Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,041,671	(T)6→7	intergenic (+46/‑108)	dsbA → / → b3861	protein disulfide isomerase I/putative GTP‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,041,665	1	.	T	100.0%	64.5 / NA	22	intergenic (+40/‑114)	dsbA/b3861	protein disulfide isomerase I/putative GTP‑binding protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (10/12);  total (10/12)

CTGATACAGTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAGTATTCACGGGC‑TTTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCTGCCGCTGGACATTATTTCAGCATA  >  NC_000913/4041591‑4041735                                                                            |                                                                       cTGATACAGTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGC‑t                                                                       <  1:261541/76‑1 (MQ=255) cTGATACAGTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGC‑t                                                                       <  2:3144095/76‑1 (MQ=255)   gATACAGTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAACGCCCGTGAATATTCACGGGC‑ttt                                                                     <  2:1518953/76‑1 (MQ=255)     tACAGTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGC‑ttttt                                                                   <  2:3479224/76‑1 (MQ=255)      aCAGTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAATCCCGTGAATATTCACGGGC‑tttttt                                                                  <  2:2569587/76‑1 (MQ=255)         gTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGC‑tttttttat                                                               <  1:3012645/76‑4 (MQ=255)              atatCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTTTTTTTATTAttt                                                           >  2:3375408/1‑76 (MQ=38)                atCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTTTTTTTATTATTtaa                                                         <  1:3132781/76‑1 (MQ=38)                  cTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTTTTTTTATTATTtaata                                                       <  2:4119312/76‑1 (MQ=38)                  cTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTTTTTTTATTATTtaata                                                       <  2:3070739/76‑1 (MQ=38)                   gggccGAGAAAAAATAATTCAATGGAAATTACATAAAGCCCGTGAAGAGTCACGGGCTTTTTTTATTATTtaataa                                                      >  1:73040/4‑76 (MQ=255)                       cGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTTTTTTTATTATTTAataaatat                                                  >  2:1759554/1‑76 (MQ=38)                             aaaaTAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTTTTTTTATTATTTAATAAATATAAATAc                                            >  1:3885861/1‑76 (MQ=38)                                  aatTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTTTTTTTATTATTTAATAAATATAAATACATTCt                                       <  2:1481239/76‑1 (MQ=38)                                  aatTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTTTTTTTATTATTTAATAAATATAAATACATTCt                                       <  1:1431430/76‑1 (MQ=38)                                    ttCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTTTTTTTATTATTTAATAAATATAAATACATTCTGa                                     <  2:2620762/76‑1 (MQ=38)                                      cAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTTTTTTTATTATTTAATAAATATAAATACATTCTGATa                                   >  1:3676749/1‑76 (MQ=38)                                        aTGTAAATTACATAAAGCCCGTGAATATTCACGGGCTTTTTTTATTATTTAATAAATATAAATACATTCTGATAAt                                 <  1:698932/76‑1 (MQ=38)                                             aaTTACATAAAGCCCGTGAATATTCACGGGCTTTTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATc                            <  2:3128999/76‑1 (MQ=38)                                               ttACATAAAGCCCGTGAATATTCACGGGCTTTTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCt                          <  1:959130/76‑1 (MQ=38)                                                 aCATAAAGCCCGTGAATATTCACGGGCTTTTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCTGc                        >  2:1635869/1‑76 (MQ=38)                                                  cATAAAGCCCGTGAATATTCACGGGCTTTTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCTGcc                       >  2:3209695/1‑76 (MQ=38)                                                      aaGCCCGTGAATATTCACGGGCTTTTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCTGCCGCTg                   <  2:1364121/76‑1 (MQ=39)                                                            gTGAATATTCACGGGCTTTTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCTGCCGCTGGACatt             >  1:445027/1‑76 (MQ=255)                                                                  aTTCACGGGCTTTTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCTGCCGCTGGACATTATTTCa       <  2:2382394/76‑1 (MQ=255)                                                                  aTTCACGGGCTTTTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCTGCCGCTGGACATTATTTCa       <  2:3885861/76‑1 (MQ=255)                                                                       cGGGCTTTTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCTGCCGCTGGACATTATTTCAGCATa  >  2:1505273/1‑76 (MQ=255)                                                                       cGGGCTTTTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCTGCCGCTGGACATTATTTCAGCATa  >  1:4421739/1‑76 (MQ=255)                                                                            |                                                                       CTGATACAGTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAGTATTCACGGGC‑TTTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCTGCCGCTGGACATTATTTCAGCATA  >  NC_000913/4041591‑4041735

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑