Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,485,551	G→A	41.4%	L97L (CTG→TTG)	menF ←	isochorismate synthase 2

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,485,551	0	G	A	41.4%	25.6 / 43.6	65	L97L (CTG→TTG)	menF	isochorismate synthase 2
Reads supporting (aligned to +/- strand):  ref base G (7/31);  new base A (6/21);  total (13/52)
Fisher's exact test for biased strand distribution p-value = 7.60e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.33e-01

ACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAACGA  >  minE/1485489‑1485617                                                               |                                                                   acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa                                                              <  1:817730/69‑1 (MQ=255) acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa                                                              <  1:1295613/69‑1 (MQ=255) acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa                                                              <  1:2745576/69‑1 (MQ=255) acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa                                                              <  1:2534474/69‑1 (MQ=255) acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa                                                              <  1:2106015/69‑1 (MQ=255) acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa                                                              <  1:1806531/69‑1 (MQ=255) acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa                                                              <  1:1937171/69‑1 (MQ=255)               ccAGGCGTGGTAAAAGTAAATTGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCgg                                                >  1:681207/1‑69 (MQ=255)               ccAGGCGTGGTAAAAGTAAATTGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCgg                                                >  1:343526/1‑69 (MQ=255)               ccAGGCGTGGTAAAAGTAAATTGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCgg                                                >  1:3052186/1‑69 (MQ=255)               ccAGGCGTGGTAAAAGTAAATTGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCgg                                                >  1:3036130/1‑69 (MQ=255)               ccAGGCGTGGTAAAAGTAAATTGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCgg                                                >  1:2909552/1‑69 (MQ=255)               ccAGGCGTGGTAAAAGTAAATTGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCgg                                                >  1:2820126/1‑69 (MQ=255)                         tAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCgg                                      >  1:840529/1‑69 (MQ=255)                         tAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCgg                                      >  1:2733437/1‑69 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTTGCg                             <  1:1469996/68‑1 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGct                             <  1:3303947/68‑2 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                             <  1:508823/68‑1 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                             <  1:140717/68‑1 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                             <  1:1343013/68‑1 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                             <  1:3206394/68‑1 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                             <  1:1525590/68‑1 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                             <  1:3337505/68‑1 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                             <  1:262064/68‑1 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                             <  1:383293/68‑1 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                             <  1:412988/68‑1 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                             <  1:2346580/68‑1 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                             <  1:583848/68‑1 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                             <  1:2307967/68‑1 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                             <  1:625286/68‑1 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                             <  1:760297/68‑1 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                             <  1:1790532/68‑1 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                             <  1:1139814/68‑1 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                             <  1:19309/68‑1 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                             <  1:1078814/68‑1 (MQ=255)                                   ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTAGGCGTGTTCCGGGTGCTGGCg                             <  1:3204369/68‑1 (MQ=255)                                             aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt                   <  1:2980039/68‑1 (MQ=255)                                             aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt                   <  1:1908063/68‑1 (MQ=255)                                             aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt                   <  1:833508/68‑1 (MQ=255)                                             aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt                   <  1:1844442/68‑1 (MQ=255)                                             aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt                   <  1:802064/68‑1 (MQ=255)                                             aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt                   <  1:2222449/68‑1 (MQ=255)                                             aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt                   <  1:634954/68‑1 (MQ=255)                                             aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt                   <  1:2317539/68‑1 (MQ=255)                                             aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt                   <  1:2926232/68‑1 (MQ=255)                                             aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt                   <  1:289291/68‑1 (MQ=255)                                                  tCAAAAGCATTCAGCGCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGcc             <  1:2854663/69‑1 (MQ=255)                                                  tCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGcc             <  1:2642397/69‑1 (MQ=255)                                                  tCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGcc             <  1:1328937/69‑1 (MQ=255)                                                  tCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGAGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGcc             <  1:3435975/69‑1 (MQ=255)                                                   cAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAAc                     <  1:2531223/60‑1 (MQ=255)                                                   cAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAAc                     <  1:1522691/60‑1 (MQ=255)                                                   cAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAAc                     <  1:336524/60‑1 (MQ=255)                                                    aaaaGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAAc                     <  1:3255755/59‑1 (MQ=255)                                                    aaaaGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAAc                     <  1:1271180/59‑1 (MQ=255)                                                    aaaaGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTg           <  1:3262548/69‑1 (MQ=255)                                                    aaaaGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTg           <  1:2306614/69‑1 (MQ=255)                                                    aaaaGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTg           <  1:1294149/69‑1 (MQ=255)                                                    aaaaGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTCTGCCTg           <  1:5780/69‑1 (MQ=255)                                                        gCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTg           <  1:1905185/65‑1 (MQ=255)                                                             cAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAacga  >  1:1639696/1‑69 (MQ=255)                                                             cAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAacga  >  1:500929/1‑69 (MQ=255)                                                             cAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAacga  >  1:331053/1‑69 (MQ=255)                                                             cAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAacg   >  1:2569082/1‑68 (MQ=255)                                                             cAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAacg   >  1:374323/1‑68 (MQ=255)                                                               |                                                                   ACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAACGA  >  minE/1485489‑1485617

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑