Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006881	2,197,868	C→G	A90A (GCG→GCC)	U712_11010 ←	Chorismate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006881	2,197,868	0	C	G	98.2%	169.9 / NA	57	A90A (GCG→GCC)	U712_11010	Chorismate synthase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base G (26/30);  minor base T (1/0);  total (27/30)
Fisher's exact test for biased strand distribution p-value = 4.74e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGCTGAAGAGCGCTCAAGCACATTTCTCATATCACGGTGATTATATTTAATCGCTCCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATTTGGCGCTTCATTTCCTTTTCTTCATCCTCTGTAATCGGAGCCGCACCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACGACGAGAGCAATTGGTGAACCGAGTGTTCGTGCATGACGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCG  >  CP006881/2197733‑2198003                                                                                                                                        |                                                                                                                                        tGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGcg                                                                                                                                      >  3:183477/1‑138 (MQ=255) tGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCGTCATCTTCTGTAATCGGAGCGGcg                                                                                                                                      >  7:60014/1‑138 (MQ=255)  gCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGcg                                                                                                                                      <  4:222091/138‑2 (MQ=255)           cgcTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTACTTTTGTTCATATTCTGTTATCGTAGCTGCGCCCATGAttt                                                                                                                            >  7:322929/1‑139 (MQ=255)               cAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGt                                                                                                                        <  1:321058/139‑1 (MQ=255)                aaGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTg                                                                                                                         <  8:180844/137‑1 (MQ=255)                aaGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTc                                                                                                                       <  7:56492/139‑1 (MQ=255)                   cacaTTTCTCCTATAAAGATGATTATATTTATTTGCAACGTTTAAGTCATAGTGCCCATGTCTCGGTCTTGAAAGCTGGAGCTTCATTTCCTTTTCTTCATATGCTGTAATCGGATCGGCGCCCATGATTTTTGTCCaa                                                                                                                    <  7:278346/139‑1 (MQ=255)                        ttCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCAATTACTTTTCTTAATATTATGTAATAGGAGCGGCGCCCCATATTTTTGTCCTATgat                                                                                                                >  4:77790/1‑136 (MQ=255)                        ttCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCGACTCTTCCTTTTCGTGATCATCTGTAATCGGAGCGGCGCCCCATATTTTTTTCCAAGGCt                                                                                                                >  5:425864/1‑138 (MQ=255)                                     atGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTGCTTTTGTTCATCTTGTGTAATCGGAGCGGCGCCCATGTTTTTTGTGCAATGGTTGCAATCGTTAttt                                                                                                  >  4:168391/2‑139 (MQ=255)                                     atGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTAATTTCCTTTTCTTCGTCTTCTGTTATCGGAGCGGCGCCCATGATTTTTGTAGATTGCTTACAATCGTTAttt                                                                                                  >  8:75501/2‑139 (MQ=255)                                              tttAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTGTTCATCTTCTGTTATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCCATCGTTTTTTTCAactacg                                                                                         >  5:75066/1‑139 (MQ=255)                                                 aaTTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTTTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAActacga                                                                                        >  6:314458/1‑137 (MQ=255)                                                      caccGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATATTCTGTAATCGGAGCGGGGCCCATGATTTTTGTGGAATTCGTGCAAACGTTTTTTTAAACTTCGACTGCAAt                                                                                 >  2:76207/3‑139 (MQ=255)                                                         cGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTgg                                                                              <  4:183477/139‑1 (MQ=255)                                                         cGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTgg                                                                              <  5:263872/139‑1 (MQ=255)                                                           tttAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCATTTCTTCATCATCTGTAATAGGAGCGGCGCCCAAGATTTTTTTGCAATGCTTCCAATCCTTATTTTCAACAACTAGAGCAATTggc                                                                             >  6:186526/1‑137 (MQ=255)                                                             tAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCaa                                                                                                           <  8:288095/106‑1 (MQ=255)                                                             tAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCaa                                                                                                           >  7:288095/1‑106 (MQ=255)                                                              aaGTCAGCGTGCCCAGGTCGCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGTGaa                                                                          <  6:249005/138‑1 (MQ=255)                                                              aaGGCAGCGGGCCCAGGTCTCGGGCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGaa                                                                          <  6:75066/138‑1 (MQ=255)                                                               aggcAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAAcc                                                                        <  6:444032/136‑1 (MQ=255)                                                               aGTGAGCGTGCCCAGGTCTCGGTCAGGAAATCTGGCGCTTCTTTTCCTTTTCTTCCTCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAAcc                                                                        <  4:360783/139‑1 (MQ=255)                                                               aGTCTGCGTGCCCAGGGCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTGCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCTATCGTTATTTTCAACTACGAGAGCAATTGGCGAAcc                                                                        <  8:52533/139‑1 (MQ=255)                                                               aGTCAGCGTGCCCAGGTCTCGGGCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAAcc                                                                        <  7:269881/139‑1 (MQ=255)                                                                gTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCGTCATTTCCTTTTCTTCATCTTATGTTATCGGAGCGGCGCCCAAGATTTTTGTCCAATGCTTCGAATAGTTATTTTAAACTACGAGGGCAATTGGAGAACCg                                                                       >  8:239831/1‑139 (MQ=255)                                                                 gacaggTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGa                                                                      <  3:274562/134‑1 (MQ=255)                                                                     cGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTGATTTCCTTTTCTTCGTCTTCTGTAATCGGTGCGGCGGCCATGTTTTTTGTGCAATGGTTCCAAACGTTATTTTCAAATAGGAGAGCAATTGGCGAGCCGGgtgt                                                                  >  3:26423/1‑139 (MQ=255)                                                                     cGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTGATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCCTGATTTTTTTCCACTGCTTCCAATCGTTTTTTTGAACTACGAGAGCAATTGGCGCACCGAgtg                                                                   >  3:43522/1‑138 (MQ=255)                                                                     cGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTGTTCATCTTCTGTTATCGGAGCGGCGCCCCTGTTTTTTGTCCAATGCTTCCAATCGTTATTTTGAACTACGAGAGCAATTGGCGGACCGAggg                                                                   >  3:278188/1‑136 (MQ=255)                                                                     cGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTGATCTTCTGTAATCGGAGCGGCGCCCATGGTTTTTGTGCAATGCTTCCAATCGTTTTTTTGAACAAAGAGAGCAATTGGCGAAACGAgtg                                                                   >  1:82333/1‑138 (MQ=255)                                                                     cGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCg                                                                                                        >  7:408648/1‑101 (MQ=255)                                                                     cGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCg                                                                                                        <  8:408648/101‑1 (MQ=255)                                                                     cGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAgtgt                                                                  <  7:15602/139‑1 (MQ=255)                                                                     cGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATATTCTTTAATCCGAGCGGCGCCCCATATTTTTGTGCAAAGATTCCAATCGTTAATTTAAACAACGACACCAAATGGCGAAACGAgtg                                                                   >  5:71953/1‑138 (MQ=255)                                                                     cGTGCCCAGGTCTCGGGCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTACTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAgtgt                                                                  <  3:134128/139‑1 (MQ=255)                                                                     cGTGCCCAGGGCTCGGGCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGACCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAgtgt                                                                  <  7:22065/139‑1 (MQ=255)                                                                      gTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCAATTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAgtgta                                                                 <  2:182076/139‑2 (MQ=255)                                                                            aGGTCTCGGTCTGGAAATCTTGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCa                                                           <  5:186526/139‑1 (MQ=255)                                                                                   ggTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAAATACGATAGCAATTTGCGAACCGAGTGTACGTTCCTGGCGCa                                                    >  7:423394/1‑139 (MQ=255)                                                                                   ggTCTGGAAATCTGGCGCTTCAGTTCCTTTTAGTGATCTTCTGTAATCGGAGAGGCGCCCATGATTTTTGTCAAATGCGTACAATCGTTATTTTCAACTACGATCGGAATTGGCGCCCCGAGTGTACGTGCCTGGCGCa                                                    >  6:174228/1‑139 (MQ=255)                                                                                     tCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCAcc                                                  <  3:68683/139‑1 (MQ=255)                                                                                        ggAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAAcc                                                                        >  4:270059/1‑114 (MQ=255)                                                                                        ggAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAAcc                                                                        <  3:270059/114‑1 (MQ=255)                                                                                           aaTCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTc                                            <  4:341121/139‑1 (MQ=255)                                                                                            atctGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCa                                           <  5:398283/136‑1 (MQ=255)                                                                                            atctGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCa                                           <  3:144643/136‑1 (MQ=255)                                                                                               tGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATaa                                        >  5:419096/1‑139 (MQ=255)                                                                                                 gcgcTTCATTTGCTTTTGTTGATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTGCCATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTTGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAAtt                                      >  8:301247/1‑139 (MQ=255)                                                                                                 gcgcTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAAtt                                      <  6:259902/139‑1 (MQ=255)                                                                                                        aTTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGcc                                <  6:223694/138‑1 (MQ=255)                                                                                                                      aTCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGAt                  <  1:177708/138‑1 (MQ=255)                                                                                                                        cttctGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTg               >  3:284585/3‑139 (MQ=255)                                                                                                                            tGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGGCTGGTCGTTTTCGATCTGCATg           >  2:127216/1‑139 (MQ=255)                                                                                                                              tAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATgcg         <  1:23008/139‑1 (MQ=255)                                                                                                                                     aGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGgcggccg  >  3:400046/1‑139 (MQ=255)                                                                                                                                        |                                                                                                                                        TGCTGAAGAGCGCTCAAGCACATTTCTCATATCACGGTGATTATATTTAATCGCTCCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATTTGGCGCTTCATTTCCTTTTCTTCATCCTCTGTAATCGGAGCCGCACCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACGACGAGAGCAATTGGTGAACCGAGTGTTCGTGCATGACGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCG  >  CP006881/2197733‑2198003

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑