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%	124.4 / NA	28	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 . (11/17);  total (11/17)

GTTGAAGAAATAGGGGCTTTTGCGCCCGGATTTCAGCGTAAACTCGCCAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCT  >  NC_000913_3_vch_tpiA/3815661‑3815948                                                                                                                                                     |                                                                                                                                            gTTGAAGAAATAGGGGCTTTTGCGCCCGGATTTCAGCGTAAACTCGCCAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTGACTTTTCTACAGACAAAAAAAAg                                                                                                                                             >  1:299780/1‑149 (MQ=255)        aaaTAGGGGCTTTTGCGCCCGGATTTCAGCGTAAACTCGCCAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACtca                                                                                                                                     <  1:171634/149‑1 (MQ=255)                               tttCAGCGTAAACTCGCCAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGATTCATGCCTTCGCTCCTCATCTTACTTTTCTACAAACAAAAAAAA‑GCTACTCATCAGTCGCCTTAAAAATCAAttt                                                                                                              >  2:634121/1‑149 (MQ=255)                                   aGCGTAAACTCGCCAAACTTTAAAGCTTGCTTGCGAAGCGCAAATTCAATAAACTGGCGCTGAGATGGTTTCATGCCTTCGCTCCTCATCTTACTTATCTAAAGAAAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCa                                                                                                          <  2:233567/149‑1 (MQ=255)                                    gCGTAAACTCGCCAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCaa                                                                                                         >  1:432745/1‑148 (MQ=255)                                               ccAAACTTTAACACCTGCTGGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCt                                                                                              <  2:776657/149‑1 (MQ=255)                                                                    ctAAGCGCAAATTCAATAAACTGGCGCTGCTATGGTTTCATGCCTTCGCTCATAATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCATCGCCGCCTCCTGCGTCGCTACAATGcattagc                                                                         >  1:194833/1‑146 (MQ=255)                                                                    ctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGgattcga                                                                         <  2:760193/149‑1 (MQ=255)                                                                      aaGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGACAACACCGGCTTCTGCGTCGCTACAATGgattcgatt                                                                       <  1:200900/149‑1 (MQ=255)                                                                       agggcAAAGTCAATCAACTTGCGCTGTTACGGTTTCATGCCTTGCTTCCTCATTTTTCTTCTCTACCGTCAAAAGAGA‑TTGGTTCATTAGTCGCCTTAACAATCCGTTTGCCAGCGCCGCCTTCTGTTTCGCTACAATGgattcgattc                                                                      <  2:569696/146‑1 (MQ=255)                                                                       aGCGCAAATTCAATAAACTGGTGCTGATATGGTTTAATGCCTCCGCTCCGCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGgattcgattc                                                                      <  1:779208/149‑1 (MQ=255)                                                                         cgcAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTccc                                                                    <  1:444263/149‑1 (MQ=255)                                                                              aTTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCgg                                                               >  2:306889/1‑149 (MQ=255)                                                                                  aaTAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGCTTCCCCTCGGGCCa                                                           >  1:542644/1‑149 (MQ=255)                                                                                    tAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCaga                                                         >  1:662144/1‑149 (MQ=255)                                                                                     aaaCTGGCGCTTATATGTTTTCATGCCTTCGCTCCTCATCTTACTTTTCTCCAGACAAAAAAAA‑GCGACTCATCAGTCGGCTTAAAAATCCCTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCagag                                                        <  1:162035/149‑1 (MQ=255)                                                                                               tGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGAt                                              <  1:333052/149‑1 (MQ=255)                                                                                                 atatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGAt                                              <  1:466864/147‑1 (MQ=255)                                                                                                 atatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGAt                                              >  2:466864/1‑147 (MQ=255)                                                                                                         tCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGctct                                    <  1:431796/149‑1 (MQ=255)                                                                                                             gCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCAt                                >  2:448656/1‑149 (MQ=255)                                                                                                               cTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATgg                              <  1:642818/149‑1 (MQ=255)                                                                                                                  cGCTCCTCATCTTACTTTATTACAGACAAAAAAAA‑GCGACGTATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCGCGTGCTATAGCCAACAAGATGAGTAGCTCTTCATGGGTg                           <  2:766866/149‑1 (MQ=255)                                                                                                                         cATCTCACTTGTCCACAGACAAAAAACA‑GCTCCTCTTCAGTCGCCTTAGATATCAGTTTGACAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGTTTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAGCGGCt                    <  2:811229/149‑1 (MQ=255)                                                                                                                             ttACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGcc                >  2:737198/1‑149 (MQ=255)                                                                                                                                 ttttCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCt            <  1:397775/149‑1 (MQ=255)                                                                                                                                         aGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTccc    >  1:772671/1‑149 (MQ=255)                                                                                                                                          gACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCa                                 <  2:457793/119‑1 (MQ=255)                                                                                                                                          gACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCa                                 >  1:457793/1‑119 (MQ=255)                                                                                                                                            acaaaaaaaaGCGACTCATCAGTCGCCTTAAAAAGCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCt  <  1:642732/147‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                            GTTGAAGAAATAGGGGCTTTTGCGCCCGGATTTCAGCGTAAACTCGCCAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCT  >  NC_000913_3_vch_tpiA/3815661‑3815948

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑