Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,485,543	A→C	44.5%	A99A (GCT→GCG)	menF ←	isochorismate synthase 2

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,485,543	0	A	C	44.5%	4.1 / 70.3	63	A99A (GCT→GCG)	menF	isochorismate synthase 2
Reads supporting (aligned to +/- strand):  ref base A (11/24);  new base C (7/21);  total (18/45)
Fisher's exact test for biased strand distribution p-value = 7.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.53e-01

GCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTG  >  minE/1485478‑1485608                                                                  |                                                                  gCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCa                                                                >  1:1668593/1‑69 (MQ=255)            acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa                                                     <  1:817730/69‑1 (MQ=255)            acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa                                                     <  1:1937171/69‑1 (MQ=255)            acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa                                                     <  1:2106015/69‑1 (MQ=255)            acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa                                                     <  1:2534474/69‑1 (MQ=255)            acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa                                                     <  1:1806531/69‑1 (MQ=255)            acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa                                                     <  1:2745576/69‑1 (MQ=255)            acaGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCa                                                     <  1:1295613/69‑1 (MQ=255)                          ccAGGCGTGGTAAAAGTAAATTGCCCTGCGACGGGTCAAACGc                                                                 >  1:2464112/1‑43 (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)                          ccAGGCGTGGTAAAAGTAAATTGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCgg                                       >  1:343526/1‑69 (MQ=255)                          ccAGGCGTGGTAAAAGTAAATTGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCgg                                       >  1:681207/1‑69 (MQ=255)                          ccAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCa                                                                >  1:2792288/1‑44 (MQ=255)                          ccAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCa                                                                >  1:3145361/1‑44 (MQ=255)                          ccAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCa                                                                >  1:3267705/1‑44 (MQ=255)                          ccAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCa                                                                >  1:243178/1‑44 (MQ=255)                          ccAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCa                                                                >  1:860818/1‑44 (MQ=255)                          ccAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCa                                                                >  1:1594694/1‑44 (MQ=255)                          ccAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCa                                                                >  1:1880900/1‑44 (MQ=255)                          ccAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCa                                                                >  1:1876927/1‑44 (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                    <  1:412988/68‑1 (MQ=255)                                              ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                    <  1:140717/68‑1 (MQ=255)                                              ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                    <  1:19309/68‑1 (MQ=255)                                              ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                    <  1:3206394/68‑1 (MQ=255)                                              ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                    <  1:3337505/68‑1 (MQ=255)                                              ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                    <  1:383293/68‑1 (MQ=255)                                              ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                    <  1:1343013/68‑1 (MQ=255)                                              ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                    <  1:508823/68‑1 (MQ=255)                                              ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                    <  1:583848/68‑1 (MQ=255)                                              ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                    <  1:625286/68‑1 (MQ=255)                                              ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                    <  1:760297/68‑1 (MQ=255)                                              ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                    <  1:1139814/68‑1 (MQ=255)                                              ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                    <  1:1078814/68‑1 (MQ=255)                                              ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                    <  1:1525590/68‑1 (MQ=255)                                              ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                    <  1:2307967/68‑1 (MQ=255)                                              ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                    <  1:1790532/68‑1 (MQ=255)                                              ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                    <  1:2346580/68‑1 (MQ=255)                                              ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCg                    <  1:262064/68‑1 (MQ=255)                                              ttGCCCTGCGACGGGTCAAACGCATTCAACCCCCAGATGCGTAAGTAGGCGTGTTCCGGGTGCTGGCg                    <  1:3204369/68‑1 (MQ=255)                                                        aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt          <  1:2980039/68‑1 (MQ=255)                                                        aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt          <  1:1908063/68‑1 (MQ=255)                                                        aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt          <  1:2222449/68‑1 (MQ=255)                                                        aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt          <  1:833508/68‑1 (MQ=255)                                                        aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt          <  1:802064/68‑1 (MQ=255)                                                        aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt          <  1:634954/68‑1 (MQ=255)                                                        aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt          <  1:2317539/68‑1 (MQ=255)                                                        aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt          <  1:1844442/68‑1 (MQ=255)                                                        aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt          <  1:289291/68‑1 (MQ=255)                                                        aCGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt          <  1:2926232/68‑1 (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            <  1:336524/60‑1 (MQ=255)                                                              cAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAAc            <  1:2531223/60‑1 (MQ=255)                                                              cAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAAc            <  1:1522691/60‑1 (MQ=255)                                                               aaaaGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAAc            <  1:1271180/59‑1 (MQ=255)                                                               aaaaGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAAc            <  1:3255755/59‑1 (MQ=255)                                                               aaaaGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTg  <  1:1294149/69‑1 (MQ=255)                                                               aaaaGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTg  <  1:3262548/69‑1 (MQ=255)                                                               aaaaGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTg  <  1:2306614/69‑1 (MQ=255)                                                               aaaaGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTCTGCCTg  <  1:5780/69‑1 (MQ=255)                                                                  |                                                                  GCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTG  >  minE/1485478‑1485608

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: ‑