Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009273	4,390,235	T→C	I44T (ATC→ACC)	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
*	CP009273	4,390,235	0	T	C	100.0%	151.4 / NA	45	I44T (ATC→ACC)	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 C (18/27);  total (18/27)

GAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAG  >  CP009273/4390094‑4390367                                                                                                                                              |                                                                                                                                     gAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTg                                                                                                                               >  1:319521/1‑149 (MQ=255)     agagagAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGaaaa                                                                                                                           <  1:678311/149‑1 (MQ=255)           gaTGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGaaaa                                                                                                                           <  2:643278/142‑1 (MQ=255)                 tAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACgg                                                                                                                     >  2:620202/1‑143 (MQ=255)                         aaTCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGtt                                                                                                       <  1:240042/149‑1 (MQ=255)                          aTCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGttt                                                                                                      <  1:57236/149‑1 (MQ=255)                            cTTGACCAGAGCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAAGCGAGGCGTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTAc                                                                                                    <  1:243608/149‑1 (MQ=255)                              ttACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACaa                                                                                                  <  1:668612/149‑1 (MQ=255)                               tACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTACTGTTTAGGTGGGGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAg                                                                                                 <  1:416978/149‑1 (MQ=255)                               gaCAAGATCCGTTCCGGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGtt                                                                                                       <  2:647083/142‑1 (MQ=255)                                aCAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGc                                                                                                <  1:644684/149‑1 (MQ=255)                                   acacgcGTTTCTTAGCGCACTGCGTCGGTAACGGGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACa                                                                                                   <  2:465607/138‑1 (MQ=255)                                      tCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGACTGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGc                                                                                                >  2:201567/1‑143 (MQ=255)                                                 aCGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACtgtt                                                                               <  1:442161/149‑1 (MQ=255)                                                 aCGCACGGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACtgtt                                                                               <  1:740570/149‑1 (MQ=255)                                                  cGCACTGCGTCGGGAACGGGTTCCAGTGTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGGCAGCCAGATGGTTTACAAGCACGCGATTTCTa                                                                                    >  2:206145/1‑143 (MQ=255)                                                      cTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTccc                                                                          >  1:58897/1‑149 (MQ=255)                                                          gTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTc                                                                            <  2:375755/143‑1 (MQ=255)                                                           tCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGtctc                                                                     >  1:258850/1‑149 (MQ=255)                                                               gAACGTGTTCCAGTTTCTATTTCTCTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGtc                                                                       >  2:254435/1‑143 (MQ=255)                                                               gAACGTGTTCCAGGTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGtc                                                                       >  2:418185/1‑143 (MQ=255)                                                                    tgtTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGttt                                                            <  1:470902/149‑1 (MQ=255)                                                                          aGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGttt                                                            <  2:24681/143‑1 (MQ=255)                                                                                   ttatttGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATcaca                                                   <  2:518605/143‑1 (MQ=255)                                                                                     atttGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTaacaac                                           >  1:183221/1‑149 (MQ=255)                                                                                       ttGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTaa                                               <  2:317984/143‑1 (MQ=255)                                                                                         ggTGAATGGTATTAAGCGGGAGGGGCAAATCGAGGCTTTCGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTATCGCCCCTTGCCTCATCACAGTaaca                                             <  2:156209/143‑1 (MQ=255)                                                                                             aagtgTATTACGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGCGACCCTGCTGAAAAACCCGGTCAGCCAGATGGTTTACAAGCACGCGATTCCTACTGTTGTCCCGTCTCGCCCGGTCCCTCATCAAAGTAACAACGCCGGTgg                                   <  1:168315/145‑1 (MQ=255)                                                                                              atcgTATTAAGCTGCAAGGCCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGcc                                        <  2:562039/140‑1 (MQ=255)                                                                                              aTGGTAGTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGc                                  <  1:114982/149‑1 (MQ=255)                                                                                                 gttttAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGt                                     <  2:14684/140‑1 (MQ=255)                                                                                                           gCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACca                           <  2:231249/143‑1 (MQ=255)                                                                                                            cAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTaa                    <  1:695234/149‑1 (MQ=255)                                                                                                              aGGGCAAATCGCGGCTTTTGGTCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACcagca                        <  2:185722/143‑1 (MQ=255)                                                                                                               gggCAAATCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACCACGCCGGTGGCGGTACCAGCAGTAACTa                 <  1:387940/149‑1 (MQ=255)                                                                                                                   aaaTCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACcat             >  1:283712/1‑149 (MQ=255)                                                                                                                     aTCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACcatca           >  1:30538/1‑149 (MQ=255)                                                                                                                      tCGAGTCTTTTGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTAc                >  2:208313/1‑143 (MQ=255)                                                                                                                      tCGAGTCTTTTGATCAGTTCGTGACCCCGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACcatcat          <  1:688853/149‑1 (MQ=255)                                                                                                                             ttttGATCAGTTCGTGACCCTGTTGAAAAAGACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACACCGGTGGCGGTACCAGCAGTAACTACCATCATg         >  2:485912/1‑143 (MQ=255)                                                                                                                             ttttGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGTTACCAGCAGTAACTCCcaacacg         >  2:446768/1‑141 (MQ=255)                                                                                                                             ttttGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATg         >  2:526504/1‑143 (MQ=255)                                                                                                                             ttttGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTATCGCCCGGTTTCTCATCACATTAACAACGCCGGTGGCGGTACCAGACGTGACTAACAGCATg         >  2:329590/1‑143 (MQ=255)                                                                                                                              tttGATCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCGCGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACACCGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTagcag  >  1:167870/1‑149 (MQ=255)                                                                                                                                   tCAGTTCGTGACCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTagca   >  2:591597/1‑143 (MQ=255)                                                                                                                                              |                                                                                                                                     GAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAG  >  CP009273/4390094‑4390367

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑