Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,877,816	T→C	pseudogene (408/1482 nt)	yeaV →	BCCT family transporter YeaV

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,877,816	0	T	C	91.7%	58.6 / ‑0.1	24	pseudogene (408/1482 nt)	yeaV	BCCT family transporter YeaV
Reads supporting (aligned to +/- strand):  ref base T (2/0);  new base C (10/12);  total (12/12)
Fisher's exact test for biased strand distribution p-value = 4.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.90e-01

GGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTTCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCTTG  >  NZ_CP009273/1877729‑1877895                                                                                        |                                                                                ggCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTTCg                                                                               >  2:109497/1‑90 (MQ=255) ggCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCg                                                                               >  1:132289/1‑90 (MQ=255) ggCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCg                                                                               >  1:23709/1‑90 (MQ=255) ggCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCg                                                                               >  2:572575/1‑90 (MQ=255) ggCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCg                                                                               >  1:317381/1‑90 (MQ=255) ggCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCg                                                                               >  2:238956/1‑90 (MQ=255) ggCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCg                                                                               >  2:66149/1‑90 (MQ=255)       aTTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCa                                                                         <  2:505136/90‑1 (MQ=255)        ttAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCaa                                                                        <  2:63643/90‑1 (MQ=255)                ggCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATg                                                                >  2:460241/1‑90 (MQ=255)                   ttATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATgggg                                                             <  1:363328/90‑1 (MQ=255)                    tATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGa                                                            >  1:557965/1‑90 (MQ=255)                            tCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGt                                                    <  1:460241/90‑1 (MQ=255)                            tCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGt                                                    <  1:325926/90‑1 (MQ=255)                                     gAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGAt                                           <  1:469473/90‑1 (MQ=255)                                          aCAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTcc                                      <  2:132289/90‑1 (MQ=255)                                                         tttCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCAAGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCg                       >  1:242429/1‑90 (MQ=255)                                                               gCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCAc                 <  2:458076/90‑1 (MQ=255)                                                                cATTATTGTTGCTATTCCCGGCGTCCGCCCGCCAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACt                <  1:352867/90‑1 (MQ=255)                                                                       gctgctATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCAtt         <  1:536671/90‑1 (MQ=255)                                                                       gctgctATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCAtt         <  1:414763/90‑1 (MQ=255)                                                                         tgctATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTc       <  1:148311/90‑1 (MQ=255)                                                                             aTTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCtt   >  2:145345/1‑90 (MQ=255)                                                                              ttACCGGCGTTCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCttg  >  2:66926/1‑90 (MQ=255)                                                                                        |                                                                                GGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTTCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCTTG  >  NZ_CP009273/1877729‑1877895

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑