Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	284,869	C→T	P557S (CCG→TCG)	yagF →	CP4‑6 prophage, dehydratase family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	284,869	0	C	T	100.0%	113.8 / NA	36	P557S (CCG→TCG)	yagF	CP4‑6 prophage, dehydratase family protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (17/19);  total (17/19)

CTACCAGCTCACCTCCGCGCTAAAGCATATCTCGTGGGGCAAGACGGTGTCGCTCATCACCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGCCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGTCTGACGTTAACTGGCAGCGTGAACTTCATCGGCACCGCGGACAACCCGCTGACGCCGGAAGAGGGCGC  >  NC_000913/284736‑284987                                                                                                                                      |                                                                                                                       cTACCAGCTCACCTCCGCGCTAAAGCATATCTCGTGGGGCAAGACGGTGTCGCTCATCACCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGAtt                                                                                                                   >  2:904983/1‑139 (MQ=255)        cTCACCTCCGCGCTAAAGCATATCTCGTGGGGCAAGACGGTGTCGCTCATCACCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGTGCGGGTCGATTGGCAAGc                                                                                                            <  1:1042909/139‑1 (MQ=255)            ccTCCGCGCTAAAGCATATCTCGTGGGGCAAGACGGTGTCGCTCATCGCCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTgcg                                                                                                        <  1:962584/139‑1 (MQ=255)            ccTCCGCGCTAAAGCATATCTCGTGGGGCAAGACGGTGTCGCTCATCACCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTgcg                                                                                                        <  2:1718554/139‑1 (MQ=255)                       aaGCATATCTCGTGGGGCAAGACGGTGTCGCTCATCACCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGAca                                                                                             <  2:1446457/139‑1 (MQ=255)                               ctcGTGGGGCAAGACGGTGTCGCTCATCACCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCgag                                                                                     >  2:451564/1‑139 (MQ=255)                                tcGTGGGGCAAGACGGTGTCGCTCATCACCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCgaga                                                                                    <  1:295584/139‑1 (MQ=255)                                tcGTGGGGCAAGACGGTGTCGCTCATCACCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCgaga                                                                                    <  1:451564/139‑1 (MQ=255)                                tcGTGGGGCAAGACGGTGTCGCTCATCACCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCgaga                                                                                    <  1:904983/139‑1 (MQ=255)                                   tGGGGCAAGACGGTGTCGCTCATCACCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTg                                                                                 >  2:771467/1‑139 (MQ=255)                                   tGGGGCAAGACGGTGTCGCTCATCACCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTg                                                                                 >  2:223306/1‑139 (MQ=255)                                    ggggCAAGACGGTGTCGCTCATCACCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGc                                                                                >  1:428102/1‑139 (MQ=255)                                                  tCGCTCATCACCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGTCTGa                                                                  <  2:895996/139‑1 (MQ=255)                                                     cTCATCACCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGTCTGACGt                                                               >  1:1522913/1‑139 (MQ=255)                                                               aTGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGTCTGACGTTAACTGGCAg                                                     >  1:272363/1‑139 (MQ=255)                                                                         ctcGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTg                                                                                                          <  2:154254/76‑1 (MQ=255)                                                                         ctcGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTg                                                                                                          >  1:154254/1‑76 (MQ=255)                                                                         ctcGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGTCTGACGTTAACTGGCAGCGTGAACTTc                                           >  2:116195/1‑139 (MQ=255)                                                                                gtgtCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGTCTGACGTTAACTGGCAGCGTGAACTTCATCGGCa                                    <  2:1522913/139‑1 (MQ=255)                                                                                 tgtCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGAcatcat                                                                                         <  2:965385/85‑1 (MQ=255)                                                                                 tgtCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGAcatcat                                                                                         >  1:965385/1‑85 (MQ=255)                                                                                 tgtCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGTc                                                                     >  2:1856137/1‑105 (MQ=255)                                                                                 tgtCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGTc                                                                     <  1:1856137/105‑1 (MQ=255)                                                                                 tgtCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGTCTGACGTTAACTGGCAGCGTTAACTTCATCGGCAc                                   >  1:1198817/1‑139 (MQ=255)                                                                                   tCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAg                                                                                                             <  1:504351/63‑1 (MQ=255)                                                                                   tCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAg                                                                                                             >  2:504351/1‑63 (MQ=255)                                                                                   tCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGTCTGACGTTAAc                                                           <  2:1629431/113‑1 (MQ=255)                                                                                   tCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGTCTGACGTTAAc                                                           >  1:1629431/1‑113 (MQ=255)                                                                                   tCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGTCTGACGTTAACTGGCAGCGTGAACTTCATCGGCACcg                                 >  1:584158/1‑139 (MQ=255)                                                                                     gACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGTCTGACGTTAACTGGCAGCGTGAACTTCATCGGCACcgcg                               <  2:1180055/139‑1 (MQ=255)                                                                                                gCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGTCTGACGTTAACTGGCAGCGTGAACTTCATCGGCACCGCGGACAACCCGCt                    <  1:771467/139‑1 (MQ=255)                                                                                                  ttCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGTCTGACGTTAACTGGCAGCGTGAACTTCATCGGCACCGCGGACAACCCGCTGa                  <  1:880451/139‑1 (MQ=255)                                                                                                  ttCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGTCTGACGTTAACTGGCAGCGTGAACTTCATCGGCACCGCGGACAACCCGCTGa                  <  1:116195/139‑1 (MQ=255)                                                                                                         aCGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGt                                                                      >  1:630008/1‑80 (MQ=255)                                                                                                         aCGTGTCGCCGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGt                                                                      <  2:630008/80‑1 (MQ=255)                                                                                                                  cGGAGGCGCTGGCGGGCGGGTCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGTCTGACGTTAACTGGCAGCGTGAACTTCATCGGCACCGCGGACAACCCGCTGACGCCGGAAGAGGgcgc  >  1:44426/1‑139 (MQ=255)                                                                                                                                      |                                                                                                                       CTACCAGCTCACCTCCGCGCTAAAGCATATCTCGTGGGGCAAGACGGTGTCGCTCATCACCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTCGCCGGAGGCGCTGGCGGGCGGGCCGATTGGCAAGCTGCGCGATAACGACATCATCGAGATTGCCGTGGATCGTCTGACGTTAACTGGCAGCGTGAACTTCATCGGCACCGCGGACAACCCGCTGACGCCGGAAGAGGGCGC  >  NC_000913/284736‑284987

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑