Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,215,948	T→C	pseudogene (487/2243 nt)	BW25113_RS25990 →	autotransporter outer membrane beta‑barrel domain‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,215,948	0	T	C	100.0%	84.6 / NA	24	pseudogene (487/2243 nt)	BW25113_RS25990	autotransporter outer membrane beta‑barrel domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (16/8);  total (16/8)

GATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCACTATTA  >  NZ_CP009273/1215867‑1216034                                                                                  |                                                                                       gATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTc                                                                                >  1:812688/1‑90 (MQ=255)  atatAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCa                                                                               >  1:630500/1‑90 (MQ=255)   tataAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCAc                                                                              <  1:48892/90‑1 (MQ=255)       aaaaaTAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACcgcg                                                                          >  1:231031/1‑90 (MQ=255)       aaaaaTAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACcgcg                                                                          >  2:750559/1‑90 (MQ=255)       aaaaaTAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACcgcg                                                                          >  1:858019/1‑90 (MQ=255)           aTAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTAt                                                                      >  2:293504/1‑90 (MQ=255)              gTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCaa                                                                   >  2:169668/1‑90 (MQ=255)                 cTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAAc                                                                <  1:750559/90‑1 (MQ=255)                 cTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAAc                                                                >  1:763656/1‑90 (MQ=255)                       caacaacaGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATa                                                          <  2:147339/90‑1 (MQ=255)                        aacaacaGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATaa                                                         >  2:559414/1‑90 (MQ=255)                         acaacaGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAAc                                                                <  1:351145/82‑1 (MQ=255)                         acaacaGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAAc                                                                >  2:351145/1‑82 (MQ=255)                           aacaGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAgg                                                      >  2:591322/1‑90 (MQ=255)                               ggCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAata                                                  <  2:858019/90‑1 (MQ=255)                                     aaaGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAAtt                                            >  2:791436/1‑90 (MQ=255)                                          ccccATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGc                                       >  2:378506/1‑90 (MQ=255)                                             cATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGaa                                                    >  1:234411/1‑74 (MQ=255)                                             cATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGaa                                                    <  2:234411/74‑1 (MQ=255)                                             cATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATc                                    >  2:218332/1‑90 (MQ=255)                                               ttGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCaa                                  <  2:901383/90‑1 (MQ=255)                                                                ggtggAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGcc                 >  1:591405/1‑90 (MQ=255)                                                                          tATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCAc       <  1:791436/90‑1 (MQ=255)                                                                               tttcCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCACTATTa  <  2:91424/90‑1 (MQ=255)                                                                                  |                                                                                       GATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCACTATTA  >  NZ_CP009273/1215867‑1216034

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑