Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,485,005	C→T	19.1%	D279N (GAT→AAT)	menF ←	isochorismate synthase 2

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,485,005	0	C	T	19.1%	157.1 / 30.0	68	D279N (GAT→AAT)	menF	isochorismate synthase 2
Reads supporting (aligned to +/- strand):  ref base C (26/28);  new base T (10/3);  total (37/31)
Fisher's exact test for biased strand distribution p-value = 7.25e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.72e-01

GTATCGGCCTGTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTACTG  >  minE/1484941‑1485067                                                                 |                                                               gTATCGGCCTGTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGc                                                          <  1:2813800/71‑1 (MQ=255)  tATCGGCCTGTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGc                                                          <  1:3893579/70‑1 (MQ=255)    tCGGCCTGTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCa                                                        >  1:3725457/1‑70 (MQ=255)      ggCCTGTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATTATCCGCCAt                                                       >  1:2958438/1‑69 (MQ=255)        ccTGTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGc                                                   <  1:4338/71‑1 (MQ=255)           gTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTattatc                                                             <  1:2412594/58‑1 (MQ=255)            tAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCa                                                 <  1:3960316/69‑1 (MQ=255)            tAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCAct                                               <  1:1114144/71‑1 (MQ=255)            tAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCAc                                                <  1:834083/70‑1 (MQ=255)            tAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCAc                                                <  1:607130/70‑1 (MQ=255)            tAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCAc                                                <  1:46971/70‑1 (MQ=255)             aaTCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCctct                                               <  1:1899510/70‑1 (MQ=255)             aaTCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCa                                                 >  1:4117606/1‑68 (MQ=255)              aTCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCActc                                              <  1:1331731/70‑1 (MQ=255)              aTCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCActc                                              <  1:1272149/70‑1 (MQ=255)              aTCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCActc                                              <  1:979677/70‑1 (MQ=255)                cGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACtctc                                            >  1:3220371/1‑70 (MQ=255)                cGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTcc                                           >  1:3851378/1‑71 (MQ=255)                cGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTcc                                           >  1:693560/1‑71 (MQ=255)                 gTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTtattat                                                              >  1:1076668/1‑51 (MQ=255)                 gTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCt                                          <  1:985012/71‑1 (MQ=255)                 gTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCt                                          <  1:3209623/71‑1 (MQ=255)                  ttGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTa                                         <  1:2014948/71‑1 (MQ=255)                  ttGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTa                                         <  1:13717/71‑1 (MQ=255)                      cAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTAActg                                     <  1:1667682/71‑1 (MQ=255)                       aGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTAActgc                                    >  1:1843356/1‑71 (MQ=255)                          tatCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTattatc                                                             >  1:1305984/1‑43 (MQ=255)                          tatCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTattatc                                                             >  1:1487374/1‑43 (MQ=255)                          tatCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTattatc                                                             >  1:2906208/1‑43 (MQ=255)                          tatCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTattatc                                                             >  1:3799944/1‑43 (MQ=255)                          tatCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTattatc                                                             >  1:3718630/1‑43 (MQ=255)                          tatCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACtgctgc                                 <  1:2114226/71‑1 (MQ=255)                           atCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTgcg                                >  1:1921220/1‑71 (MQ=255)                           atCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTgcg                                >  1:837079/1‑71 (MQ=255)                           atCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTgcg                                >  1:3933409/1‑71 (MQ=255)                            tCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCActc                                              <  1:888014/56‑1 (MQ=255)                            tCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTgcgc                               >  1:1663723/1‑71 (MQ=255)                             cTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAActgct                                   >  1:4022172/1‑66 (MQ=255)                                ccaccaccaGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGc                           >  1:1591741/1‑71 (MQ=255)                                    caccaGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTaa                                        >  1:22547/1‑54 (MQ=255)                                    caccaGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTaa                                        >  1:1714269/1‑54 (MQ=255)                                    caccaGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTaa                                        >  1:3892060/1‑54 (MQ=255)                                    caccaGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTaa                                        >  1:3701132/1‑54 (MQ=255)                                     accaGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTatc                      <  1:3434081/71‑1 (MQ=255)                                     accaGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTatc                      <  1:3953927/71‑1 (MQ=255)                                     accaGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCCCCTGCTTatc                      <  1:50951/71‑1 (MQ=255)                                       caGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTatcat                    <  1:1254054/71‑1 (MQ=255)                                        aGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAg                                                    >  1:916949/1‑38 (MQ=255)                                        aGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAg                                                    >  1:2705214/1‑38 (MQ=255)                                        aGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTatcat                    >  1:2083456/1‑70 (MQ=255)                                         gCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTatcat                    >  1:3356049/1‑69 (MQ=255)                                         gCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTatcat                    >  1:668980/1‑69 (MQ=255)                                         gCATGTTCTCGAGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTatcat                    >  1:736725/1‑69 (MQ=255)                                           aTGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAg                 >  1:2122027/1‑70 (MQ=255)                                           aTGTTCTCGCGCTGGTTTTTATGATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAg                 >  1:3837205/1‑70 (MQ=255)                                           aTGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGcc                              >  1:162070/1‑57 (MQ=255)                                           aTGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAg                 >  1:622851/1‑70 (MQ=255)                                           aTGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAg                 >  1:4103686/1‑70 (MQ=255)                                           aTGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAg                 >  1:3585743/1‑70 (MQ=255)                                           aTGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAg                 >  1:3966310/1‑70 (MQ=255)                                           aTGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAg                 >  1:1548474/1‑70 (MQ=255)                                            tGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTa                        <  1:3204500/62‑1 (MQ=255)                                            tGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTa                        <  1:1057591/62‑1 (MQ=255)                                            tGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTa                        <  1:3209426/62‑1 (MQ=255)                                            tGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTa                        <  1:3904854/62‑1 (MQ=255)                                            tGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTa                        <  1:3933011/62‑1 (MQ=255)                                                ctcGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGattat           >  1:272038/1‑71 (MQ=255)                                                ctcGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGattat           >  1:1136619/1‑71 (MQ=255)                                                ctcGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGattat           >  1:4244483/1‑71 (MQ=255)                                                     gcTGGTTTTTATTATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGc       >  1:714648/1‑70 (MQ=255)                                                     gcTGGTTTTTATTATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGc       >  1:2593569/1‑70 (MQ=255)                                                     gcTGGTTTTTATTATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGc       >  1:1344186/1‑70 (MQ=255)                                                         gTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTACTg  <  1:1910918/71‑1 (MQ=255)                                                         gTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTACTg  <  1:263385/71‑1 (MQ=255)                                                         gTTTTTAACATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTACTg  <  1:3786878/71‑1 (MQ=255)                                                                 |                                                               GTATCGGCCTGTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTACTG  >  minE/1484941‑1485067

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: ‑