Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,041,654	G→A	intergenic (+29/‑125)	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	4,041,654	0	G	A	100.0%	105.3 / NA	33	intergenic (+29/‑125)	dsbA/b3861	protein disulfide isomerase I/putative GTP‑binding protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (14/19);  total (14/19)

GCAGTATGCTGATACAGTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAGTATTCACGGGC‑T‑TTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCTGCCGCTGGACATT  >  NC_000913/4041583‑4041724                                                                        |                                                                         gcagTATGCTGATACAGTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATAtt                                                                      <  2:3491610/76‑1 (MQ=255)  cagTATGCTGATACAGTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTc                                                                     <  1:2806205/76‑1 (MQ=255)    gTATGCTGATACAGTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCAc                                                                   <  1:307348/76‑1 (MQ=255)     tATGCTGATACAGTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACg                                                                  <  2:4510340/76‑1 (MQ=255)          tGATACAGTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGC‑t‑t                                                           <  1:136518/76‑1 (MQ=255)          tGATACAGTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGC‑t‑t                                                           <  2:3450475/76‑1 (MQ=255)          tGATACAGTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGC‑t‑t                                                           >  2:5420728/1‑76 (MQ=255)           gATACAGTCAAATATCTGTCCGGGAAAAAATAATTCGATGTAAATTACATAAAGCCCGTGAATATTCACGGGC‑t‑tt                                                          <  1:2860403/76‑1 (MQ=38)            aTACAGTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGC‑t‑ttt                                                         <  2:2326617/76‑1 (MQ=255)             tACAGTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGC‑t‑tttt                                                        <  2:2220205/76‑1 (MQ=255)                aGTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGC‑t‑tttttta                                                     <  2:5600158/76‑3 (MQ=255)                    aaaTATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTT‑TTTTtattat                                                  <  2:3296230/76‑1 (MQ=38)                    aaaTATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTT‑TTTTtattat                                                  <  2:4439807/76‑1 (MQ=38)                        atCTGTCCGAGGAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTT‑TTTTTATTATTtaa                                              <  2:733665/76‑1 (MQ=38)                        atCTGTCCGAGAAAAACTAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTT‑TTTTTATTATTtaa                                              >  2:4003012/1‑76 (MQ=38)                        atCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTT‑TTTTTATTATTtaa                                              >  1:4317437/1‑76 (MQ=38)                        atCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTT‑TTTTTATTATTtaa                                              >  2:3950977/1‑76 (MQ=38)                         tCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTT‑TTTTTATTATTtaat                                             <  2:3731012/76‑1 (MQ=38)                           tGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTT‑TTTTTATTATTtaataa                                           >  2:5487034/1‑76 (MQ=38)                           tGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTT‑TTTTTATTATTtaataa                                           <  2:2152859/76‑1 (MQ=38)                                  gaAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTT‑TTTTTATTATTTAataaatataaa                                    >  2:4121821/1‑76 (MQ=38)                                   aaaaaaTAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTT‑TTTTTATTATTTAataaatataaat                                   >  1:3511344/1‑76 (MQ=38)                                      aaaTAATTCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTT‑TTTTTATTATTTAATAAATATAAATACa                                <  2:961622/76‑1 (MQ=38)                                        ataatTCAATGCAAATTACATAAAGCCCGTGAATATGCACGGGCTT‑TTTTTATTATTTAATAAATATAAATACaat                              >  2:3939792/1‑74 (MQ=255)                                             tCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTT‑TTTTTATTATTTAATAAATATAAATACATTCTGAt                         >  1:4118446/1‑76 (MQ=38)                                             tCAATGTAAATTACATAAAGCCCGTGAATATTCACGGGCTT‑TTTTTATTATTTAATAAATATAAATACATTCTGAt                         >  1:4094155/1‑76 (MQ=38)                                                        tACATAAAGCCCGTGAATATTCACGGGCTT‑TTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCTg              >  2:4891752/1‑76 (MQ=38)                                                          cATAAAGCCCGTGAATATTCACGGGCTT‑TTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCTGcc            <  2:4984474/76‑1 (MQ=38)                                                          cATAAAGCCCGTGAATATTCACGGGCTT‑TTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCTGcc            >  1:5788422/1‑76 (MQ=38)                                                          cATAAAGCCCGTGAATATTCACGGGCTT‑TTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCTGcc            <  1:4121822/76‑1 (MQ=38)                                                                gCCCGTGAATATTCACGGGCTT‑TTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCTGCCGCTGGa      <  1:1696316/76‑1 (MQ=255)                                                                   cctGAATATTCACGGGC‑TGTTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCTGCCGCTGGACat   >  2:1037863/3‑76 (MQ=255)                                                                    gTGAATATTCACGGGCTT‑TTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCTGCCGCTGGACatt  >  2:5031146/1‑76 (MQ=255)                                                                        |                                                                         GCAGTATGCTGATACAGTGAAATATCTGTCCGAGAAAAAATAATTCAATGTAAATTACATAAAGCCCGTGAGTATTCACGGGC‑T‑TTTTTATTATTTAATAAATATAAATACATTCTGATAATGCATCCTGCCGCTGGACATT  >  NC_000913/4041583‑4041724

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑