Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,071,500	A→G	noncoding (184/195 nt)	isrC →	novel sRNA, CP4‑44, putative prophage remnant

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,071,500	0	A	G	100.0%	122.7 / NA	33	noncoding (184/195 nt)	isrC	novel sRNA, CP4‑44, putative prophage remnant
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (16/17);  total (16/17)

CCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAA  >  NC_000913/2071369‑2071633                                                                                                                                    |                                                                                                                                      ccTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCtt                                                                                                                                >  2:43151/1‑139 (MQ=255)     tGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCtttttt                                                                                                                            >  2:99035/1‑139 (MQ=255)     tGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCtttttt                                                                                                                            >  2:316740/1‑139 (MQ=255)     tGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCtttttt                                                                                                                            >  1:170288/1‑139 (MQ=255)      gTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTa                                                                                                                           >  2:243281/1‑139 (MQ=255)      gTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTa                                                                                                                           >  1:402744/1‑139 (MQ=255)        cAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTAtt                                                                                                                         <  1:43151/139‑1 (MQ=255)        cAGAAACATGCACAAATACGTACAGAAAGACATTCAGGGAACAACAGACCCACATTTCAGAAACCCCCACAGCGGGACCCCCGGCATTGTAACCCTTTCCCTGCCGGTATCCACGTTTGGGGGGGCCGGTTTTTTTAtc                                                                                                                         <  1:294826/139‑2 (MQ=255)                       aTACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAg                                                                                                          >  1:550878/1‑139 (MQ=255)                                        ttCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACg                                                                                         <  1:316740/139‑1 (MQ=255)                                         tCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTAtt                                                                                                                         >  1:220939/1‑106 (MQ=255)                                         tCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTAtt                                                                                                                         <  2:220939/106‑1 (MQ=255)                                           aGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACa                                                                                      >  2:114007/1‑139 (MQ=255)                                                acaacaGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGa                                                                                 <  1:99035/139‑1 (MQ=255)                                                acaacaGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGa                                                                                 <  2:170288/139‑1 (MQ=255)                                                    caGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATAc                                                                             <  1:114007/139‑1 (MQ=255)                                                       aaCCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCt                                                                                                                   <  1:36289/98‑1 (MQ=255)                                                       aaCCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCt                                                                                                                   >  2:36289/1‑98 (MQ=255)                                                                 cAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTg                                                                >  1:127070/1‑139 (MQ=255)                                                                      aCTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATg                                                           <  1:31665/139‑1 (MQ=255)                                                                        tCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGa                                                         <  2:402744/139‑1 (MQ=255)                                                                                          ggCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCt                                                                                                                   <  2:58638/63‑1 (MQ=255)                                                                                          ggCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCt                                                                                                                   >  1:58638/1‑63 (MQ=255)                                                                                          ggCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCtt                                       <  1:243281/139‑1 (MQ=255)                                                                                              cTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCt                                                                                                                   >  1:547366/1‑59 (MQ=255)                                                                                              cTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCt                                                                                                                   <  2:547366/59‑1 (MQ=255)                                                                                               tGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATc                                                                                    <  2:400523/89‑1 (MQ=255)                                                                                               tGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATc                                                                                    >  1:400523/1‑89 (MQ=255)                                                                                                 tAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGa                                                                                        >  2:286025/1‑83 (MQ=255)                                                                                                 tAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGa                                                                                        <  1:286025/83‑1 (MQ=255)                                                                                                                   tATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCcg              <  2:550878/139‑1 (MQ=255)                                                                                                                        aCGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAGTCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCAc         <  2:82991/139‑1 (MQ=255)                                                                                                                               tgGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTaa  >  1:126455/1‑139 (MQ=255)                                                                                                                                    |                                                                                                                                      CCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAA  >  NC_000913/2071369‑2071633

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑