Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,201,626	A→G	pseudogene (34/786 nt)	BW25113_RS05980 →	baseplate J/gp47 family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,201,626	0	A	G	100.0%	124.4 / NA	33	pseudogene (34/786 nt)	BW25113_RS05980	baseplate J/gp47 family protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (11/22);  total (11/22)

GAAAGCATTTGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGC  >  NZ_CP009273/1201540‑1201713                                                                                       |                                                                                        gAAAGCATTTGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGt                                                                                     >  1:177419/1‑91 (MQ=255)   aaGCATTTGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGa                                                                                   <  1:268731/91‑1 (MQ=255)   aaGCATTTGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGa                                                                                   <  1:238626/91‑1 (MQ=255)           ggCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTAGATGCGCTGGGAAGGGGTCAGCGATGGCCTGGAGGTGACCGCCggg                                                                           <  2:439910/91‑1 (MQ=255)             cGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAg                                                                         <  2:776811/91‑1 (MQ=255)             cGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAg                                                                         <  1:537449/91‑1 (MQ=255)               aaGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCggg                                                                           <  1:191575/87‑1 (MQ=255)               aaGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCggg                                                                           >  2:191575/1‑87 (MQ=255)               aaGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAgtg                                                                       >  1:468666/1‑91 (MQ=255)                aGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGGGACCGCCGGGAgggt                                                                      >  1:853713/1‑91 (MQ=255)                     cTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTc                                                                 <  2:281050/91‑1 (MQ=255)                        aaCTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAgc                                                              <  1:644864/91‑1 (MQ=255)                           tgctgcCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGcgcg                                                           >  1:275311/1‑91 (MQ=255)                            gctgcCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGa                                                          <  1:438374/91‑1 (MQ=255)                                 ccGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGAcc                                                     <  2:336820/91‑1 (MQ=255)                                  cGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCt                                                    <  2:777751/91‑1 (MQ=255)                                  cGTCGATCCCGGCTGTGTGCTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCt                                                    <  2:166096/91‑1 (MQ=255)                                       aTCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGc                                               <  2:177419/91‑1 (MQ=255)                                       aTCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGc                                               <  2:556054/91‑1 (MQ=255)                                       aTCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGc                                               <  1:829743/91‑1 (MQ=255)                                               tgtgtgGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACg                                       >  2:138545/1‑91 (MQ=255)                                                gtgtgGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGa                                      >  1:234420/1‑91 (MQ=255)                                                 tgtgGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGAc                                     <  2:210025/91‑1 (MQ=255)                                                 tgtgGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGAc                                     <  2:275311/91‑1 (MQ=255)                                                          tGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAgc                                                              <  1:89642/57‑1 (MQ=255)                                                          tGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAgc                                                              >  2:89642/1‑57 (MQ=255)                                                            cgcTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATg                          <  2:593161/91‑1 (MQ=255)                                                               tGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCaa                       >  1:108282/1‑91 (MQ=255)                                                                  gAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCa                    <  2:563124/91‑1 (MQ=255)                                                                  gAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCa                    <  2:627116/91‑1 (MQ=255)                                                                        gtCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCg              >  2:858051/1‑91 (MQ=255)                                                                            acGATGGCCTGGAGGTGACCGCCGTGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACCGACGATGCAACCAGCTCCggtgg          <  2:374051/90‑1 (MQ=255)                                                                               aTGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGgtgt       >  1:43721/1‑91 (MQ=255)                                                                               aTGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGgtgt       >  1:284794/1‑91 (MQ=255)                                                                                    cTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTgc  <  2:837003/91‑1 (MQ=255)                                                                                       |                                                                                        GAAAGCATTTGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGC  >  NZ_CP009273/1201540‑1201713

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑