Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	1,197,502	C→T	G11R (GGA→AGA)	ymfD ←	e14 prophage; putative SAM‑dependent methyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	1,197,502	0	C	T	100.0%	83.1 / NA	28	G11R (GGA→AGA)	ymfD	e14 prophage; putative SAM‑dependent methyltransferase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (15/13);  total (15/13)

TGATTAATTCATCAGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCCGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGATAATACCACTCACTGAG  >  NC_000913_3_pae_tpiA/1197358‑1197647                                                                                                                                                 |                                                                                                                                                  tGATTAATTCATCAGAATATCTAAATTTTCCGCAGCCAAAATCACGGGCGTGGCCATTTTTCTCAATGCGTCTAATATACTCGCAAAGATCTCTAGAGGGCATCGTATGAGGTTTTGCGGCATTCTTAGAGCGGATATTAACACtgtgg                                                                                                                                               >  1:385286/1‑148 (MQ=255)   aTTAATTCATCAGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCat                                                                                                                                             >  2:628369/1‑149 (MQ=255)          catcaGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAg                                                                                                                                      <  1:942925/149‑1 (MQ=255)            tcaGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTTAGCGAATATTAACTCTGTGCATATTATAGtt                                                                                                                                    >  2:647796/1‑149 (MQ=255)                aaTATCCAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCaaa                                                                                                                                <  1:525480/149‑1 (MQ=255)                  tatCTAAGTTTTCCGCAGCCAACATCAAGGGCCTCCCAGATTTACTTAGCTCTTATAACAAACTCAGAAGGGTAGCGACAAGGCAGTGGATTAGGGTTTGCTTGATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGc                                                                                                                              <  2:100263/149‑1 (MQ=255)                  tatCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGc                                                                                                                              >  1:929843/1‑149 (MQ=255)                    tCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCaa                                                                                                                            <  1:570268/149‑1 (MQ=255)                    acaaaGGTTTCGACAGCAAAAGTCAACGGAGTGGCCATTTTTCTCAATGCTTCCAATATACTCGCAAAGATATCGAGAGGCCATCGGATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCaa                                                                                                                            <  2:171046/146‑1 (MQ=255)                      tAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGt                                                                                                                          >  1:260513/1‑149 (MQ=255)                        aGTTGTCCGCAACCAAAATCAAGGGCGTGGACATTTTTCACAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTAc                                                                                                                        <  1:19540/149‑1 (MQ=255)                                   gCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTaa                                                                                                             >  2:724312/1‑149 (MQ=255)                                    ccAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAAt                                                                                                            <  1:724312/149‑1 (MQ=255)                                    ccAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCAATCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAAt                                                                                                            >  2:867891/1‑149 (MQ=255)                                                       cATTTTTCTCAATGCTTCTAATATACTCGCAAAAATATCTAGAGGGCATCGTATGAGGGTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACAATTAAATTAATGTTATTTTTAGTAACAAAt                                                                                         >  2:1003241/1‑149 (MQ=255)                                                           tttCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCtt                                                                                     <  1:225245/149‑1 (MQ=255)                                                               tcAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCttttat                                                                                 >  2:304621/1‑149 (MQ=255)                                                                           atatACTAGAAAAAAAAAGTAGAGGGCATCTTATGAGGTTTTGGTGGATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCATTTAATGTTAAAAAAAAAAAAAAATTCTTTTATTTTATCGTCCgg                                                                     <  2:1136066/149‑1 (MQ=255)                                                                                cTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGAttt                                                                <  1:628369/149‑1 (MQ=255)                                                                                          tatCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGGTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCgacttg                                                      >  1:936964/1‑149 (MQ=255)                                                                                               agagGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGTGATTTTTCCGACTTGACttt                                                 <  1:1133374/149‑1 (MQ=255)                                                                                                                      ctgcATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTTTGGGCTTAACTGTtaaa                          >  1:91222/1‑149 (MQ=255)                                                                                                                        gcATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGTGCTTAACTGTcaaaac                        >  2:796696/1‑147 (MQ=255)                                                                                                                                  aGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGataata              <  1:766415/149‑1 (MQ=255)                                                                                                                                   gCGAATATTAACTTTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCAATCTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGATAATAc             <  2:1044671/149‑1 (MQ=255)                                                                                                                                   gCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGATAATAc             >  1:287028/1‑149 (MQ=255)                                                                                                                                    cGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAAGGAATGTTCTTTTTAGTGAAACATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGATAATAcc            >  1:842372/1‑149 (MQ=255)                                                                                                                                         atTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGATAATACcactca       >  1:729244/1‑149 (MQ=255)                                                                                                                                            aaCTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTTGTGTTAACTGTCACAGCAACGATAATACcattccatg    >  1:299081/1‑145 (MQ=255)                                                                                                                                              ctctGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGATAATACCACTCACTgag  <  1:183316/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                  TGATTAATTCATCAGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCCGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGATAATACCACTCACTGAG  >  NC_000913_3_pae_tpiA/1197358‑1197647

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑