Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,995,231	(A)7→8	intergenic (‑139/+83)	ygeK ← / ← ygeN	pseudogene, response regulator family, part of T3SS PAI ETT2 remnant, putative 2‑component transcriptional regulator/pseudogene, orgB family, part of T3SS PAI ETT2 remnant

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,995,224	1	.	A	100.0%	20.5 / NA	8	intergenic (‑132/+90)	ygeK/ygeN	pseudogene, response regulator family, part of T3SS PAI ETT2 remnant, putative 2‑component transcriptional regulator/pseudogene, orgB family, part of T3SS PAI ETT2 remnant
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base A (4/4);  total (4/4)

CCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCA  >  NC_000913/2995140‑2995351                                                                                      |                                                                                                                                 cccTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTA‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAAtt                                                                            >  2:32375/1‑139 (MQ=255)                                    tACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTA‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGa                                         <  2:1472450/139‑1 (MQ=255)                                                           atatAATTAAAAATAAAATTTTTGCGTA‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGcc                  >  2:1079929/1‑139 (MQ=255)                                                               aaTTAAAAATAAAATTTTTGCGTA‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCaaaa              <  1:1079929/139‑1 (MQ=255)                                                               aaTTAAAAATAAAATTTTTGCGTA‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCaaaa              >  1:196660/1‑139 (MQ=255)                                                                   aaaaaTAAAATTTTTGCGTAAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAg           >  1:970929/1‑139 (MQ=255)                                                                          aaatTTTTGCGTAAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAattatt    <  2:970929/139‑1 (MQ=255)                                                                           aatTTTTGCGTA‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCa  <  1:32375/139‑1 (MQ=255)                                                                                      |                                                                                                                                 CCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCA  >  NC_000913/2995140‑2995351

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑