Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,741,977	T→C	36.1%	L38L (TTA→TTG)	rseA ←	anti‑sigma factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,741,977	0	T	C	36.1%	50.4 / 50.0	83	L38L (TTA→TTG)	rseA	anti‑sigma factor
Reads supporting (aligned to +/- strand):  ref base T (33/20);  new base C (13/17);  total (46/37)
Fisher's exact test for biased strand distribution p-value = 1.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.47e-01

ATCACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGTTCGTTAAGC  >  minE/1741912‑1742034                                                                  |                                                          aTCACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTaa                                                         >  1:3309291/1‑68 (MQ=255) aTCACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTaa                                                         >  1:3387930/1‑68 (MQ=255)  tCACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGt                                                       <  1:220100/69‑1 (MQ=255)   cACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGt                                                       >  1:917301/1‑68 (MQ=255)   cACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGt                                                       >  1:2288032/1‑68 (MQ=255)   cACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGt                                                       >  1:1809235/1‑68 (MQ=255)   cACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGt                                                       >  1:414712/1‑68 (MQ=255)   cACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGt                                                       >  1:3387888/1‑68 (MQ=255)   cACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGt                                                       >  1:393890/1‑68 (MQ=255)            agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGGttt                                              >  1:725871/1‑68 (MQ=255)            agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:937003/1‑68 (MQ=255)            agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:2670518/1‑68 (MQ=255)            agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:2911011/1‑68 (MQ=255)            agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:1706180/1‑68 (MQ=255)            agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:3367011/1‑68 (MQ=255)            agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:1491293/1‑68 (MQ=255)            agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:818934/1‑68 (MQ=255)            agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:528884/1‑68 (MQ=255)            agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:11585/1‑68 (MQ=255)            agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:738566/1‑68 (MQ=255)            agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCtt                                               >  1:1801892/1‑67 (MQ=255)            agagATATCGAAATGGAGCACCTAGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:2587764/1‑68 (MQ=255)                atatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAg                                         >  1:417707/1‑69 (MQ=255)                atatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAg                                         >  1:2337008/1‑69 (MQ=255)                atatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAg                                         >  1:2288379/1‑69 (MQ=255)                atatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAg                                         >  1:2168728/1‑69 (MQ=255)                atatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAg                                         >  1:2996478/1‑69 (MQ=255)                atatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAATCACGGATTAAGTGATAGCTTTCCCAg                                         >  1:2907737/1‑69 (MQ=255)                 tatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAgg                                        <  1:3178185/69‑1 (MQ=255)                 tatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAgg                                        <  1:376387/69‑1 (MQ=255)                 tatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAgg                                        <  1:660467/69‑1 (MQ=255)                 tatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAgg                                        <  1:1726216/69‑1 (MQ=255)                   tCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGt                                       >  1:3204744/1‑68 (MQ=255)                   tCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCAAGGt                                       >  1:1907560/1‑68 (MQ=255)                     gAAATGGAGCACCTCGGTAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:1712667/68‑1 (MQ=255)                     gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:3156300/68‑1 (MQ=255)                     gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:3258945/68‑1 (MQ=255)                     gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:3345234/68‑1 (MQ=255)                     gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:2904983/68‑1 (MQ=255)                     gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:434/68‑1 (MQ=255)                     gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:2782969/68‑1 (MQ=255)                     gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:2639297/68‑1 (MQ=255)                     gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:1012565/68‑1 (MQ=255)                     gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:1189426/68‑1 (MQ=255)                     gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:132256/68‑1 (MQ=255)                     gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:1362083/68‑1 (MQ=255)                     gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:1540150/68‑1 (MQ=255)                     gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:1803180/68‑1 (MQ=255)                     gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:1807187/68‑1 (MQ=255)                     gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCAAGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:3237671/68‑1 (MQ=255)                                  tCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTgg                        >  1:891725/1‑68 (MQ=255)                                  tCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTgg                        >  1:841606/1‑68 (MQ=255)                                  tCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTgg                        >  1:3008975/1‑68 (MQ=255)                                  tCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGT‑ATAGCTTTCCCAGGTTTTCTGCATTTCTGGGt                      <  1:499304/69‑1 (MQ=255)                                   cGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGt                      <  1:1020078/69‑1 (MQ=255)                                   cGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGt                      <  1:1641977/69‑1 (MQ=255)                                   cGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGt                      <  1:1795144/69‑1 (MQ=255)                                   cGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGt                      <  1:3147320/69‑1 (MQ=255)                                       aGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:1795553/50‑1 (MQ=255)                                           tCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTg                                 <  1:2070706/50‑1 (MQ=255)                                           tCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTg                                 <  1:3184830/50‑1 (MQ=255)                                           tCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAgac              >  1:1170337/1‑67 (MQ=255)                                           tCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGcc              >  1:1925551/1‑69 (MQ=255)                                           tCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGcc              >  1:3122576/1‑69 (MQ=255)                                           tCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGcc              >  1:1119267/1‑69 (MQ=255)                                           tCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGcc              >  1:2330146/1‑69 (MQ=255)                                           tCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGcc              >  1:1127040/1‑69 (MQ=255)                                             aCCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAg            <  1:2646218/69‑1 (MQ=255)                                             aCCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAg            <  1:822207/69‑1 (MQ=255)                                             aCCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAg            <  1:2176963/69‑1 (MQ=255)                                             aCCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAg            <  1:528252/69‑1 (MQ=255)                                             aCCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAg            <  1:2109707/69‑1 (MQ=255)                                             aCCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAg            <  1:3055743/69‑1 (MQ=255)                                             aCCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAg            <  1:3069533/69‑1 (MQ=255)                                               cccGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGtt          >  1:1441132/1‑69 (MQ=255)                                                      tGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGTTCGTTAag   <  1:2605027/69‑1 (MQ=255)                                                       gAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCa             >  1:1285915/1‑58 (MQ=255)                                                       gAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGTTCGTTAagc  >  1:2133250/1‑69 (MQ=255)                                                       gAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGTTCGTTAagc  >  1:125015/1‑69 (MQ=255)                                                       gAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGTTCGTTAagc  >  1:419646/1‑69 (MQ=255)                                                       gAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGTTCGTTAagc  >  1:152891/1‑69 (MQ=255)                                                       gAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGTTCGTTAagc  >  1:1591906/1‑69 (MQ=255)                                                       gAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGTTCGTTAagc  >  1:1634104/1‑69 (MQ=255)                                                                  |                                                          ATCACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGTTCGTTAAGC  >  minE/1741912‑1742034

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: ‑