Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	402,421	C→T	27.9%	P114P (CCG→CCA)	rlpA ←	minor lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	402,421	0	C	T	27.9%	88.8 / 32.5	82	P114P (CCG→CCA)	rlpA	minor lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (29/30);  new base T (12/11);  total (41/41)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGATCATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGCCGTCAGGTTACT  >  minE/402353‑402489                                                                     |                                                                     cgATCATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATc                                                                      <  1:466533/69‑1 (MQ=255) cgATCATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATc                                                                      <  1:1918073/69‑1 (MQ=255) cgATCATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATc                                                                      <  1:621741/69‑1 (MQ=255)     cATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGaa                                                                  >  1:2713119/1‑69 (MQ=255)     cATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGaa                                                                  >  1:2763588/1‑69 (MQ=255)     cATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGaa                                                                  >  1:692085/1‑69 (MQ=255)     cATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGaa                                                                  >  1:2040923/1‑69 (MQ=255)     cATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGaa                                                                  >  1:869105/1‑69 (MQ=255)     cATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGaa                                                                  >  1:1957597/1‑69 (MQ=255)     cATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGaa                                                                  >  1:358678/1‑69 (MQ=255)         aaTGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGGTCGGAAGCGt                                                              >  1:3107767/1‑69 (MQ=255)         aaTGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGt                                                              >  1:2630088/1‑69 (MQ=255)         aaTGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGt                                                              >  1:2227880/1‑69 (MQ=255)         aaTGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGt                                                              >  1:2210440/1‑69 (MQ=255)         aaTGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGt                                                              >  1:406827/1‑69 (MQ=255)            gcgcACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCTTTg                                                            <  1:1239432/68‑1 (MQ=255)            gcgcACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTg                                                            <  1:460869/68‑1 (MQ=255)            gcgcACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTg                                                            <  1:973157/68‑1 (MQ=255)            gcgcACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTg                                                            <  1:425039/68‑1 (MQ=255)            gcgcACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTg                                                            <  1:2476219/68‑1 (MQ=255)            gcgcACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTg                                                            <  1:1806396/68‑1 (MQ=255)            gcgcACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTg                                                            <  1:199320/68‑1 (MQ=255)                   acGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCgg                                                                    >  1:219049/1‑53 (MQ=255)                   acGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCgg                                                                    >  1:422418/1‑53 (MQ=255)                   acGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCt                                                    >  1:1182645/1‑69 (MQ=255)                   acGATCATTCGCCAGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCgg                                                                    >  1:1098043/1‑53 (MQ=255)                        cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:290044/69‑1 (MQ=255)                        cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:1268807/69‑1 (MQ=255)                        cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:1104614/69‑1 (MQ=255)                        cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:637922/69‑1 (MQ=255)                        cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:42939/69‑1 (MQ=255)                        cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:3036366/69‑1 (MQ=255)                        cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:3036513/69‑1 (MQ=255)                        cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:3107094/69‑1 (MQ=255)                        cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:2040457/69‑1 (MQ=255)                        cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:2033016/69‑1 (MQ=255)                        cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:3124410/69‑1 (MQ=255)                        cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:1697393/69‑1 (MQ=255)                         aTTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:1753807/68‑1 (MQ=255)                           tCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCa                                             >  1:1597855/1‑68 (MQ=255)                           tCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAg                                            >  1:1000212/1‑69 (MQ=255)                           tCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAg                                            >  1:488834/1‑69 (MQ=255)                           tCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAg                                            >  1:1552158/1‑69 (MQ=255)                           tCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAg                                            >  1:1488208/1‑69 (MQ=255)                             gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGTGATTGGAAGCGTTGGATGGGCCGCCGt                                               >  1:2071737/1‑64 (MQ=39)                             gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCg                                                               >  1:2822654/1‑48 (MQ=255)                             gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGt                                                              >  1:1436965/1‑49 (MQ=255)                             gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGt                                               >  1:3395396/1‑64 (MQ=255)                             gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                              >  1:2551327/1‑65 (MQ=255)                             gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                              >  1:3378078/1‑65 (MQ=255)                             gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                              >  1:578810/1‑65 (MQ=255)                             gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                              >  1:3245024/1‑65 (MQ=255)                             gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                              >  1:1359775/1‑65 (MQ=255)                             gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                              >  1:430022/1‑65 (MQ=255)                             gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                              >  1:2402175/1‑65 (MQ=255)                             gCCCGTTAGCCAGCTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                              >  1:2146022/1‑65 (MQ=255)                                        aGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:924781/69‑1 (MQ=255)                                        aGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:2147862/69‑1 (MQ=255)                                        aGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:2703464/69‑1 (MQ=255)                                        aGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:2316265/69‑1 (MQ=255)                                        aGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:730776/69‑1 (MQ=255)                                         ggTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:1337781/68‑1 (MQ=255)                                         ggTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:482531/68‑1 (MQ=255)                                         ggTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:948595/68‑1 (MQ=255)                                         ggTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:1619540/68‑1 (MQ=255)                                         ggTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:2212511/68‑1 (MQ=255)                                                gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:614126/69‑1 (MQ=255)                                                gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:935301/69‑1 (MQ=255)                                                gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:818027/69‑1 (MQ=255)                                                gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:1017732/69‑1 (MQ=255)                                                gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:658763/69‑1 (MQ=255)                                                gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:3343576/69‑1 (MQ=255)                                                gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:3322893/69‑1 (MQ=255)                                                gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:3182526/69‑1 (MQ=255)                                                gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:3033369/69‑1 (MQ=255)                                                gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:2040722/69‑1 (MQ=255)                                                gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:1671126/69‑1 (MQ=255)                                                          tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCtgt                                        >  1:1716445/1‑42 (MQ=255)                                                          tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCagag                >  1:2422958/1‑66 (MQ=255)                                                          tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGcc             >  1:3146556/1‑69 (MQ=255)                                                          tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGcc             >  1:2946713/1‑69 (MQ=255)                                                          tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGcc             >  1:216056/1‑69 (MQ=255)                                                          tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGcc             >  1:1559347/1‑69 (MQ=255)                                                          tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGcc             >  1:1062652/1‑69 (MQ=255)                                                          tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGcc             >  1:974659/1‑69 (MQ=255)                                                                     cGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGCCGTCAGGTTACt  >  1:53299/1‑69 (MQ=255)                                                                     cGGAAGCGGTGGATGGGCTGCCGTCAGCTGTGTCGGGTCGAATGCTTCGCCAGAGGCCGTCAGGTTACt  >  1:2809471/1‑69 (MQ=255)                                                                     |                                                                     CGATCATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGCCGTCAGGTTACT  >  minE/402353‑402489

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑