Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,486,821	T→C	S202P (TCC→CCC)	lptF →	lipopolysaccharide transport system protein LptF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,486,821	0	T	C	100.0%	145.3 / NA	41	S202P (TCC→CCC)	lptF	lipopolysaccharide transport system protein LptF
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (19/22);  total (19/22)

AATTCGACCAAAAGGTAATGCACGTCCTTCTGTGGTGGTGGCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCTCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCATTGTTACGTGATTTCCGCATTACGGACT  >  NC_000913/4486745‑4486896                                                                             |                                                                            aaTTCGACCAAAAGGTAATGCACGTCCTTCTGTGGTGGTGGCCGATTCCGGACATTTAACCCAGCTGCGCGACGGcccc                                                                           >  2:858989/1‑79 (MQ=255) aaTTCGACCAAAAGGTAATGCACGTCCTTCTGTGGTGGTGGCCGATTCCGGACATTTAACCCAGCTGCGCGACGGcccc                                                                           >  2:858984/1‑79 (MQ=255)  aTTCGACCAAAAGGTAATGCACGTCCTTCTGTGGTGGTGGCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAg                                                                        <  1:858928/81‑1 (MQ=255)    tCGACCAAAAGGTAATGCACGTCCTTCTGTGGTGGTGGCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGgt                                                                      >  2:859007/1‑81 (MQ=255)      gACCAAAAGGTAATGCACGTCCTTCTGTGGTGGTGGCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGgtc                                                                     <  2:858928/80‑1 (MQ=255)       aCCAAAAGGTAATGCACGTCCTTCTGTGGTGGTGGCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGgtcgt                                                                   <  2:858929/81‑1 (MQ=255)             aGGTAATGCACGTCCTTCTGTGGTGGTGGCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCActct                                                             <  2:858930/81‑1 (MQ=255)              ggTAATGCACGTCCTTCTGTGGTGGTGGCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCActct                                                             >  1:858989/1‑80 (MQ=255)                 aaTGCACGTCCTTCTGTGGTGGTGGCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAAc                                                         >  1:858991/1‑81 (MQ=255)                 aaTGCACGTCCTTCTGTGGTGGTGGCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAAc                                                         >  1:858987/1‑81 (MQ=255)                  aTGCACGTCCTTCTGTGGTGGTGGCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAAc                                                         >  2:859002/1‑80 (MQ=255)                   tGCACGTCCTTCTGTGGTGGTGGCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCa                                                       <  1:858932/81‑1 (MQ=255)                        gTCCTTCTGTGGTGGTGGCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGaa                                                  >  1:859000/1‑81 (MQ=255)                         tCCTTCTGTGGTGGTGGCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAAc                                                 <  2:858932/81‑1 (MQ=255)                             tCTGTGGTGGTGGCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACgcgc                                             >  1:858999/1‑81 (MQ=255)                                gtggtggtgGCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTc                                          >  2:858995/1‑81 (MQ=255)                                 tggtggtggCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCt                                            <  2:858933/78‑1 (MQ=255)                                  ggtggtggCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCg                                         >  1:859009/1‑80 (MQ=255)                                      gtggCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAgg                                     <  2:858935/80‑1 (MQ=255)                                      gtggCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGc                                    <  1:858935/81‑1 (MQ=255)                                      gtggCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGc                                    <  1:858937/81‑1 (MQ=255)                                       tggCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCa                                   <  1:858938/81‑1 (MQ=255)                                         gCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCAc                                  <  2:858938/80‑1 (MQ=255)                                          ccGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTg                                >  1:858981/1‑81 (MQ=255)                                          ccGATTCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTg                                >  2:859009/1‑81 (MQ=255)                                              ttCCGGACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCAtt                            <  1:858940/81‑1 (MQ=255)                                                   gACATTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCATTGTTAc                       <  1:858941/81‑1 (MQ=255)                                                      aTTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCATTGTTAtgtg                    <  2:858941/81‑1 (MQ=255)                                                      aTTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCATTGTTACGt                     >  2:859018/1‑80 (MQ=255)                                                      aTTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCATTGTTACGt                     >  1:859018/1‑80 (MQ=255)                                                      aTTTAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCATTGTTACGTg                    <  1:858943/81‑1 (MQ=255)                                                       tttAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCATTGTTACGTGa                   >  1:859028/1‑81 (MQ=255)                                                         tAACCCAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCATTGTTACGTGAt                  <  1:858944/80‑1 (MQ=255)                                                           aCCCAGCTGCGCGTCGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCATTGTTACGTGAttt                <  1:858945/80‑1 (MQ=255)                                                            cccAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCATTGTTACGTGATTTcc              <  1:858946/81‑1 (MQ=255)                                                              cAGCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCATTGTTACGTGATTTCCGc            <  1:858947/81‑1 (MQ=255)                                                                gCTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCATTGTTACGTGATTTCCGCAt          >  2:859021/1‑81 (MQ=255)                                                                 cTGCGCGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCATTGTTACGTGATTTCCGCAt          >  1:859024/1‑80 (MQ=255)                                                                   gcgcGACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCATTGTTACGTGATTTCCGCATTAc       >  2:859006/1‑81 (MQ=255)                                                                    cgcgACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCATTGTTACGTGATTTCCGCATTAc       <  1:858948/80‑1 (MQ=255)                                                                     gcgACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCATTGTTACGTGATTTCCGCATTACg      >  2:859013/1‑80 (MQ=255)                                                                       gACGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCATTGTTACGTGATTTCCGCATTACGGAc   <  1:858949/81‑1 (MQ=255)                                                                        aCGGCCCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCATTGTTACGTGATTTCCGCATTACGGACt  >  1:858998/1‑81 (MQ=255)                                                                             |                                                                            AATTCGACCAAAAGGTAATGCACGTCCTTCTGTGGTGGTGGCCGATTCCGGACATTTAACCCAGCTGCGCGACGGCTCCCAGGTCGTCACTCTCAACCAGGGAACGCGCTTCGAAGGCACTGCATTGTTACGTGATTTCCGCATTACGGACT  >  NC_000913/4486745‑4486896

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑