Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006881	2,197,268	T→A	T290T (ACA→ACT)	U712_11010 ←	Chorismate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006881	2,197,268	0	T	A	98.3%	170.7 / NA	58	T290T (ACA→ACT)	U712_11010	Chorismate synthase
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base A (34/23);  total (35/23)
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

TGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATTCCTGTCGTCATGCCGCCTTCCAGTCCTCCGAGTCTGTTTGTAGCGCGGGTATATCCCTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCTTCCGGCTGCTTCAAAGCCGATGCCGAATTCCACACCTTTAAATGCGTTAATTGACAGAACAGC  >  CP006881/2197132‑2197396                                                                                                                                         |                                                                                                                                 ttgCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGTAGGAATCGTCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGt                                                                                                                                <  5:448148/137‑1 (MQ=255)     aGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAgca                                                                                                                            <  3:256493/139‑2 (MQ=255)     aGAAAACGGTTCTTTAGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAgca                                                                                                                            <  8:445879/139‑2 (MQ=255)      gAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAgcac                                                                                                                           <  2:49339/139‑3 (MQ=255)       aaaaCGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGATTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGACTTCCAGTCCGCCAAGTCTGTTAGTAgcaag                                                                                                                          >  8:233716/1‑136 (MQ=255)           cGGTTCTTTCGTTTCAATCTCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGtg                                                                                                                      <  6:261707/139‑2 (MQ=255)                 tttCGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGGCTGTTAGTAGCACGGGTGTATcct                                                                                                                >  2:375946/1‑138 (MQ=255)                    cGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCAGCGTACAACAATCGGCATCCCTGTCGTAATTCCGCCTTCCAGTCAGCCAAGTCTGTTATTAGCACGGGTGTTTCCtttt                                                                                                             >  6:315636/1‑139 (MQ=255)                      tttCAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTc                                                                                                           >  7:337300/1‑139 (MQ=255)                         cAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCt                                                                                                         <  7:146871/138‑1 (MQ=255)                                gacacTTTTAAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATAGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCaa                                                                                                 <  6:288502/135‑1 (MQ=255)                                       ttCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGAtct                                                                                          >  3:14687/1‑139 (MQ=255)                                       ttCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGAtct                                                                                          >  6:91346/1‑139 (MQ=255)                                       ttCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGAtc                                                                                           <  1:126382/138‑1 (MQ=255)                                            ctgTTTATAGAAAGTCGGAATCGTCTTCATGACTCCGCGGACAACAATCGTCATCCCTGTCGTCATGCCGCCTTCGAGTCCGACAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCa                                                                                     <  6:134870/137‑1 (MQ=255)                                               tttATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTATTAGCACGGGTGTATCATTTTTCCTCTTCCCAAATGATATCGTCATg                                                                                   >  5:134870/1‑138 (MQ=255)                                               tttATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATgg                                                                                  >  6:412915/1‑139 (MQ=255)                                                 tataCAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTTGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGAc                                                                                >  4:423553/1‑139 (MQ=255)                                                 tataCAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGa                                                                                 <  8:348650/138‑1 (MQ=255)                                                       aaGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCt                                                                          <  5:91346/139‑1 (MQ=255)                                                        aGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGAtc                                                                                           >  7:104759/1‑121 (MQ=255)                                                        aGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGAtc                                                                                           <  8:104759/121‑1 (MQ=255)                                                        aGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGAtc                                                                                           >  5:72761/1‑121 (MQ=255)                                                        aGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCtt                                                                         >  1:17903/1‑139 (MQ=255)                                                        aGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCtt                                                                         >  1:401808/1‑139 (MQ=255)                                                        aGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCtt                                                                         >  2:7603/1‑139 (MQ=255)                                                        aGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCt                                                                          >  4:126194/1‑138 (MQ=255)                                                        aGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGGGTATCCTTTTTCCTCGTCCCAAATGAtc                                                                                           <  6:72761/121‑1 (MQ=255)                                                                  ggCTTCATGACTCCGCGGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATttcgcc                                                               >  8:238416/1‑136 (MQ=255)                                                                               cgcgGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCaaa                                                  >  5:186762/1‑139 (MQ=255)                                                                               cgcgGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCaaa                                                  >  1:216402/1‑139 (MQ=255)                                                                               cgcgGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCaa                                                   >  7:351700/1‑138 (MQ=255)                                                                                 cgGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCaaatc                                                >  7:302402/1‑137 (MQ=255)                                                                                 cgGACAACAATCGGCATCCCTGTCGTCATGCCGCCTTCCACTCCGCCAACTCTGTTAGTATCACCGGTGTATACTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTACATTTCGCCCTGCTGCCTCaaatc                                                >  4:151282/1‑137 (MQ=255)                                                                                           tCGGCATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGACCTGCTGCCTCAAATCCGATGcgcaa                                      >  5:385499/1‑135 (MQ=255)                                                                                               cATCCCTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTcc                                  <  5:405785/139‑1 (MQ=255)                                                                                                atcccTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTCca                                 >  8:287665/4‑139 (MQ=255)                                                                                                atcccTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTCca                                 <  7:238416/136‑1 (MQ=255)                                                                                                atcccTGTCGTCATGACGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTCca                                 <  1:375946/136‑1 (MQ=255)                                                                                                 tcccTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTCcac                                <  5:59107/137‑1 (MQ=255)                                                                                                 tcccTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTCcac                                <  5:412915/137‑1 (MQ=255)                                                                                                 tcccTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTATCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTCcac                                <  5:99702/137‑1 (MQ=255)                                                                                                  cccTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCa                                                                                     >  7:165719/2‑85 (MQ=255)                                                                                                  cccTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCa                                                                                     <  8:165719/84‑1 (MQ=255)                                                                                                  cccTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTCcaca                               >  4:399272/2‑139 (MQ=255)                                                                                                  cccTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTCcaca                               >  5:16561/2‑139 (MQ=255)                                                                                                   ccTGTCGTCATGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCGCAAATCCGATGCCGAATTCCacac                              >  2:59021/1‑139 (MQ=255)                                                                                                            aTGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTCCACACCTTTAAATg                     >  1:364205/1‑139 (MQ=255)                                                                                                            aTGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTCCACACCTTTAAATg                     >  8:21503/1‑139 (MQ=255)                                                                                                             tGCCGCCTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTCCACACCTTTAAATGc                    >  8:103443/1‑139 (MQ=255)                                                                                                              gccgccTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTCCACACCTTTAAATGCg                   >  7:276400/1‑139 (MQ=255)                                                                                                               ccgccTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTCCACACCTTTAAATGCGt                  >  8:72275/1‑139 (MQ=255)                                                                                                                 gccTTCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTCCACACCTTTAAATGCGTTa                <  2:397004/139‑1 (MQ=255)                                                                                                                    ttCCAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTCCACACCTTTAAATGCGTTAAtt             >  4:343039/1‑139 (MQ=255)                                                                                                                       cAGTCCGCCAAGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTCCACACCTTTAAATGCGTTAATTGa           <  6:16561/138‑1 (MQ=255)                                                                                                                            cgccaaGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTCca                                 >  3:236886/6‑111 (MQ=255)                                                                                                                            cgccaaGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTCca                                 <  4:236886/106‑1 (MQ=255)                                                                                                                               caaGTCTGTTAGTAGCACGGGTGTATCCTTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCGCCCTGCTGCCTCAAATCCGATGCCGAATTCCACACCTTTAAATGCGTTAATTGACAGAAcagc  >  2:301238/3‑139 (MQ=255)                                                                                                                                         |                                                                                                                                 TGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATTCCTGTCGTCATGCCGCCTTCCAGTCCTCCGAGTCTGTTTGTAGCGCGGGTATATCCCTTTTCCTCGTCCCAAATGATCTCGTCATGGACTTCGCTTCCATTTCTTCCGGCTGCTTCAAAGCCGATGCCGAATTCCACACCTTTAAATGCGTTAATTGACAGAACAGC  >  CP006881/2197132‑2197396

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑