Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,160,790	T→C	24.9%	R224R (CGT→CGC)	xthA →	exonuclease III

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,160,790	0	T	C	24.9%	84.1 / 24.6	72	R224R (CGT→CGC)	xthA	exonuclease III
Reads supporting (aligned to +/- strand):  ref base T (19/35);  new base C (13/5);  total (32/40)
Fisher's exact test for biased strand distribution p-value = 1.23e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.35e-01

CGAATCCGCAAACAGCAGATCGTTTCTCATGGTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAGAAACCGGCATC  >  minE/1160723‑1160856                                                                    |                                                                   cGAATCCGCAAACAGCAGATCGTTTCTCATGGTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTg                                                                   >  1:1767139/1‑69 (MQ=255) cGAATCCGCAAACAGCAGATCGTTTCTCATGGTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTg                                                                   >  1:1606014/1‑69 (MQ=255)     tCCGCAAACAGCAGATCGTTTCTCATGGTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTc                                                                >  1:2287957/1‑68 (MQ=255)             cagcagATCGTTTCTCATGGTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCg                                                       <  1:947744/69‑1 (MQ=255)             cagcagATCGTTTCTCATGGTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCg                                                       <  1:171081/69‑1 (MQ=255)              agcagATCGTTTCTCATGGTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCg                                                       >  1:584390/1‑68 (MQ=255)              agcagATCGTTTCTCATGGTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGa                                                      >  1:22054/1‑69 (MQ=255)              agcagATCGTTTCTCATGGTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGa                                                      >  1:865906/1‑69 (MQ=255)              agcagATCGTTTCTCATGGTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGa                                                      >  1:621126/1‑69 (MQ=255)              agcagATCGTTTCTCATGGTTTGATTACCCCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCg                                                       >  1:2912044/1‑68 (MQ=255)                            cATGGTTTGATTACCGCTCAAAAGGTTTTGACGATAATCGCGGTCTGCGCATCGACCTGCTGCTCgcc                                         <  1:1935323/68‑1 (MQ=255)                            cATGGTTTGATTACCGCTCAAAAGGTTTTGACGATAATCGCGGTCTGCGCATCGACCTGCTGCTCgcc                                         <  1:3230892/68‑1 (MQ=255)                            cATGGTTTGATTACCGCTCAAAAGGTTTTGACGATAATCGCGGTCTGCGCATCGACCTGCTGCTCgcc                                         <  1:2948198/68‑1 (MQ=255)                            cATGGTTTGATTACCGCTCAAAAGGTTTTGACGATAATCGCGGTCTGCGCATCGACCTGCTGCTCgcc                                         <  1:1360140/68‑1 (MQ=255)                            cATGGTTTGATTACCGCTCAAAAGGTTTTGACGATAATCGCGGTCTGCGCATCGACCTGCTGCTCgcc                                         <  1:2535436/68‑1 (MQ=255)                                gTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCgccagcca                                    >  1:1652200/1‑69 (MQ=255)                                gTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCgccagcca                                    <  1:1832480/69‑1 (MQ=255)                                gTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCgccagcca                                    <  1:1826530/69‑1 (MQ=255)                                gTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCgccagcca                                    <  1:3078216/69‑1 (MQ=255)                                gTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCgccagcca                                    >  1:517268/1‑69 (MQ=255)                                gTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCgccagcca                                    <  1:1731571/69‑1 (MQ=255)                                gTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCgccagcca                                    >  1:593437/1‑69 (MQ=255)                                gTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCgccagcca                                    >  1:694320/1‑69 (MQ=255)                                gTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCgccagcca                                    <  1:697181/69‑1 (MQ=255)                                gTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCgccagcca                                    <  1:1405715/69‑1 (MQ=255)                                gTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCgccagcca                                    <  1:81944/69‑1 (MQ=255)                                gTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCgccagcca                                    >  1:927539/1‑69 (MQ=255)                                gTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCgccagcca                                    >  1:1125400/1‑69 (MQ=255)                                gTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCgccagcc                                     >  1:2672975/1‑68 (MQ=255)                                  ttGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCaa                                   >  1:1213169/1‑68 (MQ=255)                                  ttGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAAc                                  >  1:2749532/1‑69 (MQ=255)                                           gCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAg                         <  1:1224868/69‑1 (MQ=255)                                           gCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAg                         <  1:2477432/69‑1 (MQ=255)                                            cTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAg                         <  1:1562529/68‑1 (MQ=255)                                              cAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAAt                      >  1:1056029/1‑69 (MQ=255)                                              cAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAAt                      >  1:1390461/1‑69 (MQ=255)                                                 aaGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATg                     <  1:2110886/67‑1 (MQ=255)                                                 aaGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATg                     <  1:1010787/67‑1 (MQ=255)                                                 aaGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATg                     <  1:247880/67‑1 (MQ=255)                                                     ttttGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATg                     <  1:1748246/63‑1 (MQ=255)                                                       ttGACGATAATCGCGGTCTGCGCATCGACCTGCTGCTCGCCAGCCCACCGCTGGCAGAATGTTGCGTa              >  1:2382696/1‑68 (MQ=255)                                                       ttGACGATAATCGCGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGt               >  1:394905/1‑67 (MQ=255)                                                       ttGACGATAATCGCGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGt               >  1:1855492/1‑67 (MQ=255)                                                       ttGACGATAATCGCGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTa              >  1:3029244/1‑68 (MQ=255)                                                       ttGACGATAATCGCGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTa              >  1:690622/1‑68 (MQ=255)                                                       ttGACGATAATCGCGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTa              >  1:1435708/1‑68 (MQ=255)                                                       ttGACGATAATCGCGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTa              >  1:2597178/1‑68 (MQ=255)                                                       ttGACGATAATCGCGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTa              >  1:465641/1‑68 (MQ=255)                                                       ttGACGATAATCGCGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTa              >  1:2395807/1‑68 (MQ=255)                                                       ttGACGATAATCGCGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTa              >  1:2890856/1‑68 (MQ=255)                                                       ttGACGATAATCGCGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTa              >  1:2859020/1‑68 (MQ=255)                                                       ttGACGATAATCGCGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTa              >  1:2300390/1‑68 (MQ=255)                                                       ttGACGATAATCGCGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTa              >  1:2318137/1‑68 (MQ=255)                                                       ttGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAg             <  1:2967150/69‑1 (MQ=255)                                                       ttGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAg             <  1:3167954/69‑1 (MQ=255)                                                       ttGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAg             <  1:3240155/69‑1 (MQ=255)                                                       ttGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAg             <  1:430027/69‑1 (MQ=255)                                                       ttGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAg             <  1:2720212/69‑1 (MQ=255)                                                       ttGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAg             <  1:2488151/69‑1 (MQ=255)                                                       ttGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGCTGCGTAg             <  1:1131223/69‑1 (MQ=255)                                                       ttGACGATAACCGTGGTCTGCGCATCGACCTGATGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAg             <  1:920227/69‑1 (MQ=255)                                                                  cGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAGAAACCGGCATc  <  1:1257336/69‑1 (MQ=255)                                                                  cGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAGAAACCGGCATc  <  1:2503533/69‑1 (MQ=255)                                                                  cGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAGAAACCGGCATc  <  1:2628084/69‑1 (MQ=255)                                                                  cGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAGAAACCGGCATc  <  1:1456589/69‑1 (MQ=255)                                                                  cGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAGAAACCGGCATc  <  1:1521191/69‑1 (MQ=255)                                                                  cGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAGAAACCGGCATc  <  1:1620998/69‑1 (MQ=255)                                                                  cGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAGAAACCGGCATc  <  1:2185807/69‑1 (MQ=255)                                                                  cGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAGAAACCGGCATc  <  1:2291040/69‑1 (MQ=255)                                                                  cGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAGAAACCGGCATc  <  1:2667194/69‑1 (MQ=255)                                                                  cGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAGAAACCGGCATc  <  1:264605/69‑1 (MQ=255)                                                                  cGTGGTCTGAGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAGAAACCGGCATc  <  1:1430060/69‑1 (MQ=255)                                                                    |                                                                   CGAATCCGCAAACAGCAGATCGTTTCTCATGGTTTGATTACCGCTCAAAAGGTTTTGACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGTTGCGTAGAAACCGGCATC  >  minE/1160723‑1160856

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: ‑