Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,242,341	C→T	31.1%	D259D (GAC→GAT)	pykA →	pyruvate kinase II

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,242,341	0	C	T	31.1%	74.0 / 36.8	80	D259D (GAC→GAT)	pykA	pyruvate kinase II
Reads supporting (aligned to +/- strand):  ref base C (35/20);  new base T (8/17);  total (43/37)
Fisher's exact test for biased strand distribution p-value = 1.47e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01

GATGACATCATCCTCGCCTCTGACGTGGTAATGGTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTAAACCGAGCGGT  >  minE/1242273‑1242403                                                                     |                                                               gATGACATCATCCTCGCCTCTGACGTGGTAATGGTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGAc                                                                >  1:406948/1‑69 (MQ=255)     aCATCATCCTCGCCTCTGACGTGGTAATGGTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCgg                                                            <  1:1675835/69‑1 (MQ=255)          atcCTCGCCTCTGACGTGGTAATGGTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTg                                                       >  1:1708515/1‑69 (MQ=255)          atcCTCGCCTCTGACGTGGTAATGGTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTg                                                       >  1:157096/1‑69 (MQ=255)                  ctctGACGTGGTAATGGTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCa                                                <  1:2697898/68‑1 (MQ=255)                  ctctGACGTGGTAATGGTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCa                                                <  1:2941810/68‑1 (MQ=255)                            gTAATGGTTGCTCGCGGCGACCTCGGTGTGGAAATTGGCGATCCGGAACTGGTCGGCATTCAGAAAGCg                                     >  1:734777/1‑69 (MQ=255)                            gTAATGGTTGCTCGCGGCGACCTCGGTGTGGAAATTGGCGATCCGGAACTGGTCGGCATTCAGAAAGCg                                     >  1:2507675/1‑69 (MQ=255)                            gTAATGGTTGCTCGCGGCGACCTCGGTGTGGAAATTGGCGATCCGGAACTGGTCGGCATTCAGAAAGCg                                     >  1:2149044/1‑69 (MQ=255)                            gTAATGGTTGCTCGCGGCGACCTCGGTGTGGAAATTGGCGATCCGGAACTGGTCGGCATTCAGAAAGCg                                     >  1:2037226/1‑69 (MQ=255)                            gTAATGGTTGCTCGCGGCGACCTCGGTGTGGAAATTGGCGATCCGGAACTGGTCGGCATTCAGAAAGCg                                     >  1:2570766/1‑69 (MQ=255)                            gTAATGGTTGCTCGCGGCGACCTCGGTGTGGAAATTGGCGATCCGGAACTGGTCGGCATTCAGAAAGCg                                     >  1:1585299/1‑69 (MQ=255)                            gTAATGGTTGCTCGCGGCGACCTCGGTGTGGAAATTGGCGATCCGGAACTGGTCGGCATTCAGAAAGCg                                     >  1:2839850/1‑69 (MQ=255)                            gTAATGGTTGCTCGCGGCGACCTCGGTGTGGAAATTGGCGATCCGGAACTGGTCGGCATTCAGAAAGCg                                     >  1:2615288/1‑69 (MQ=255)                              aaTGGTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGtt                                   >  1:2917065/1‑69 (MQ=255)                              aaTGGTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGtt                                   >  1:2122770/1‑69 (MQ=255)                              aaTGGTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGtt                                   >  1:2091480/1‑69 (MQ=255)                              aaTGGTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGtt                                   >  1:1956580/1‑69 (MQ=255)                              aaTGGTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGtt                                   >  1:190586/1‑69 (MQ=255)                              aaTGGTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGtt                                   >  1:3318434/1‑69 (MQ=255)                              aaTGGTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGtt                                   >  1:1005567/1‑69 (MQ=255)                                  gTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGCCCCGGAACTGGTCGGCATTCAGAAAGCGTTGATc                               >  1:2294690/1‑69 (MQ=255)                                  gTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATc                               >  1:2037089/1‑69 (MQ=255)                                  gTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATc                               >  1:2290760/1‑69 (MQ=255)                                  gTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATc                               >  1:3183806/1‑69 (MQ=255)                                  gTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATc                               >  1:820354/1‑69 (MQ=255)                                  gTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATc                               >  1:948159/1‑69 (MQ=255)                                  gTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATc                               >  1:1511414/1‑69 (MQ=255)                                  gTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATc                               >  1:576154/1‑69 (MQ=255)                                  gTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATc                               >  1:2810217/1‑69 (MQ=255)                                  gTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATc                               >  1:570021/1‑69 (MQ=255)                                  gTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATc                               >  1:1899154/1‑69 (MQ=255)                                  gTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATc                               >  1:161212/1‑69 (MQ=255)                                  gTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATc                               >  1:2718906/1‑69 (MQ=255)                                  gTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATc                               >  1:1761252/1‑69 (MQ=255)                                  gTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATc                               >  1:3423065/1‑69 (MQ=255)                                  gTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATc                               >  1:1623589/1‑69 (MQ=255)                                           ggCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTgcg                      <  1:985847/69‑1 (MQ=255)                                           ggCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTgcg                      <  1:1211718/69‑1 (MQ=255)                                              gACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGt                   <  1:3425032/69‑1 (MQ=255)                                              gACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGt                   <  1:1482705/69‑1 (MQ=255)                                              gACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGt                   <  1:1487002/69‑1 (MQ=255)                                                      tgtgGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTaa            <  1:3033526/68‑1 (MQ=255)                                                      tgtgGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTaa            <  1:709517/68‑1 (MQ=255)                                                      tgtgGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTaa            <  1:2244053/68‑1 (MQ=255)                                                      tgtgGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTaa            <  1:1542863/68‑1 (MQ=255)                                                      tgtgGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTaa            <  1:575249/68‑1 (MQ=255)                                                      tgtgGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTaa            <  1:3415032/68‑1 (MQ=255)                                                      tgtgGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTaa            <  1:489957/68‑1 (MQ=255)                                                        tgGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTaaa           >  1:1144986/1‑67 (MQ=255)                                                        tgGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTaaa           >  1:18267/1‑67 (MQ=255)                                                          gAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTAAACCGa       >  1:996827/1‑69 (MQ=255)                                                               tGGCGATCCGGAACTGGTCGGCATTCAGAAAGCTTTGATCCGTCGTGCGCGTCAGCtta            <  1:1259184/59‑3 (MQ=255)                                                               tGGCGATCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCTTGCGCGTCAGCtta            <  1:531120/59‑3 (MQ=255)                                                               tGGCGATCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCtta            <  1:1736582/59‑3 (MQ=255)                                                               tGGCGATCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCtta            <  1:1267750/59‑3 (MQ=255)                                                               tGGCGATCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCtta            <  1:1559506/59‑3 (MQ=255)                                                               tGGCGATCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCtta            <  1:906221/59‑3 (MQ=255)                                                               tGGCGATCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCtta            <  1:1636148/59‑3 (MQ=255)                                                               tGGCGATCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCtta            <  1:1658898/59‑3 (MQ=255)                                                               tGGCGATCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCtta            <  1:2659011/59‑3 (MQ=255)                                                               tGGCGATCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCtta            <  1:1688222/59‑3 (MQ=255)                                                               tGGCGATCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCtta            <  1:2611915/59‑3 (MQ=255)                                                               tGGCGATCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCtta            <  1:189102/59‑3 (MQ=255)                                                               tGGCGATCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCtta            <  1:3318096/59‑3 (MQ=255)                                                               tGGCGATCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCtta            <  1:2452998/59‑3 (MQ=255)                                                               tGGCGATCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCtta            <  1:1226284/59‑3 (MQ=255)                                                               tGGCGATCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCtta            <  1:2891302/59‑3 (MQ=255)                                                               tGGCGATCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCtta            <  1:2587375/59‑3 (MQ=255)                                                               tGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTAAACCGATCGGt  >  1:2273117/1‑69 (MQ=255)                                                               tGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTAAACCGATCGGt  >  1:2276954/1‑69 (MQ=255)                                                               tGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTAAACCGAGCgg   >  1:1547518/1‑68 (MQ=255)                                                               tGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTAAACCGAGCGGt  <  1:353728/69‑1 (MQ=255)                                                               tGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTAAACCGAGCGGt  <  1:899193/69‑1 (MQ=255)                                                               tGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTAAACCGAGCGGt  >  1:817945/1‑69 (MQ=255)                                                               tGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTAAACCGAGCGGt  <  1:1403437/69‑1 (MQ=255)                                                               tGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTAAACCGAGCGGt  >  1:1406920/1‑69 (MQ=255)                                                               tGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTAAACCGAGCGGt  >  1:1601670/1‑69 (MQ=255)                                                               tGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTAAACCGAGCGGt  >  1:3169923/1‑69 (MQ=255)                                                               tGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTAAACCGAGCGGt  <  1:2464700/69‑1 (MQ=255)                                                               tGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTAAACCGAGCGGt  <  1:2612844/69‑1 (MQ=255)                                                                     |                                                               GATGACATCATCCTCGCCTCTGACGTGGTAATGGTTGCACGTGGCGACCTCGGTGTGGAAATTGGCGACCCGGAACTGGTCGGCATTCAGAAAGCGTTGATCCGTCGTGCGCGTCAGCTAAACCGAGCGGT  >  minE/1242273‑1242403

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: ‑