                     ctcCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCATTCata                                           <  1:300397/140‑1 (MQ=255)                                                                                      tcCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCATTCatat                                          <  2:448872/140‑1 (MQ=255)                                                                                                ggTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCATTCATATTAATACACtt                                >  1:184375/1‑140 (MQ=255)                                                                                                       ggAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCATTCATATTAATACACTTCATCCAg                         <  2:316572/140‑1 (MQ=255)                                                                                                             cGAGTCTCTCCGCCCCTGCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCATTCATATTAATACACTTCATCCAGCACGtt                   >  2:163184/1‑140 (MQ=255)                                                                                                                              gCCAGAAATCATACTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCATTCATATTAATACACTTCATCCAGCACGTTAATTTTCAAAAGATcgc  >  2:602002/1‑140 (MQ=255)                                                                                                                                          |                                                                                                                                CTGTCACGCAGGGGGTCGCGGGTTCGAGTCCCGTCCGTTCCGCCACCCTAATTAGGGGCGTAGTTCAATTGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATCATCCTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATAACCCTCTCCGAAGTAAATCCTTCTACCGGCATCCTTGCCAGCCATTCATATTAATACACTTCATCCAGCACGTTAATTTTCAAAAGATCGC  >  NC_000913/3946904‑3947168

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑