Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,205,731	G→A	*61* (TAG→TAA)  pseudogene (1/412 nt)	ymfR → beeE →	e14 prophage, uncharacterized protein pseudogene, portal protein family, e14 prophage,Phage or Prophage Related

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,205,731	0	G	A	100.0%	144.7 / NA	45	*61* (TAG→TAA)  pseudogene (1/412 nt)	ymfR beeE	e14 prophage, uncharacterized protein pseudogene, portal protein family, e14 prophage,Phage or Prophage Related
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (22/23);  total (22/23)

TTGCTGGCGTATGGTGCCTGGCTGATTTATCCCCCGGCGGGTTTTGTTGTTGCCGGGGCGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAGTGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCGGGCTGTCGTATGACACCTATACCGGAAAGCAGATCAGCAGTCAGCGGG  >  NC_000913/1205597‑1205854                                                                                                                                       |                                                                                                                            ttGCTGGCGTATGGTGCCTGGCTGATTTATCCCCCGGCGGGTTTTGTTGTTGCCGGGGCGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGtt                                                                                                                         <  1:403891/139‑1 (MQ=255)                 ccTGGCTGATTTATCCCCCGGCGGGTTTTGTTGTTGCCGGGGCGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCtttt                                                                                                                    <  2:938695/128‑1 (MQ=255)                 ccTGGCTGATTTATCCCCCGGCGGGTTTTGTTGTTGCCGGGGCGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCtttt                                                                                                                    <  2:882164/128‑1 (MQ=255)                 ccTGGCTGATTTATCCCCCGGCGGGTTTTGTTGTTGCCGGGGCGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCtttt                                                                                                                    >  1:938695/1‑128 (MQ=255)                 ccTGGCTGATTTATCCCCCGGCGGGTTTTGTTGTTGCCGGGGCGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCtttt                                                                                                                    >  1:882164/1‑128 (MQ=255)                    ggCTGATTTATCCCCCGGCGGGTTTTGTTGTTGCCGGGGCGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCaa                                                                                                      >  2:812132/1‑139 (MQ=255)                         aTTTATCCCCCGGCGGGTTTTGTTGTTGCCGGGGCGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGaaa                                                                                                 >  1:1316955/1‑139 (MQ=255)                              tCCCCCGGCGGGTTTTGTTGTTGCCGGGGCGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGtt                                                                                                                         <  2:477810/110‑1 (MQ=255)                              tCCCCCGGCGGGTTTTGTTGTTGCCGGGGCGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACAGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGtt                                                                                                                         >  1:477810/1‑110 (MQ=255)                                ccccGGCGGGTTTTGTTGTTGCCGGGGCGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGAc                                                                                          <  2:614596/139‑1 (MQ=255)                                 cccGGCGGGTTTTGTTGTTGCCGGGGCGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACg                                                                                         <  1:1299669/139‑1 (MQ=255)                                 cccGGCGGGTTTTGTTGTTGCCGGGGCGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACg                                                                                         <  2:1316955/139‑1 (MQ=255)                                    ggcggGTTTTGTTGTTGCCGGGGCGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTg                                                                                            >  2:1020620/1‑133 (MQ=255)                                    ggcggGTTTTGTTGTTGCCGGGGAGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTg                                                                                            <  1:1020620/133‑1 (MQ=255)                                         gTTTTGTTGTTGCCGGGGCGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTg                                                                                 >  2:1004301/1‑139 (MQ=255)                                           tttGTTGTTGCCGGGGCGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGAc                                                                               >  2:503231/1‑139 (MQ=255)                                              gttgttgCCGGGGCGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCAc                                                                            <  2:475217/139‑1 (MQ=255)                                                        gggCGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGTAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGGagag                                                                  <  2:876780/139‑1 (MQ=255)                                                              tgtgCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCg                                                            >  2:896353/1‑139 (MQ=255)                                                                          ggTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCggg                                                <  2:4973/139‑1 (MQ=255)                                                                          ggTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCggg                                                <  1:896353/139‑1 (MQ=255)                                                                           gTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGaaa                                                                                                 <  1:876563/89‑1 (MQ=255)                                                                           gTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGaaa                                                                                                 >  2:876563/1‑89 (MQ=255)                                                                           gTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCGGGc                                               <  1:584280/139‑1 (MQ=255)                                                                           gTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCGGGc                                               >  1:343142/1‑139 (MQ=255)                                                                           gTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCGGGc                                               >  1:43302/1‑139 (MQ=255)                                                                                   tggtggCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCGGGCTGTCGTAt                                       <  2:343142/139‑1 (MQ=255)                                                                                     gtggCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTc                                                                                                                   <  2:554003/61‑1 (MQ=255)                                                                                     gtggCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTc                                                                                                                   >  1:554003/1‑61 (MQ=255)                                                                                                        gTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCAcc                                                                                     >  2:1189474/1‑72 (MQ=255)                                                                                                        gTACACAGTCGTCTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCAcc                                                                                     <  1:1189474/72‑1 (MQ=255)                                                                                                                tcgtcTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCggg                                                <  1:1500567/101‑1 (MQ=255)                                                                                                                tcgtcTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCggg                                                >  2:1500567/1‑101 (MQ=255)                                                                                                                tcgtcTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCGGGCTGTCGTATGACACCTATACCGGAAAg                     <  2:179104/128‑1 (MQ=255)                                                                                                                tcgtcTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCGGGCTGTCGTATGACACCTATACCGGAAAg                     >  1:179104/1‑128 (MQ=255)                                                                                                                tcgtcTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCGGGCTGTCGTATGACACCTATACCGGAAAGCAGATcagcag          >  2:1455126/1‑139 (MQ=255)                                                                                                                   tcTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCGGGCTGTCGTATGacac                                  <  2:771159/112‑1 (MQ=255)                                                                                                                   tcTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCGGGCTGTCGTATGacac                                  >  1:771159/1‑112 (MQ=255)                                                                                                                   tcTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCGGGCTGTCGTATGACACCTATACCGGAAAGCAGATCAGCAGTCa       >  2:1193754/1‑139 (MQ=255)                                                                                                                   tcTGTCGGCGGAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCGGGCTGTCGTATGACACCTATACCGGAAAGCAGATCAGCAGTCa       >  1:1180064/1‑139 (MQ=255)                                                                                                                        cggcggAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGAc                                                                                          >  2:156989/1‑51 (MQ=255)                                                                                                                        cggcggAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGAc                                                                                          <  1:156989/51‑1 (MQ=255)                                                                                                                        cggcggAGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCGGGCTGTCGTATGACACCTATACCGGAAAGCAGATCAGCAGTCAGCggg  <  1:503231/139‑1 (MQ=255)                                                                                                                              aGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCGGGCTGTCGTATGACACCTATACCGGAAAg                     >  2:823204/1‑114 (MQ=255)                                                                                                                              aGGTAAATAATGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCGGGCTGTCGTATGACACCTATACCGGAAAg                     <  1:823204/114‑1 (MQ=255)                                                                                                                                       |                                                                                                                            TTGCTGGCGTATGGTGCCTGGCTGATTTATCCCCCGGCGGGTTTTGTTGTTGCCGGGGCGCTGTGCCTGTTCTGGTCGTGGCTGGTGGCGCGATATCTCGACCGTACACAGTCGTCTGTCGGCGGAGGTAAATAGTGTTCTTTTCGGGATTATTTCAACGAAAAAGTGACGCACCGGTGACCACGCCAGCAGAGCTGGCGGATGCCATCGGGCTGTCGTATGACACCTATACCGGAAAGCAGATCAGCAGTCAGCGGG  >  NC_000913/1205597‑1205854

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑