Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	291,906	C→T	S136L (TCA→TTA)	yagJ →	CP4‑6 prophage; protein YagJ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	291,906	0	C	T	100.0%	131.4 / NA	36	S136L (TCA→TTA)	yagJ	CP4‑6 prophage; protein YagJ
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (19/17);  total (19/17)

CAAGGTTTTTGAGATCGAAACCAAACGTGAAGGATTTGCTTTCTGGTATCGTAATCCACAGTACACAGGGCAGTCGTCACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTCGTCCCGATTTCCTGTTCTTTGCCGAACAGG  >  NC_000913/291829‑291980                                                                              |                                                                           cAAGGTTTTTGAGATCGAAACCAAACGTGAAGGATTTGCTTTCTGGTATCGTAATCCACAGTACACAGGGCAGTCGTTACt                                                                         >  2:66427/1‑81 (MQ=255)        tttGAGATCGAAACCAAACGTGAAGGATTTGCTTTCTGGTATCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAAt                                                                   <  1:66392/80‑1 (MQ=255)         ttGAGATCGAAACCAAACGTGAAGGATTTGCTTTCTGGTATCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATc                                                                  <  2:66393/80‑1 (MQ=255)            agaTCGAAACCAAACGTGAAGGATTTGCTTTCTGGTATCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCt                                                               >  1:66472/1‑80 (MQ=255)               tCGAAACCAAACGTGAAGGATTTGCTTTCTGGTATCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATg                                                           <  2:66394/81‑1 (MQ=255)                 gAAACCAAACGTGAAGGATTTGCTTTCTGGTATCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGtt                                                         >  2:66430/1‑81 (MQ=255)                 gAAACCAAACGTGAAGGATTTGCTTTCTGGTATCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGtt                                                         >  1:66456/1‑81 (MQ=255)                  aaaCCAAACGTGAAGGATTTGCTTTCTGGTATCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTg                                                        <  2:66395/81‑1 (MQ=255)                   aaCCAAACGTGAAGGATTTGCTTTCTGGTATCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTg                                                        >  1:66446/1‑80 (MQ=255)                       aaaCGTGAAGGATTTGCTTTCTGGTATCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCt                                                   >  1:66440/1‑81 (MQ=255)                       aaaCGTGAAGGATTTGCTTTCTGGTATCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCt                                                   >  2:66439/1‑81 (MQ=255)                            tGAAGGATTTGCTTTCTGGTATCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGaa                                                >  1:66442/1‑79 (MQ=255)                               aGGATTTGCTTTCTGGTATCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTa                                           >  1:66444/1‑81 (MQ=255)                               aGGATTTGCTTTCTGGTATCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTa                                           <  2:66396/81‑1 (MQ=255)                                 gATTTGCTTTCTGGTATCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTAc                                          >  1:66447/1‑80 (MQ=255)                                 gATTTGCTTTCTGGTATCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACa                                         <  2:66397/81‑1 (MQ=255)                                       cTTTCTGGTATCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGAtt                                    <  2:66398/80‑1 (MQ=255)                                           cTGGTATCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTc                                <  1:66399/80‑1 (MQ=255)                                              gTATCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTCGTc                             <  2:66400/80‑1 (MQ=255)                                                aTCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTCGTccc                           >  2:66460/1‑80 (MQ=255)                                                 tCGTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTCGTCCCGa                         >  2:66448/1‑81 (MQ=255)                                                   gTAATCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTCGTCCCGAtt                       >  1:66468/1‑81 (MQ=255)                                                     aaTCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTCGTCCCGATTTc                     >  2:66466/1‑81 (MQ=255)                                                     aaTCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTCGTCCCGATTTc                     >  2:66459/1‑81 (MQ=255)                                                      aTCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTCGTCCCGATTTcc                    <  1:66401/81‑1 (MQ=255)                                                       tCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTCGTCCCGATTTCCt                   <  2:66402/81‑1 (MQ=255)                                                       tCCACAGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTCGTCCCGATTTCCt                   <  1:66403/81‑1 (MQ=255)                                                         cacaGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTCGTCCCGATTTCCTg                  <  2:66404/80‑1 (MQ=255)                                                          acaGTACACAGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTCGTCCCGATTTCCTGtt                >  2:66450/1‑81 (MQ=255)                                                                cacaGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTCGTCCCGATTTCCTGTTCTTTGc          <  2:66405/81‑1 (MQ=255)                                                                 acaGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTCGTCCCGATTTCCTGTTCTTTGcc         <  1:66406/81‑1 (MQ=255)                                                                  caGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTCGTCCCGATTTCCTGTTCTTTGcc         >  2:66452/1‑80 (MQ=255)                                                                  caGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTCGTCCCGATTTCCTGTTCTTTGCCg        <  1:66407/81‑1 (MQ=255)                                                                   aGGGCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTTGTCCCGATTTCCTGTTCTTTGCCg        >  2:66467/1‑80 (MQ=255)                                                                    gggCAGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTCGTCCCGATTTCCTGTTCTTTGCCGaa      >  1:66451/1‑81 (MQ=255)                                                                        aGTCGTTACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTCGTCCCGATTTCCTGTTCTTTGCCGAACAgg  <  2:66408/81‑1 (MQ=255)                                                                              |                                                                           CAAGGTTTTTGAGATCGAAACCAAACGTGAAGGATTTGCTTTCTGGTATCGTAATCCACAGTACACAGGGCAGTCGTCACTGGGAATCGCTTATGTTGAAGCTGAACAGTACAAGATTGTTCGTCCCGATTTCCTGTTCTTTGCCGAACAGG  >  NC_000913/291829‑291980

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑