Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AE015451	6,132,542	A→G	16.8%	D437D (GAT→GAC)	copA‑II ←	copper resistance protein A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AE015451	6,132,542	0	A	G	16.8%	110.2 / 4.7	45	D437D (GAT→GAC)	copA‑II	copper resistance protein A
Reads supporting (aligned to +/- strand):  ref base A (23/14);  new base G (5/3);  total (28/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01

CATGTCGACCAAGGGGTTGTTAGTCTCTGAGGCTGGGTGAGACTGCATGGCGCCACCCATACCTTCCATGCTGCTGTGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATACCGGCCATGTTGCCGTGGTCCATGCCGGCCATGCTGCCGTGATC  >  AE015451/6132320‑6132736                                                                                                                                                                                                                               |                                                                                                                                                                                                   cATGTCGACCAAGGGGTTGTTAGTCACTGAGGCTGGGTGAGACTGCATGGCGCCACCCATACCTTCCATGCTGCTGTGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCg                                                                                                                                                                                           >  1:565519/1‑232 (MQ=255)       gACCAAGGGGTTGTTAGTCTCTGAGGCTGGGTGAGACTGCATGGCGCCACCCATACCTTCCATGCTGCTGTGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCTGCCGTGGTCCATCTCAGCCATTTTGCTGTGGTCCATGCCGGCCAtgctgc                                                                                                                                                                                 >  1:599396/1‑236 (MQ=255)       gACCAAGGGGTTGTTAGTCTCTGAGGCTGGGTGAGACTGCATGGCGCCACCCATACCTTCCATGCTGCTGTGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCAtgctg                                                                                                                                                                                  <  1:608589/235‑1 (MQ=255)                 ttgttAGTCGCTGAGGCTGGGTGAGACTGCATGGCGCCACCCATACCTTCCATGCTGCTGTGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCa                                                                                                                                                                        <  1:589348/235‑1 (MQ=255)                      aGTCTCTGAGGCTGGGTGAGACTGCATGGCGCCACCCATACCTTCCATGCTGCTGTGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATg                                                                                                                                                                                              >  1:1083743/1‑208 (MQ=255)                      aGTCTCTGAGGCTGGGTGAGACTGCATGGCGCCACCCATACCTTCCATGCTGCTGTGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCAt                                                                                                                                                                                      >  1:252924/1‑216 (MQ=255)                              aGGCTGGGTGAGACTGCATGGCGCCACCCATACCTTCCATGCTGCTGTGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTg                                                                                                                                                          <  1:242305/236‑1 (MQ=255)                                               aTGGCGCCACCCATACCTTCCATGCTGCTGTGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCAtgctg                                                                                                                                                                                  <  2:760127/195‑1 (MQ=255)                                                               cTTCCATGCTGCTGTGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCAtttt                                                                                                                                                           <  1:64514/202‑1 (MQ=255)                                                                ttCCATGCTGCTGTGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATACCGGCCATGCTGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATTCCGGCCa                                                                                                                                                                                       >  2:518052/1‑173 (MQ=14)                                                                        tgctgTGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCCTGGTCCATCCCAGCCATTTTGCCGTGGTCCa                                                                                                                                                >  2:1008829/1‑204 (MQ=255)                                                                         gctgTGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCACCCATTTCGCTGTGGTCCacacc                                                                                                                                                                                            >  2:876750/1‑155 (MQ=255)                                                                                  cATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGGCCATGCCGGCCATGCGGCCGCGGTCCATCTCAGACATTTTGCTGTGATc                                                                                                                                                                                                  >  2:208915/1‑144 (MQ=255)                                                                                       cGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCGTGGTCCATCCCAGCCAttt                                                                                                                                                            >  1:1082107/1‑177 (MQ=255)                                                                                             tGCCGCCTTGGTCCATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCTTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCg                                                                                                                                           >  1:877517/1‑188 (MQ=255)                                                                                              gccgcaTTGGTCCATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATcc                                                                                                                     <  1:425410/209‑1 (MQ=255)                                                                                                                     tCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCCCAGCCATTTTGCTGTTATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGt                                                                                                                                         >  2:45458/1‑166 (MQ=255)                                                                                                                                     atCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCCCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATCGTCCACCCCAGCCa                                                                                                                                                               >  2:8999/1‑128 (MQ=255)                                                                                                                                       cGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGc                                                                                             >  1:332514/1‑192 (MQ=255)                                                                                                                                            aTGCCGCCTTGTTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATACCAGCCATTTTTCTGTGATCCATTCCGGCCGTGCTGCCATGGTCCATCCCAGCCATTTTGCGGTTGTCCATGcc                                                                                                                                            >  2:735868/1‑140 (MQ=17)                                                                                                                                              cccgccTTGGCCCATCCCCGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCAtttt                                                                                                                                                           <  2:370082/122‑1 (MQ=255)                                                                                                                                                cgccTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCAtttt                                                                                                           <  1:911615/169‑1 (MQ=255)                                                                                                                                                 gccTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCGTGGTGCATCCCGGCCATTTTGCTGTGGTCCATGCCCGTCa                                                                                                                                       >  1:1059847/1‑140 (MQ=255)                                                                                                                                                  ccTGGGTCTATCCTAGACATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCCACCATTTTGCTGTGATCCATGCCGGCCATGCCGCCATGCTCCATCCCAGcc                                                                                                                                                                <  1:1029815/114‑1 (MQ=255)                                                                                                                                                      ggTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCAtttttc                                                         >  1:91837/1‑211 (MQ=255)                                                                                                                                                               cAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCgg                                                                                          >  1:610604/1‑171 (MQ=255)                                                                                                                                                                    aTCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCACACCgg                                          >  1:270027/1‑214 (MQ=255)                                                                                                                                                                    aTCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCAATGCCGGTCATGTTGCCGTGGTGCATCCCCGCCATTTTGCTGTGGTCCATGCCGGcc                                                                                        >  1:430353/1‑168 (MQ=255)                                                                                                                                                                    aTCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATGTTGCTGTGGTCCATGCCGACCATGCTGCCATGGTCCATCCCGGCCATCTTGCTGTGGCCCATGc                                                                                                                                             >  2:745464/1‑115 (MQ=18)                                                                                                                                                                         gCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTCTGCTGTGGTCGATACCGGCCAt                                                                                                                                      >  2:93727/1‑117 (MQ=18)                                                                                                                                                                         gCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCCCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATccc                                                                                                                                                                    >  2:1030118/1‑87 (MQ=255)                                                                                                                                                                                tCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCAtttt                                                           >  1:766429/1‑185 (MQ=255)                                                                                                                                                                                tCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCATTTTGCtgt                                                      <  1:812738/190‑1 (MQ=255)                                                                                                                                                                                  cATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGCTGCCGTGATCCATacccata                                                                >  2:456230/1‑174 (MQ=255)                                                                                                                                                                                    tGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGGTCCATGCCGGCCATGCTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCAtttt                                                           <  1:142149/181‑1 (MQ=255)                                                                                                                                                                                             tGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCTCTTTGccg                                                       >  1:597545/1‑174 (MQ=255)                                                                                                                                                                                                cgccgTGGTCCATGCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGt                                                                                    <  2:599393/144‑1 (MQ=255)                                                                                                                                                                                                        tCCATCCCATCCTTTTTGCTGTGGGCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGt                                                                              <  2:496337/142‑1 (MQ=11)                                                                                                                                                                                                        cccATCCCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCTTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTg                                                                                  <  1:466803/137‑1 (MQ=255)                                                                                                                                                                                                          cttaccggCCATGTTGCCGTGGTCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATATTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCGTGTTGCCGTGGTcc                                                                         >  2:667720/8‑145 (MQ=14)                                                                                                                                                                                                               cAGCCATTTTGCTGTGATCCATGCCGGCCAtgctg                                                                                                                                                                                  >  2:37476/1‑35 (MQ=255)                                                                                                                                                                                                               cAGCCATTTTGCTGTGATCCATGCCGGCCAtgctg                                                                                                                                                                                  <  1:37477/35‑1 (MQ=255)                                                                                                                                                                                                                  ccATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATACCGGCCATGTTGCCGTGGTCCATGcc                    >  1:138591/1‑190 (MQ=255)                                                                                                                                                                                                                    aTTTTGCTGTGATCCATGCCGGCCATGCTGCCTTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTgg                                                                            <  2:911880/132‑1 (MQ=255)                                                                                                                                                                                                                          cTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATACCGGCCATGTTGCCGTGGTCCATGCCGGCCATGCTGCCGTGATc  <  1:626960/200‑1 (MQ=255)                                                                                                                                                                                                                               |                                                                                                                                                                                                   CATGTCGACCAAGGGGTTGTTAGTCTCTGAGGCTGGGTGAGACTGCATGGCGCCACCCATACCTTCCATGCTGCTGTGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATACCGGCCATGTTGCCGTGGTCCATGCCGGCCATGCTGCCGTGATC  >  AE015451/6132320‑6132736

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑