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 (5/3);  total (5/3)

ATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATT  >  NC_000913/2995138‑2995346                                                                                        |                                                                                                                           atcCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTaaa                                                                                                     >  1:1470827/1‑111 (MQ=255) atcCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTaaa                                                                                                     <  2:1470827/111‑1 (MQ=255)                                              tgaAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAg                            >  1:1087314/1‑139 (MQ=255)                                               gaAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTAAAATCATTAAACTTGAGCCAGGGAGTTATAAGt                           >  2:1075259/1‑139 (MQ=255)                                                                      aaaataaaatTTTTGCGTAAAAAAAATACCACAGGCATTAACAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGaa    <  1:1075259/139‑1 (MQ=255)                                                                        aataaaatTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAatt  >  1:215675/1‑139 (MQ=255)                                                                                  ttGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATaa                             <  1:1332550/102‑1 (MQ=255)                                                                                  ttGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATaa                             >  2:1332550/1‑102 (MQ=255)                                                                                        |                                                                                                                           ATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATT  >  NC_000913/2995138‑2995346

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑