Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,484,894	T→C	54.1%	M316V (ATG→GTG)	menF ←	isochorismate synthase 2

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,484,894	0	T	C	54.1%	5.2 / 44.9	37	M316V (ATG→GTG)	menF	isochorismate synthase 2
Reads supporting (aligned to +/- strand):  ref base T (6/11);  new base C (9/11);  total (15/22)
Fisher's exact test for biased strand distribution p-value = 7.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.55e-01

CTGATGTAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCTGTAATCGTTGACA  >  minE/1484826‑1484963                                                                     |                                                                      cTGATGTAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCActt                                                                     <  1:267821/71‑1 (MQ=255)    aTGTAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCActtt                                                                    <  1:3923551/69‑1 (MQ=255)    aTGTAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCActtt                                                                    <  1:2231836/69‑1 (MQ=255)    aTGTAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTac                                                                  >  1:3678170/1‑71 (MQ=255)       tAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacgc                                                                <  1:2678512/70‑1 (MQ=255)         aaCAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacgcaga                                                             <  1:1499191/71‑1 (MQ=255)          aCAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTacgcagac                                                            <  1:1212710/71‑1 (MQ=255)           cAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCAttt                                                                     >  1:2357484/1‑61 (MQ=255)           cAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTacgcagacg                                                           >  1:1954848/1‑71 (MQ=255)           cAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacgcagacg                                                           <  1:2262654/71‑1 (MQ=255)           cAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacgcagacg                                                           <  1:1318273/71‑1 (MQ=255)              aTCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTacgcagacgcag                                                        <  1:2299114/71‑1 (MQ=255)              aTCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacgcagacgcag                                                        >  1:2176289/1‑71 (MQ=255)              aTCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacgcagacgcag                                                        >  1:1770849/1‑71 (MQ=255)              aTCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacgcagacg                                                           <  1:2615989/68‑1 (MQ=255)                   atcatcCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTACGCAGACGCAGTACCt                                                   >  1:2261845/1‑71 (MQ=255)                    tcatcCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTg                                                  <  1:2791201/71‑1 (MQ=255)                     catcCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTacgcagacgc                                                          <  1:1479947/62‑1 (MQ=255)                      atcCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAATATGCTGCATTTTACGCAGACGCAGTACCTgcg                                                <  1:3799074/71‑1 (MQ=255)                      atcCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTgcg                                                <  1:193237/71‑1 (MQ=255)                             ttgttgAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTACGCAGAAGCAGTACCTGCGGCGGTa                                          >  1:2486156/1‑70 (MQ=255)                                ttgAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAAc                                      <  1:3303441/71‑1 (MQ=255)                                 tgAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACa                                     >  1:253792/1‑71 (MQ=255)                                  gAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTgcg                                                >  1:191262/1‑59 (MQ=255)                                  gAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACAt                                    >  1:3193498/1‑71 (MQ=255)                                  gAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGAAGCAGTACCTGCGGCGGTAAAACAt                                    >  1:2956127/1‑71 (MQ=255)                                   aGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATc                                   <  1:1698877/71‑1 (MQ=255)                                       aaGTCCAGATACAGCGGCGAAGATTCTGCACTTTACGCAGACGCAGTACCTgcggc                                              <  1:3179676/56‑1 (MQ=255)                                       aaGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGc                               <  1:2388129/71‑1 (MQ=255)                                          tCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCt                                                   <  1:3777752/48‑1 (MQ=255)                                            cAGATACAGCGGCGAAGATGCTGCACTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCt                           <  1:84632/70‑1 (MQ=255)                                            cAGATACAGCGGCGAAGATGCTGCACTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTg                          >  1:2362768/1‑71 (MQ=255)                                                   aGCGGCGAAGATGCTGCACTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCg                   <  1:2128403/71‑1 (MQ=255)                                                   aGCGGCGAAGATGCTGCACTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCg                   <  1:550595/71‑1 (MQ=255)                                                     cggcgAAGATGCTGCACTTTACGCAGACGCAGTACCTGCGGCGGTaaaa                                       >  1:2339887/1‑49 (MQ=255)                                                     cggcgAAGATGCTGCACTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGc                 <  1:2399439/71‑1 (MQ=255)                                                     cggcgAAGATGCTGCACTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGc                 <  1:2394736/71‑1 (MQ=255)                                                       gcgAAGATGCTGCACTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCa                                 >  1:1645907/1‑53 (MQ=255)                                                                 tgcACTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTgg                         >  1:1257045/1‑51 (MQ=255)                                                                   cATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCTGTAATCGTTGa    >  1:2584339/1‑70 (MQ=255)                                                                    aTTTTAAGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCTGTAATCGTTGACa  <  1:3252505/71‑1 (MQ=255)                                                                     |                                                                      CTGATGTAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCTGTAATCGTTGACA  >  minE/1484826‑1484963

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑