Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,461,422	(G)5→4	pseudogene (1774/2526 nt)	BW25113_RS07350 →	autotransporter domain‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,461,418	0	G	.	100.0%	100.7 / NA	23	pseudogene (1770/2526 nt)	BW25113_RS07350	autotransporter domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (14/9);  total (14/9)

AGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCACAACCAACAGTGGGAAGGTTTC  >  NZ_CP009273/1461330‑1461504                                                                                         |                                                                                       agaACATTGGTGACAACGGCACGGTTAACAACAAAGAAGATGTTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAggg                                                                                      >  1:841492/1‑91 (MQ=255)     cATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAggggcaa                                                                                  >  2:811972/1‑88 (MQ=255)     cATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAggggcaa                                                                                  >  2:689113/1‑88 (MQ=255)     cATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAggggcaa                                                                                  >  2:599191/1‑88 (MQ=255)     cATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAggggcaa                                                                                  >  2:596223/1‑88 (MQ=255)     cATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAggggcaa                                                                                  >  1:240095/1‑88 (MQ=255)     cATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAggggcaa                                                                                  >  1:24082/1‑88 (MQ=255)     cATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAggggcaa                                                                                  >  1:800720/1‑88 (MQ=255)     cATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAggggcaa                                                                                  >  1:621261/1‑88 (MQ=255)     cATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAggggcaa                                                                                  >  1:484095/1‑88 (MQ=255)        tGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAg                                                                              <  2:263811/91‑1 (MQ=255)                 cGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAGTATCCAATa                                                                     <  1:144929/91‑1 (MQ=255)                     aCGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAGTATCCAATACggg                                                                 <  1:16301/91‑1 (MQ=255)                        gTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAGTATCCAATCCGGGTGa                                                              >  1:276098/1‑91 (MQ=255)                        gTTAACAACAAAGGAGATAATGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAGGATCCAATACGGGTgc                                                              >  1:276099/1‑90 (MQ=255)                           aacaacAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAg                                                                              <  1:316331/72‑1 (MQ=255)                           aacaacAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAg                                                                              >  2:316331/1‑72 (MQ=255)                           aacaacAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAGTATCCAATACGGGTGATGt                                                           <  2:679354/91‑1 (MQ=255)                           aacaacAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAGTATCCAATACGGGTGATGt                                                           >  1:848570/1‑91 (MQ=255)                                  aaGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAGTATCCAATACGGGTGATGTTAACGtt                                                    >  1:112848/1‑91 (MQ=255)                                   aGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAGTATCCAATACGGGTGATGTTAACGTTa                                                   <  2:514426/91‑1 (MQ=255)                                    ggAGATATTGTTGTTTCCGATACTGGATCGCTTGGCGTGGTCATCAACGGTGA‑GGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAg                                                  >  2:869916/1‑91 (MQ=255)                                                gttTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGAc                                      <  2:522678/91‑1 (MQ=255)                                                           tGGATCGATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCa                           >  1:62661/1‑91 (MQ=255)                                                            ggATCGATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCAt                          >  1:425686/1‑91 (MQ=255)                                                                 gATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAg                                    <  1:7373/76‑1 (MQ=255)                                                                 gATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAg                                    >  2:7373/1‑76 (MQ=255)                                                                 gATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCAcaa                     >  2:279230/1‑91 (MQ=255)                                                                 gATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCAcaa                     >  2:440372/1‑91 (MQ=255)                                                                 gATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCAcaa                     >  2:239237/1‑91 (MQ=255)                                                                 gATTGGCGTGCTCATCAACGGTGA‑GGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCAcaa                     >  1:180746/1‑91 (MQ=255)                                                                   ttGGCGTGCTCATCAACGGTGA‑GGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCAcaacc                   >  1:781882/1‑91 (MQ=255)                                                                      gCGTGCTCATCAACGGGGA‑GGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCAcaaccaac                >  2:289714/1‑91 (MQ=255)                                                                                    ggTGA‑GGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCACAACCAACAGTGGGAAGGTTTc  <  2:140531/91‑1 (MQ=255)                                                                                    ggTGA‑GGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCACAACCAACAGTGGGAAGGTTTc  >  1:228173/1‑91 (MQ=255)                                                                                    ggTGA‑GGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCACAACCAACAGTGGGAAGGTTTc  >  1:696467/1‑91 (MQ=255)                                                                                         |                                                                                       AGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCACAACCAACAGTGGGAAGGTTTC  >  NZ_CP009273/1461330‑1461504

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑