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%	89.6 / NA	25	pseudogene (34/786 nt)	BW25113_RS05980	baseplate J/gp47 family protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (10/15);  total (10/15)

CTGTCTGTGCCTGAGGGGAAACTTTTACGCCTACAAAGTGAAAGCATTTGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGT  >  NZ_CP009273/1201501‑1201742                                                                                                                              |                                                                                                                     ctgtctgtGCCTGAGGGGAAACTTTTACGCCTACAAAGTGAAAGCATTTGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCgg                                                                                                         <  2:264872/139‑1 (MQ=255)   gtctgtGCCTGAGGGGAAACTTTTACGCCTACAAAGTGAAAGCATTTGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCgg                                                                                                         >  2:301161/1‑137 (MQ=255)    tctgtGCCTGAGGGGAAACTTTTACGCCTACAAAGTGAAAGCATTTGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCggta                                                                                                       <  1:221175/138‑3 (MQ=255)    tctgtGCCTGAGGGGAAACTTTTACGCCTACAAAGTGAAAGCATTTGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAg                                                                                                      >  1:663647/1‑139 (MQ=255)              aGGGGAAACTTTTACGCCTACAAAGTGAAAGCATTTGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAg                                                                                            >  1:278936/1‑139 (MQ=255)                     aCTTTTACGCCTACAAAGTGAAAGCATTTGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATg                                                                                     <  2:278936/139‑1 (MQ=255)                                      gTGAAAGCATTTGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACg                                                                    <  1:301161/139‑1 (MQ=255)                                           aGCATTTGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAAc                                                               >  2:396207/1‑139 (MQ=255)                                                        gTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAAcc                                                  <  2:65008/139‑1 (MQ=255)                                                               aaCTGCTGCCCGTCGGTCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCg                                           <  1:182544/139‑1 (MQ=255)                                                               aaCTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTc                                             <  1:606706/137‑1 (MQ=255)                                                                       cccGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTc                                   <  1:396207/139‑1 (MQ=255)                                                                         cGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATg                                                                                     <  1:190581/87‑1 (MQ=255)                                                                         cGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATg                                                                                     >  2:190581/1‑87 (MQ=255)                                                                                        tgtgGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACTACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGc                  >  1:192651/1‑139 (MQ=255)                                                                                        tgtgGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGc                  <  2:452250/139‑1 (MQ=255)                                                                                          tgGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGcc                 <  1:766229/138‑1 (MQ=255)                                                                                               tatGCGCTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTc            <  2:401249/138‑1 (MQ=255)                                                                                                    gcTGGGAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTg       >  1:401723/1‑138 (MQ=255)                                                                                                       gggAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTc            >  2:72545/1‑130 (MQ=255)                                                                                                       gggAAGGTGTCAGCGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTc            <  1:72545/130‑1 (MQ=255)                                                                                                                    cGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGt  <  1:396965/127‑1 (MQ=255)                                                                                                                    cGATGGCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGGGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGt  >  2:396965/1‑127 (MQ=255)                                                                                                                         gCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTc            <  2:594195/112‑1 (MQ=255)                                                                                                                         gCCTGGAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTc            >  1:594195/1‑112 (MQ=255)                                                                                                                              |                                                                                                                     CTGTCTGTGCCTGAGGGGAAACTTTTACGCCTACAAAGTGAAAGCATTTGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGT  >  NZ_CP009273/1201501‑1201742

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑