Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,486,041	T→C	intergenic (‑90/‑177)	pepA ← / → lptF	aminopeptidase A/I/lipopolysaccharide transport system protein LptF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,486,041	0	T	C	100.0%	77.2 / NA	23	intergenic (‑90/‑177)	pepA/lptF	aminopeptidase A/I/lipopolysaccharide transport system protein LptF
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (10/13);  total (10/13)

GAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCTGAGAGGTGAATCCGTTGAGTATAAT  >  NC_000913/4485965‑4486115                                                                             |                                                                           gAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTCCgtg                                                                        >  1:858770/1‑81 (MQ=255)   aTCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTCCGTGtt                                                                      <  2:858735/81‑1 (MQ=255)         aaGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTCCGTGTTAATCtt                                                                <  2:858736/81‑1 (MQ=255)             cAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTCCGTGTTAATCTTAACg                                                            <  2:858737/81‑1 (MQ=255)               aCGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTCCGTGTTAATCTTAACGt                                                           >  2:858771/1‑80 (MQ=255)                              gATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTCCGTGTTAATCTTAACGTTATTACGGCATTGGCa                                           <  2:858738/81‑1 (MQ=255)                               aTAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTCCGTGTTAATCTTAACGTTATTACGGCATTGGCAc                                          >  1:858776/1‑81 (MQ=255)                                tAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTCCGTGTTAATCTTAACGTTATTACGGCATTGGCACg                                         <  1:858740/81‑1 (MQ=255)                                 aGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTCCGTGTTAATCTTAACGTTATTACGGCATTGGCACGt                                        >  1:858774/1‑81 (MQ=255)                                  gAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTCCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTc                                       <  2:858740/81‑1 (MQ=255)                                         aaGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTCCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACaa                                <  1:858743/81‑1 (MQ=255)                                         aaGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTCCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACaa                                <  2:858741/81‑1 (MQ=255)                                            cTTTCGTAACTCATGTCCGCTGTTGCGATGACTCCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAAt                             <  2:858743/81‑1 (MQ=255)                                               tCGTAACTCATGTCCGCTGTTGCGATGACTCCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCt                           >  1:858792/1‑80 (MQ=255)                                                 gTAACTCATGTCCGCTGTTGCGATGACTCCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCt                           >  1:858780/1‑78 (MQ=255)                                                 gTAACTCATGTCCGCTGTTGCGATGACTCCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCTgag                        <  2:858744/81‑1 (MQ=255)                                                   aaCTCATGTCCGCTGTTGCGATGACTCCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCTGagag                      >  2:858781/1‑81 (MQ=255)                                                     cTCATGTCCGCTGTTGCGATGACTCCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCTGAGAGGt                    >  2:858772/1‑81 (MQ=255)                                                             cGCTGTTGCGATGACTCCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCTGAGAGGTGAATCCGt            <  1:858746/81‑1 (MQ=255)                                                                  ttGCGATGACTCCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCTGAGAGGTGAATCCGTTGAGt       <  1:858747/81‑1 (MQ=255)                                                                      gATGACTCCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCTGAGAGGTGAATCCGTTGAGTATaa   <  2:858747/81‑1 (MQ=255)                                                                       aTGACTCCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCTGAGAGGTGAATCCGTTGAGTATAAt  >  1:858779/1‑81 (MQ=255)                                                                        tGACTCCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCTGAGAGGTGAATCCGTTGAGTATAAt  >  1:858784/1‑80 (MQ=255)                                                                             |                                                                           GAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCTGAGAGGTGAATCCGTTGAGTATAAT  >  NC_000913/4485965‑4486115

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑