Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AE015451	4,741,245	A→C	65.7%	intergenic (+482/+271)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AE015451	4,741,245	0	A	C	65.7%	81.5 / 45.4	35	intergenic (+482/+271)	gltA/yeiW	citrate synthase/putative oxidoreductase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base C (7/16);  minor base . (7/5);  total (14/21)
Fisher's exact test for biased strand distribution p-value = 1.53e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.33e-03

GCCACCCGAACAAAACCCTTCTCTTCCGGCAGGTAAGTCGGCTCTTCTTTCAGGTTACGGGTCAGGCTGCCATCCGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AACC‑TCC‑GCCAAC‑TGCAATTCGTGAA‑CCAAGCAAAAGGCCCCGAAAAGGCCCTCC‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTTTTCAGCCCAGGCCACAGGCGACAGCAGAACACCCACACC  >  AE015451/4741050‑4741449                                                                                                                                                                                                        |                                                                                                                                                                                                               gCCACCCGAACAAAACCCTTCTCTTCCGGCAGGTAAGTCGGCTCTTCTTTCAGGTTACGGGTCAGGCTGCCATCCGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGtcctcctg                                                                                                                                                                       <  1:80989/236‑3 (MQ=255)                      tctTCCGGCAGGTAAGTCGGCTCTTCTTTCAGGTTACGGGTCAGGCTGCCATCCGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAg                                                                                                                                                  <  1:879841/236‑1 (MQ=255)                                ggTAAGTCGGCTCTTCTTTCAGGTTACGGGTCAGGCTGCCATCCGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCt                                                                                                                                          >  2:780397/1‑234 (MQ=255)                                    cgTCGGCTCTTCTTTCAGGTTACGGGTCAGGCCGCCCTCCGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCa                                                                                                                                                   <  2:134996/220‑1 (MQ=255)                                                 ttCAGGTTACGGGTCAGGCTGCCATCCGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACcgc                                                                                                                        <  1:491412/235‑1 (MQ=255)                                                                aGGCTGCCATCCTCCTCCTGGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACtt                                                                                                        <  1:713873/236‑1 (MQ=255)                                                                           cacctcctTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCT‑GCGACT‑TGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGc                                                                                               <  2:793282/232‑1 (MQ=255)                                                                              ctcctTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCT‑GCGACT‑TGC‑ATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCt                                                                                          <  1:849295/236‑1 (MQ=255)                                                                              ctcctTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCt                                                                                          <  1:738822/236‑1 (MQ=255)                                                                                             aaTGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCT‑GCGACT‑TGC‑ATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGacac                                                                             >  2:916053/1‑234 (MQ=255)                                                                                             aaTGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCT‑GCGACT‑TGC‑ATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACAcc                                                                            >  1:333091/1‑235 (MQ=255)                                                                                                 tgCAGCACGGAATCACGCGGCGGCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGa                                                                                    <  2:170079/223‑1 (MQ=255)                                                                                                      caCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCT‑GCGACT‑TGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCcg                                                                   >  1:865898/1‑235 (MQ=255)                                                                                                      caCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAg                                                                                                                   >  2:746295/1‑187 (MQ=255)                                                                                                           aaTCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGACTTGC‑ATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCcgt                                                                  <  1:521322/231‑1 (MQ=255)                                                                                                                   ggcgTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGc                                                     >  1:232281/1‑236 (MQ=255)                                                                                                                    gcgTCACCGGCCCTGGCGTAGTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACcgc                                                                                                                        <  2:248014/168‑1 (MQ=255)                                                                                                                      gTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCATCTCTGGTCACCTGCGTGCTTGAG‑CAGC‑TGC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACcgc                                                                                                                        <  2:71841/166‑1 (MQ=255)                                                                                                                                     gTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTTTTCAGc                                   >  1:236017/1‑236 (MQ=255)                                                                                                                                           aaCTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTTTTCAGCCCAGGc                             >  1:77983/1‑236 (MQ=255)                                                                                                                                           aaCTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATACCGTCCTCGTCCTTGGCCACTTGCCAGttt                                        >  1:32888/1‑225 (MQ=255)                                                                                                                                                   ataGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGCTCACGGTCACACcg                                                                                                                         >  2:254276/1‑136 (MQ=255)                                                                                                                                                   ataGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTTTTCAGCCCAGGCCACAgg                       <  2:567150/234‑1 (MQ=255)                                                                                                                                                    taGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGC‑TACTGCGACT‑TGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGACTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTTTTCAGCCCAGGCCACAgg                       <  2:865895/233‑1 (MQ=255)                                                                                                                                                             ctctGGTCACCTTCGTGCTTGAGCAGCT‑TCT‑GCGACT‑TGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTTTTCAGCCCAGGCCACAGGCGACAGCAGaa            >  1:656571/1‑235 (MQ=255)                                                                                                                                                             ctctGGTCACCTTCGTGCTTGAGCAGCT‑TCT‑GCGACT‑TGC‑ATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTTTTCAGCCCAGGCCACAGGCGACAGCAGa             >  2:629475/1‑234 (MQ=255)                                                                                                                                                             ctctGGTCACCTTCGTGCTTGAG‑CAGCTTCT‑GCGACT‑TGC‑ATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTTTTCAGCCCAGGCCACAGGCGAcagcag              >  2:670748/1‑233 (MQ=255)                                                                                                                                                             ctctGGTCACCTTCGTGCTTGAG‑CAGC‑TTCTGCGACT‑TGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTTTTCAGCCCAGGCCACAGGCGa                    >  2:368693/1‑227 (MQ=255)                                                                                                                                                             ctctGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTTTTCAGCCCAGGCCACAGGCGACAGCAGaa            <  1:472059/235‑1 (MQ=255)                                                                                                                                                               ctGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTTTTCAGCCCAGGCCACAGGCGACAGCAGAacac         <  1:368696/236‑1 (MQ=255)                                                                                                                                                               ctGGTCACCTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTTTTCAGCCCAGGCCACAGGCGACAGCAGAacac         <  1:318820/236‑1 (MQ=255)                                                                                                                                                                gggTCACCTTCGTGCTTGAGCAGCT‑TCT‑GCGACT‑TGC‑ATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTTTTCAGCCCAGGCCACAGGCGACAGCAGAacac         <  2:726689/234‑1 (MQ=255)                                                                                                                                                                  gTCACCTTCGGGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTTTTCAGCCCAGGCCACAGGCGACAGCAGAacac         <  2:801234/233‑1 (MQ=255)                                                                                                                                                                       cTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTTTTCAGCCCAGGCCACAGGCGAcagcag              <  1:776410/223‑1 (MQ=255)                                                                                                                                                                       cTTCGTGCTTGAG‑CAGC‑TTC‑TGCGAC‑TTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTTTTCAGCCCAGGCCACAGGCGACAGCAGAACACccacacc  <  1:721530/235‑1 (MQ=255)                                                                                                                                                                                                        |                                                                                                                                                                                                               GCCACCCGAACAAAACCCTTCTCTTCCGGCAGGTAAGTCGGCTCTTCTTTCAGGTTACGGGTCAGGCTGCCATCCGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AACC‑TCC‑GCCAAC‑TGCAATTCGTGAA‑CCAAGCAAAAGGCCCCGAAAAGGCCCTCC‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTTTTCAGCCCAGGCCACAGGCGACAGCAGAACACCCACACC  >  AE015451/4741050‑4741449

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑