Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP006881	2,197,067	T→A	10.3%	A357A (GCA→GCT)	U712_11010 ←	Chorismate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006881	2,197,067	0	T	A	10.3%	126.7 / 2.4	45	A357A (GCA→GCT)	U712_11010	Chorismate synthase
Reads supporting (aligned to +/- strand):  ref base T (14/25);  new base A (3/2);  total (18/27)
Fisher's exact test for biased strand distribution p-value = 3.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGGTTTGAACATGCAGTGTTTTCATTAAAATTCCCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCTTTTCAGCGGTTTATACAAAGTCGGAA  >  CP006881/2196941‑2197194                                                                                                                               |                                                                                                                                cGGTTTGAACATGCAGTGTTTTCATTAAAATTCCCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCt                                                                                                                     <  2:279601/139‑1 (MQ=255) cGGTTGGAACATGCAGTGTTTTCATAAAAATTCCCTCGACAGTTTTCTAATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCt                                                                                                                     <  4:104476/139‑1 (MQ=255)   ggttGAACATGCAGTGTTTTCATTAAAATTCCCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTc                                                                                                                   <  4:308045/137‑1 (MQ=255)   gTTTGAACATGCAGTGTTTTCATTAAAATTCCCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCACTTc                                                                                                                   <  7:221279/139‑1 (MQ=255)      tGAACATGCAGTGTTTTCATTAAAATTCCCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAg                                                                                                                 <  5:8923/138‑1 (MQ=255)         ccATGCAGTGTTTTCATTAAAATTCCCTCGACAGTTTGCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTCATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGctac                                                                                                             <  4:25327/138‑1 (MQ=255)            tGCAGTGTTTTCATTAAAATTCCCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGctacta                                                                                                           >  7:197807/1‑138 (MQ=255)             gCAGTGTTTTCATTAAAATTCCCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTaca                                                                                                         >  5:253383/1‑139 (MQ=255)              cAGTGTTTTCATTAAAATTCCCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCt                                                                                                                     <  4:50482/126‑1 (MQ=255)              cAGTGTTTTCATTAAAATTCCCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCt                                                                                                                     >  3:50482/1‑126 (MQ=255)              cAGTGTTTTCATTAAAATTCCCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTacac                                                                                                        <  5:249132/139‑1 (MQ=255)              cAGTGTTTTCATTAAAATTCCCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTacac                                                                                                        <  3:76258/139‑1 (MQ=255)                gtgtTATCATTAAAATTCCCTCGACCGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACtt                                                                                                      <  5:89134/139‑1 (MQ=255)                     ttCATTAAAATTCCCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGAGTTTATGTAAGCCCCATTGTGCAACGACTGCGTTCGCCATCGCCCAGACGACCGCCGCTTGAGGTACTGCCCATGCCGc                                                                                                 >  1:241252/1‑139 (MQ=255)                      tCATTAAAATTCCCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGATTTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGc                                                                                                 <  2:251772/138‑1 (MQ=255)                        aTTAAAATTCCCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGACGATTTGATCTAACACAAATTGTTCAACGACTGCCTTAGCAATCACCCAACGGACACCCGCTTCAGCTACTACACATGCCGCacg                                                                                              >  6:89134/1‑137 (MQ=255)                         ttAAAATTCCCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGGCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGc                                                                                             <  1:101447/139‑1 (MQ=255)                                tCCCTCGACCGGTGTCTCATATACTCCACCTTTTCCCTCATGCGGTGGATTTGATCTACGCCGACTTGTTCACCGACTGCGTTCGCAATCTACCAAGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGca                                                                                       <  7:84622/138‑1 (MQ=255)                                  ccTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAg                                                                                    <  6:125964/139‑1 (MQ=255)                                         aGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTg                                                                             <  8:20546/139‑1 (MQ=255)                                          gTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGa                                                                            <  5:110935/139‑1 (MQ=255)                                           ttttCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCCCTTCAGCTACAACACTTGCCGCACGCACTGCACAGCAGTCAGaa                                                                           >  2:11596/1‑139 (MQ=255)                                                                            gTCGATTTTAAATAATCCGAATTTTTAAACCACATCGTTCGCAAACTCCCCATCGACCGCCCCTTCAGCGAATACAAATTCCGCAGTCACATCACAACGCTCTGAACGGTAAATTCTGGCAGAAAACGGTTCTTTCGtt                                          >  6:216641/1‑139 (MQ=255)                                                                                          aGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCt                            >  3:107136/1‑139 (MQ=255)                                                                                           gCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGa                                                                            >  2:219325/1‑90 (MQ=255)                                                                                           gCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGa                                                                            <  1:219325/90‑1 (MQ=255)                                                                                              gAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCtttt                         >  7:936/1‑138 (MQ=255)                                                                                              gAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCTTTTc                        >  5:172169/1‑139 (MQ=255)                                                                                               aaTTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGAACGTTCAATTCTGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCTTTTCa                       <  8:618/139‑1 (MQ=255)                                                                                               aaTTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCtttt                         >  5:290792/1‑137 (MQ=255)                                                                                               aaTTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCTTTTCa                       <  5:129085/139‑1 (MQ=255)                                                                                               aaTTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCTTTTCa                       <  6:253383/139‑1 (MQ=255)                                                                                               aaTTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCTTTTCa                       <  8:197807/139‑1 (MQ=255)                                                                                               aaTTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCTTTTCa                       <  1:11596/139‑1 (MQ=255)                                                                                                 ttGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGc                     >  4:330373/1‑139 (MQ=255)                                                                                                    ttCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCTTTTCAGCGGt                  >  2:96558/1‑139 (MQ=255)                                                                                                         cGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAgg                                                                                              >  7:117797/1‑58 (MQ=255)                                                                                                         cGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAgg                                                                                              <  8:117797/58‑1 (MQ=255)                                                                                                         cGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCa                                                                                            <  2:220865/60‑1 (MQ=255)                                                                                                         cGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCa                                                                                            >  1:220865/1‑60 (MQ=255)                                                                                                              gCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCTTTTCAGCGGTTTATACAAAg        >  3:300442/1‑139 (MQ=255)                                                                                                               cGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCTTTTCAGCGGTTTATACAAAg        <  1:11219/138‑1 (MQ=255)                                                                                                                   cGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCTTTTCAGCGGTTTATACAAAGTCgg    >  4:316543/1‑138 (MQ=255)                                                                                                                    gCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGaa  <  3:330373/139‑1 (MQ=255)                                                                                                                    gCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGAACGTTCACTGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCTTTTCAGCGGTTTATACAAAGTCGGaa  <  5:69272/139‑1 (MQ=255)                                                                                                                               |                                                                                                                                CGGTTTGAACATGCAGTGTTTTCATTAAAATTCCCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCTTTTCAGCGGTTTATACAAAGTCGGAA  >  CP006881/2196941‑2197194

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: ‑