Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,907,051	C→A	M176I (ATG→ATT)	phoU ←	negative regulator of the pho regulon

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,907,051	0	C	A	100.0%	221.1 / NA	62	M176I (ATG→ATT)	phoU	negative regulator of the pho regulon
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (28/34);  total (28/34)

AATCCTGCCCCTTCACGTAGTAGAAGATAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTCATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCACGTCGTGCAGCATCTGGATGGTATG  >  NC_000913/3906915‑3907179                                                                                                                                         |                                                                                                                                 aaTCCTGCCCCTTCACGTAGTAGAAGATAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGtaatc                                                                                                                               <  1:342178/140‑1 (MQ=255)      tGCCCCTTCACGTAGTAGAAGATAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTg                                                                                                                          >  1:166606/1‑140 (MQ=255)      tGCCCCTTCACGTAGTAGAAGATAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTg                                                                                                                          >  1:819917/1‑140 (MQ=255)      tGCCCCTTCACGTAGTAGAAGATAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTg                                                                                                                          <  2:315414/140‑1 (MQ=255)       gCCCCTTCACGTAGTAGAAGATAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGa                                                                                                                         <  2:81890/140‑1 (MQ=255)        ccccTTCACGTAGTAGAAGATAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGAc                                                                                                                        >  2:318166/1‑140 (MQ=255)              cACGTAGTAGAAGATAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACaa                                                                                                                  >  2:449893/1‑140 (MQ=255)                 gtagtaGAAGATAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAAtgc                                                                                                               <  2:708422/140‑3 (MQ=255)                 gtagtaGAAGATAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATAc                                                                                                               <  2:589619/140‑1 (MQ=255)                 gtagtaGAAGATAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATAc                                                                                                               <  2:463239/140‑1 (MQ=255)                 gtagtaGAAGATAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATAc                                                                                                               <  1:867833/140‑1 (MQ=255)                  tagtagAAGATAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATAcc                                                                                                              >  1:247398/1‑140 (MQ=255)                     tagAAGATAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATa                                                                                                                >  1:881049/1‑135 (MQ=255)                     tagAAGATAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATa                                                                                                                <  2:881049/135‑1 (MQ=255)                     tagAAGATAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTc                                                                                                           >  1:478281/1‑140 (MQ=255)                      agaagaTAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCg                                                                                                          <  1:542309/140‑1 (MQ=255)                        aagaTAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTa                                                                                                        <  2:454582/140‑1 (MQ=255)                        aagaTAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTa                                                                                                        <  2:76493/140‑1 (MQ=255)                          gaTAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTAtt                                                                                                      >  1:238855/1‑140 (MQ=255)                           aTAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTc                                                                                                     >  1:82369/1‑140 (MQ=255)                                  cacaAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCg                                                                                              <  1:933862/140‑1 (MQ=255)                                  cacaAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCg                                                                                              <  1:812703/140‑1 (MQ=255)                                  cacaAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCg                                                                                              <  2:85964/140‑1 (MQ=255)                                    caAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGAc                                                                                            >  2:585057/1‑140 (MQ=255)                                          ttCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACtttttt                                                                                      <  2:238855/140‑1 (MQ=255)                                          ttCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACtttttt                                                                                      <  1:41184/140‑1 (MQ=255)                                           tCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTa                                                                                     >  2:254042/1‑140 (MQ=255)                                               gCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCtt                                                                                 <  1:92140/140‑1 (MQ=255)                                                cAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTc                                                                                <  1:254042/140‑1 (MQ=255)                                                     gTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGAt                                                                           >  1:630163/1‑140 (MQ=255)                                                     gTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGAt                                                                           >  1:134536/1‑140 (MQ=255)                                                                  tCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGa                                                                            >  1:99367/1‑126 (MQ=255)                                                                  tCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGa                                                                            <  2:99367/126‑1 (MQ=255)                                                                     aTAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTc                                                           >  2:479671/1‑140 (MQ=255)                                                                       aGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGt                                                         <  2:630163/140‑1 (MQ=255)                                                                                 cAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATCCCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCAt                                               <  2:928935/140‑1 (MQ=255)                                                                                      cAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCcgcg                                          >  2:455964/1‑140 (MQ=255)                                                                                         cgcAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGa                                       >  2:359828/1‑140 (MQ=255)                                                                                           cAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAAc                                     <  1:359828/140‑1 (MQ=255)                                                                                           cAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAAc                                     <  1:585057/140‑1 (MQ=255)                                                                                                agtaCGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTc                                <  2:166606/140‑1 (MQ=255)                                                                                                agtaCGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTc                                <  2:819917/140‑1 (MQ=255)                                                                                                   aCGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAg                             <  2:134536/140‑1 (MQ=255)                                                                                                     gCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCa                           >  2:35376/1‑140 (MQ=255)                                                                                                      cTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCAc                          >  2:868516/1‑140 (MQ=255)                                                                                                      cTCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCAc                          >  2:702853/1‑140 (MQ=255)                                                                                                       tCGGAATGGTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCAcg                         <  2:247398/140‑1 (MQ=255)                                                                                                               gTACGCGATTCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCACGTCGTgcag                 >  2:764385/1‑140 (MQ=255)                                                                                                               gTACGCGAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCACGTCGTgcag                 <  2:82369/140‑1 (MQ=255)                                                                                                                  cgcgAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCACGTCGTGCAGCAt              <  1:479671/140‑1 (MQ=255)                                                                                                                     gAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCACGTCGTGCAGCATCTg           >  1:549452/1‑140 (MQ=255)                                                                                                                     gAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCACGTCGTGCAGCATCTg           >  2:216536/1‑140 (MQ=255)                                                                                                                     gAATCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCACGTCGTGCAGCATCTg           <  1:318166/140‑1 (MQ=255)                                                                                                                       aTCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCACGTCGTGCAGCATCTGGa         <  2:137330/140‑1 (MQ=255)                                                                                                                       aTCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCACGTCGTGCAGCATCTGGa         >  1:780511/1‑140 (MQ=255)                                                                                                                       aTCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCACGTCGTGCAGCATCTGGa         >  1:506805/1‑140 (MQ=255)                                                                                                                        tCTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCACGTCGTGCAGCATCTGGAt        <  1:449893/140‑1 (MQ=255)                                                                                                                         cTTCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCACGTCGTGCAGCATCTGGATg       >  2:571928/1‑140 (MQ=255)                                                                                                                          ttCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCACGTCGTGCAGCATCTGGATgg      <  2:780511/140‑1 (MQ=255)                                                                                                                          ttCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCACGTCGTGCAGCATCTGGATgg      <  2:506805/140‑1 (MQ=255)                                                                                                                          ttCCATCATGTAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCACGTCGTGCAGCATCTGGATgg      >  2:371275/1‑140 (MQ=255)                                                                                                                                    tAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCACGTCGTGCAGCATCTGGATGGTATg  >  1:397478/1‑134 (MQ=255)                                                                                                                                    tAGGTAATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCACGTCGTGCAGCATCTGGATGGTATg  <  2:397478/134‑1 (MQ=255)                                                                                                                                         |                                                                                                                                 AATCCTGCCCCTTCACGTAGTAGAAGATAAACTCACAAATATTCTGGCAGCGGTCGCCAATACGTTCGATAGAACGCGCGCAGAACAGCGCAGTAAGTACGCTCGGAATGGTACGCGAATCTTCCATCATGTAGGTCATCAGTTGACGAACAATACCTTCGTATTCCTGATCGACTTTTTTATCTTCACGATAAATACGTACCGCTTCGTCAATGTCCATCCGCGCGAACGCGTCCAGCACGTCGTGCAGCATCTGGATGGTATG  >  NC_000913/3906915‑3907179

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑