Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_vch_tpiA	3,815,810	Δ1 bp	intergenic (‑42/+24)	pyrE ← / ← rph	orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_vch_tpiA	3,815,809	0	G	.	100.0%	80.1 / NA	19	intergenic (‑41/+25)	pyrE/rph	orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (15/4);  total (15/4)

GGGCTTTTGCGCCCGGATTTCAGCGTAAACTCGCCAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCC  >  NC_000913_3_vch_tpiA/3815674‑3815946                                                                                                                                        |                                                                                                                                          gggCTTTTGCGCCCGGATTTCAGCGTAAACTCGCCAAACTTTAACACCTGCTTGCTCAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTc                                                                                                                             >  1:11424/1‑149 (MQ=255)                        cGTAAACTCGCCAAACTTTAACACCTGCTTGCTCAACCCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCCTAAAAACCAGTTTTCCAgc                                                                                                      >  2:314715/1‑149 (MQ=255)                                 gCCAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAAACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTCTGCCTGCGCCCCCCTc                                                                                             >  1:131371/1‑149 (MQ=255)                                   cAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCCAAGTGGCGCTACCAATATTCCCGCTCGACAGACACAAAAAA‑CCGGCTGATCAGTCGCCGCAAAAATCAGTTTTCCAACGCCGCCTTcag                                                                                           >  1:103097/1‑147 (MQ=255)                                   cAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGttt                                                                                                            <  1:245664/132‑1 (MQ=255)                                   cAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGttt                                                                                                            >  2:245664/1‑132 (MQ=255)                                   cAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAATCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTg                                                                                           >  1:121185/1‑149 (MQ=255)                                     aaCTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCAGCCTTCTgac                                                                                         >  1:190449/1‑147 (MQ=255)                                                                               cgcTGATATGGTTTCATGTCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCcaacaa                                               <  1:252801/149‑1 (MQ=255)                                                                                     tatGATTTTATGTCCTCCCTTCTCACCTTACTTTTCTAAGCACGAGTAAAA‑GCGACGGATCAGTCGCCGTAAAAATCAGTCTGCCAGCTCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAg                                         <  1:278289/149‑1 (MQ=255)                                                                                      atGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAAGGATTCGATTCCCCTCGGGCCAGAGACCACAACATGAGt                                        >  2:95861/1‑149 (MQ=255)                                                                                       tGGTTTAATGCCTTCGCTCATAATCTTACTTTCCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAACGCAGCCGTCTGCATCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTa                                       <  2:269577/149‑1 (MQ=255)                                                                                                    tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGTCCAAAGCCAACAAGATGAGTAGCTCTTCATGGGt                          >  1:123851/1‑149 (MQ=255)                                                                                                         cctcATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGGACg                     >  2:293978/1‑149 (MQ=255)                                                                                                          ctcATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTGTTCATGGGTTAACgg                    >  2:346612/1‑149 (MQ=255)                                                                                                                ttACTTCTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCATCGGGCCACAGCCAACAAGATGAGTAGAGCTTCATGGGTGGACGGCTCGcc              >  2:354256/1‑149 (MQ=255)                                                                                                                    ttttCTACTGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGAGCCGACTTCTGCGTAGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCGGACAAGATGAGTCGCTCTTCATGGGTGGATGGCTCGCCTTCt          >  2:152668/1‑149 (MQ=255)                                                                                                                        cTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCg      >  2:25965/1‑149 (MQ=255)                                                                                                                            aGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCCGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCCCTTCATGGGTGAACGGCTCGCCTTCTGCCGTccc  >  1:393193/1‑149 (MQ=255)                                                                                                                                        |                                                                                                                                          GGGCTTTTGCGCCCGGATTTCAGCGTAAACTCGCCAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCC  >  NC_000913_3_vch_tpiA/3815674‑3815946

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑