Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_KO_pgi	4,160,854	C→T	intergenic (‑64/‑270)	sthA ← / → fabR	pyridine nucleotide transhydrogenase, soluble/transcriptional repressor of fabA and fabB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_KO_pgi	4,160,854	0	C	T	100.0%	164.3 / NA	53	intergenic (‑64/‑270)	sthA/fabR	pyridine nucleotide transhydrogenase, soluble/transcriptional repressor of fabA and fabB
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (26/27);  total (26/27)

TTAACCAGGCCCATTGCAGCGCCTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGCCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTATTGGATTTTTATCGACGATACTCTCCGTTTAAGCGGCAGGTTTCCGCTGTACGTAAAAGA  >  NC_000913_3_KO_pgi/4160711‑4160995                                                                                                                                                 |                                                                                                                                              ttAACCAGGCCCATTGCAGCGCCTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTGAGTCAAtt                                                                                                                                          >  1:87706/1‑149 (MQ=255) ttAACCAGGCCCATTGCAGCGCCTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAAtt                                                                                                                                          <  1:343939/149‑1 (MQ=255) ttAACCAGGCCCATTGCAGCGCCTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTAAAtt                                                                                                                                          >  2:100263/1‑149 (MQ=255)  tacccAGGCCCATTTCAGCGCCTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTg                                                                                                                                         <  1:568710/146‑1 (MQ=255)       aGGCCCATTGCAGCGCCTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATccc                                                                                                                                    >  1:813792/1‑149 (MQ=255)        ggCCCATTGCAGCGCCTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTAACTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATcccc                                                                                                                                   >  2:877744/1‑149 (MQ=255)          cccATTGCAGCGCCTTCGCCGCCGGGGCCGGAACCGTTTGCTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGt                                                                                                                                 <  1:391569/149‑1 (MQ=255)             aTTGCAGCGCCTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCCGGTAAGTCACTTGATCCCCGTCAt                                                                                                                              <  1:782040/149‑1 (MQ=255)              ttGCAGCGCCTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCAtt                                                                                                                             >  1:458837/1‑149 (MQ=255)                  aGCGCCTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATc                                                                                                                         <  1:535650/149‑1 (MQ=255)                  aGCGCCTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGAAGGGCA‑CCTGAAGCAGGGTGTACCGGGTAAGTCAATTGATCCCCGTCATTTATc                                                                                                                         >  1:429558/1‑149 (MQ=255)                        ttCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTCATCGTAGGAATGTGGCCTGGTAAGGATTGCCACATCTTATACATAAAACCAACAGA‑CTGTGAACGTTGTCTGTCGGGTAAGTCCATTTATCCCCGTCATTTATCTGGCtc                                                                                                                   >  2:648/1‑148 (MQ=255)                        ttCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGcga                                                                                                                   >  1:838120/1‑147 (MQ=255)                            ccgccgGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATc                                                                                                                                      >  2:813568/1‑126 (MQ=255)                            ccgccgGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATc                                                                                                                                      <  1:813568/126‑1 (MQ=255)                              gtcgGGGCCAGAACCTATTATCATGGCATCGCAATCGTAGGAATGTGGCATGGTAGGGCTTACCTATTCGTATATATAAGAGCAACAGA‑TTGGTAACATTTTATCGCGGGTAAGTCAATTGACCCCCGTCATTTACCTGGCTATATCCt                                                                                                             <  1:740659/147‑1 (MQ=255)                              gccgGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCt                                                                                                             <  1:2695/149‑1 (MQ=255)                               ccgGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTg                                                                                                            >  2:721410/1‑149 (MQ=255)                                   ggCTGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGTGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCg                                                                                                        <  2:222434/149‑1 (MQ=255)                                           ccTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTACTCCCCGTCATTTACCTGGCTCTATCCTGAGCGGCctttgc                                                                                                >  2:901254/1‑149 (MQ=255)                                            cTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAACAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCctttgct                                                                                               <  1:434809/149‑1 (MQ=255)                                              aTTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCctttgcttt                                                                                             <  2:458837/149‑1 (MQ=255)                                                    gtgtctccgtaatgggaGGAATGTGGCATGGTAGGGTCTCCCTGTTCTTATACATAAAAGCAACAGT‑ATGGTAACATTTTATCGCGGGTAAGTCAATTTATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCCTTGTCTGt                                                                                       <  2:447057/142‑1 (MQ=255)                                                      ggCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGttt                                                                                     <  1:318957/149‑1 (MQ=255)                                                       gCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTc                                                                                    >  2:454103/1‑149 (MQ=255)                                                                       aaTGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGAc                                                                    <  2:898482/149‑1 (MQ=255)                                                                          gtgGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCTTGACGtt                                                                 >  1:827302/1‑149 (MQ=255)                                                                           tgGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCct                                                                                                    >  1:801685/1‑113 (MQ=255)                                                                           tgGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCct                                                                                                    <  2:801685/113‑1 (MQ=255)                                                                             gCATGGTAGGGCTTACCTGTTCTTATACATGAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTa                                                              >  1:671241/1‑149 (MQ=255)                                                                              caaggTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTAt                                                             <  2:429558/146‑1 (MQ=255)                                                                               agggTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTAtt                                                            <  2:645251/147‑1 (MQ=255)                                                                                  gTAGGGCTTGCCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGTGGGTAAGTCAATTGATCCCCGCACAATATGACGCTATATCCTGAGCGGCCTTTTCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTATTGGa                                                         <  1:623367/149‑1 (MQ=255)                                                                                  gTAGGGCTCACCTGTGCTTATACAGAAAACCAAGAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCAATATCTTTAGCTTGTTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTATTGGa                                                         <  2:373957/149‑1 (MQ=255)                                                                                       gCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCTGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGCCGTTTTCTTGGAttttt                                                    >  2:374873/1‑149 (MQ=255)                                                                                        cTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGttt                                                                                     <  1:222586/115‑1 (MQ=255)                                                                                        cTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGttt                                                                                     >  2:222586/1‑115 (MQ=255)                                                                                           aCCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTATTGGATTTTTATcg                                                >  1:829593/1‑149 (MQ=255)                                                                                             cTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGCCGTTTTATTGGATTTTTATcgac                                              >  1:228956/1‑149 (MQ=255)                                                                                              tGTTCTTATACATAAAAGCAACAGACAACATAA‑AGGTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTATTGGATTTTTTTcgacg                                             >  1:670836/1‑149 (MQ=255)                                                                                                 tCTTATACATAAAAGTAACAGA‑TTGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCTGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTATTGGATTTTTATCGACGATa                                          <  2:439136/149‑1 (MQ=255)                                                                                                   ttATACATAAAAGCAACAGA‑ATGGTAACATTTTATGGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTTTTGCTGTTGCCGTTACGTTTTGTTGGATTTTTTTCGGCGTTAct                                        >  1:392171/1‑149 (MQ=255)                                                                                                        cATAAAAGCAACCGA‑ATGGTAACATTTTATCGCGCGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTATTGGATTTTTATCGACGATACTCTCCg                                   <  1:786477/149‑1 (MQ=255)                                                                                                         aTAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTATTGGATTTTTATCGGCGATACTCTCCGt                                  >  1:277262/1‑149 (MQ=255)                                                                                                         aTAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTATTGGATTTTTATCGACGATACTCTcctt                                  >  1:167631/1‑147 (MQ=255)                                                                                                                 aaCAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTATTGGATTTTTATCGACGATACTCTCCGTTTAAGCgg                          <  1:466175/149‑1 (MQ=255)                                                                                                                  aCAGA‑ATGGTAACATTTTATCGCGGGTAAGTCAATAAACCCCCGCCAATTGTCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTATTGGATTTTTATCGACGATACTCTCCGTTTAAGCGGc                         <  1:748384/149‑1 (MQ=255)                                                                                                                             aaCATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTATTGGATTTTTATCGACGATACTCTCCGTTTAAGCGGCAGGTTTCCGc               >  2:254541/1‑149 (MQ=255)                                                                                                                              aCATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTATTGGATTTTTATCGACGATACTCTCCGTTTAAGCGGCAGGTTTCCGCt              <  2:671241/149‑1 (MQ=255)                                                                                                                               cATTTTATCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTATTGGATTTTTAGCGACGATACTCTCCGTTTAAGCGGCAGGtttagcctg             >  2:621308/1‑143 (MQ=255)                                                                                                                                      tCGCGGGTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTATTGGATTTTTCTCGACGATACTCTCCGTTTAAGCGGCTGGTTTCCGCTGTACGTaa      <  1:415155/149‑1 (MQ=255)                                                                                                                                          gggTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTATTGGATTTTTATCGACGATACTCTCCGTTTAAGCGGCAGGTTTCCGCTGTACGTAAAAGa  <  1:355781/149‑1 (MQ=255)                                                                                                                                          gggTAAGTCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTATTGGATTTTTATCGACGATACTCTCCGTTTAAGCGGAAGGTTTCCCTTGTACGTAAAAGa  >  1:121339/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                              TTAACCAGGCCCATTGCAGCGCCTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGA‑ATGGTAACATTTTATCGCGGGTAAGCCAATTGATCCCCGTCATTTATCTGGCTATATCCTGAGCGGCCTTTGCTTTGTCTGTTTCTTACTTTTGCCCTGACGTTTTATTGGATTTTTATCGACGATACTCTCCGTTTAAGCGGCAGGTTTCCGCTGTACGTAAAAGA  >  NC_000913_3_KO_pgi/4160711‑4160995

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: ‑