Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,400,407	T→G	D40E (GAT→GAG)	hfq →	global sRNA chaperone; HF‑I, host factor for RNA phage Q beta replication

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,400,407	0	T	G	100.0%	202.5 / NA	52	D40E (GAT→GAG)	hfq	global sRNA chaperone; HF‑I, host factor for RNA phage Q beta replication
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (29/23);  total (29/23)

CAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTA  >  NC_000913/4400261‑4400546                                                                                                                                                   |                                                                                                                                            cAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGt                                                                                                                                         <  2:322541/151‑1 (MQ=255)    aTAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCg                                                                                                                                      <  1:947965/151‑1 (MQ=255)      aaGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGt                                                                                                                                     <  2:553186/150‑1 (MQ=255)           tataAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCt                                                                                                                               >  1:347226/1‑151 (MQ=255)             taAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGt                                                                                                                             >  2:721512/1‑151 (MQ=255)              aaGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGtt                                                                                                                            <  2:134685/151‑1 (MQ=255)                ggAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTg                                                                                                                           >  2:609983/1‑150 (MQ=255)                ggAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGa                                                                                                                          <  1:109932/151‑1 (MQ=255)                    aaGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGaaaa                                                                                                                       >  1:803860/1‑150 (MQ=255)                       agagaATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAacac                                                                                                                   >  2:141797/1‑151 (MQ=255)                          gaATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGt                                                                                                                >  2:79774/1‑151 (MQ=255)                          gaATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGt                                                                                                                <  1:644812/151‑1 (MQ=255)                           aaTGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTc                                                                                                               <  2:276549/151‑1 (MQ=255)                           aaTGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTc                                                                                                               >  1:294040/1‑151 (MQ=255)                             tGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGt                                                                                                                >  2:323045/1‑148 (MQ=255)                                  aaGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAg                                                                                                         <  1:801791/150‑1 (MQ=255)                                    ggggCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATg                                                                                                      <  2:7289/151‑1 (MQ=255)                                      ggCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGt                                                                                                    <  2:605158/151‑1 (MQ=255)                                       gCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGtt                                                                                                   <  2:213519/151‑1 (MQ=255)                                             tttACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACa                                                                                               >  1:332740/1‑149 (MQ=255)                                                aCAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCa                                                                                           <  1:180334/150‑1 (MQ=255)                                                       ccGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGAttt                                                                                   <  1:941634/151‑1 (MQ=255)                                                       ccGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGAttt                                                                                   <  1:653352/151‑1 (MQ=255)                                                       ccGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGAttt                                                                                   >  1:181489/1‑151 (MQ=255)                                                       ccGTTCCTGAACGCACTGCGTCGGGAACGTGATCCAGTTTCTATTTATTTGGTGAATGGAATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGAttt                                                                                   >  2:242043/1‑151 (MQ=255)                                                                        gCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGtct                                                                  <  1:200724/151‑1 (MQ=255)                                                                         cGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGtctc                                                                 <  2:788395/151‑1 (MQ=255)                                                                                              tCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGt                                             <  2:578155/150‑1 (MQ=255)                                                                                               cTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTa                                            >  2:77311/1‑150 (MQ=255)                                                                                                 atttatttGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTa                                            <  1:643780/148‑1 (MQ=255)                                                                                                    tatttGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTaacaac                                       <  2:129892/150‑1 (MQ=255)                                                                                                    tatttGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACg                                      >  2:319657/1‑151 (MQ=255)                                                                                                      tttGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGcc                                    >  1:643121/1‑151 (MQ=255)                                                                                                         ggTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGt                                 <  2:355177/151‑1 (MQ=255)                                                                                                            gAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTGGTGATCCTGTTGAAAAACACGGTCAGCCAGCTGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTgg                               >  2:733559/1‑150 (MQ=255)                                                                                                            gAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGc                              >  2:474957/1‑151 (MQ=255)                                                                                                                 gTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTAc                         >  2:211931/1‑151 (MQ=255)                                                                                                                  tATTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTAcc                        >  2:663204/1‑151 (MQ=255)                                                                                                                   aTTAAGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACca                       <  1:662935/151‑1 (MQ=255)                                                                                                                      aaGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCCCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACcagc                     >  1:583861/1‑150 (MQ=255)                                                                                                                       aGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACcagc                     >  1:908974/1‑149 (MQ=255)                                                                                                                       aGCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACcagc                     >  1:877630/1‑149 (MQ=255)                                                                                                                        gCTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGt                  >  1:283718/1‑151 (MQ=255)                                                                                                                         cTGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGccc                                                             >  1:65233/1‑107 (MQ=255)                                                                                                                          tGCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTa                 >  2:548889/1‑150 (MQ=255)                                                                                                                           gCAAGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAAc               >  1:254777/1‑151 (MQ=255)                                                                                                                             aaGGGCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACt              >  1:437121/1‑150 (MQ=255)                                                                                                                                 gCAAATCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACcat         <  2:611129/151‑1 (MQ=255)                                                                                                                                   aaaTCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACcatc        >  2:454521/1‑150 (MQ=255)                                                                                                                                   aaaTCGAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACcatc        >  2:31667/1‑150 (MQ=255)                                                                                                                                        gAGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTa  <  2:814311/151‑1 (MQ=255)                                                                                                                                         aGTCTTTTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGt   >  1:533539/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                            CAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTA  >  NC_000913/4400261‑4400546

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑