Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,887,571	Δ1 bp	intergenic (+163/+7)	sokX → / ← cysH	small RNA SokX/phosphoadenosine phosphosulfate reductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,887,570	0	G	.	100.0%	89.4 / NA	20	intergenic (+162/+8)	sokX/cysH	small RNA SokX/phosphoadenosine phosphosulfate reductase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (13/7);  total (13/7)

ACGTTTAAAATCAGGAATGCTGCTCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCCGGCAATATTTACCCTTCGTGTAACCCACATTCCCTTTTTAAGCCAAAGAAACGCGTTTCTTCTTCCGCCATGCCG  >  NC_000913/2887495‑2887644                                                                            |                                                                           aCGTTTAAAATCAGGAATGCTGCTCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAata                                                                      >  1:519588/1‑81 (MQ=255)  cGTTTAAAATCAGGAATGCTGCTCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAatat                                                                     >  2:519584/1‑81 (MQ=255)       aaaaTCAGGAATGCTGCTCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTAcc                                                                >  1:519592/1‑81 (MQ=255)          aTCAGGAATGCTGCTCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCtt                                                             >  2:519590/1‑81 (MQ=255)            cAGGAATGCTGCTCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCg                                                           >  2:519583/1‑81 (MQ=255)               gAATGCTGCTCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCgtg                                                         >  1:519587/1‑80 (MQ=255)                   gctgctCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAAcc                                                    >  2:519589/1‑81 (MQ=255)                    ctgctCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAAccc                                                   <  1:519566/81‑1 (MQ=255)                    ctgctCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAAccc                                                   <  2:519565/81‑1 (MQ=255)                    ctgctCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAAccc                                                   <  1:519567/81‑1 (MQ=255)                    ctgctCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAAccc                                                   <  1:519564/81‑1 (MQ=255)                          gCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAACCCACATTc                                             >  2:519586/1‑81 (MQ=255)                                tAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAACCCACATTCCCtttt                                       <  1:519568/81‑1 (MQ=255)                                    aaCGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAACCCACATTCCCTTTTTAAg                                   >  1:519585/1‑81 (MQ=255)                                               catTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAACCCACATTCCCTTTTTAAGCCAAAGAAAcg                        >  2:519599/1‑81 (MQ=255)                                                       aCAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAACCCACATTCCCTTTTTAAGCCAAAGAAACGCGTttctt                >  1:519594/1‑81 (MQ=255)                                                       aCAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAACCCACATTCCCTTTTTAAGCCAAAGAAACGCGTttct                 <  1:519569/80‑1 (MQ=255)                                                              cGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAACCCACATTCCCTTTTTAAGCCAAAGAAACGCGTTTCTTCTTCCGc         >  2:519595/1‑81 (MQ=255)                                                                    aTTTGTCC‑GCAATATTTACCCTTCGTGTAACCCACATTCCCTTTTTAAGCCAAAGAAACGCGTTTCTTCTTCCGCCATGcc   <  2:519570/81‑1 (MQ=255)                                                                     tttGTCC‑GCAATATTTACCCTTCGTGTAACCCACATTCCCTTTTTAAGCCAAAGAAACGCGTTTCTTCTTCCGCCATGCCg  >  2:519605/1‑81 (MQ=255)                                                                            |                                                                           ACGTTTAAAATCAGGAATGCTGCTCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCCGGCAATATTTACCCTTCGTGTAACCCACATTCCCTTTTTAAGCCAAAGAAACGCGTTTCTTCTTCCGCCATGCCG  >  NC_000913/2887495‑2887644

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑