Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,258,486	G→A	P271S (CCG→TCG)	psuK ←	pseudouridine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,258,486	0	G	A	100.0%	236.8 / NA	68	P271S (CCG→TCG)	psuK	pseudouridine kinase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (37/31);  total (37/31)

ATTTTTAATTCAGACATTCTGCGTTCTCCACTAACGATATAACGTTGGCAATCGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGGCATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGGCGCAGACCAGCCACTTTCACCGCTGATATCGCTGTAATAAACG  >  NC_000913/2258351‑2258613                                                                                                                                        |                                                                                                                                aTTTTTAATTCAGACATTCTGCGTTCTCCACTAACGATATAACGTTGGCAATCGATAAATCGGGGTTATTGGTGTATTCACCGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACAt                                                                                                                              <  2:1425360/139‑1 (MQ=255) aTTTTTAATTCAGACATTCTGCGTTCTCCACTAACGATATAACGTTGGCAATCGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAAAGACAt                                                                                                                              >  1:704428/1‑139 (MQ=255)   ttttAATTCAGACATTCTGCGTTCTCCACTAACGATATAACGTTGGCAATCGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTc                                                                                                                            >  2:517074/1‑139 (MQ=255)             gACATTCTGCGTTCTCCACTAACGATATAACGTTGGCAATCGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCa                                                                                                                  >  1:1375884/1‑139 (MQ=255)                      cGTTCTCCACTAACGATATAACGTTGGCAATCGATAAATCGGGTTTATTGGTGTATTCACAGGAGAGCGCAATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGc                                                                                                         <  2:1256322/139‑1 (MQ=255)                        ttCTCCACTAACGATATAACGTTGGCAATCGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCaa                                                                                                       <  2:1375884/139‑1 (MQ=255)                          ctcCACTAACGATATAACGTTGGCAATCGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGt                                                                                                     >  1:1379513/1‑139 (MQ=255)                           tcCACTAACGATATAACGTTGGCAATCGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAaca                                                                                                               <  2:833591/128‑1 (MQ=255)                           tcCACTAACGATATAACGTTGGCAATCGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAaca                                                                                                               >  1:833591/1‑128 (MQ=255)                           tcCACTAACGATATAACGTTGGCAATCGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTc                                                                                                    >  2:736809/1‑139 (MQ=255)                                     atatAACGTTGGCAATCGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCcatcat                                                                                          >  2:429224/1‑139 (MQ=255)                                     atatAACGTTGGCAATCGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCACTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCcatcat                                                                                          >  1:1345257/1‑139 (MQ=255)                                      tataACGTTGGCAATCGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCACTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATg                                                                                         <  2:1345257/139‑1 (MQ=255)                                        taACGTTGGCAATCGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGc                                                                                       <  1:875972/139‑1 (MQ=255)                                        taACGTTGGCAATCGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGc                                                                                       <  1:718560/139‑1 (MQ=255)                                              tGGCAATCGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGcc                                                                                 >  1:185865/1‑139 (MQ=255)                                               ggCAATCGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGccc                                                                                >  2:66563/1‑139 (MQ=255)                                               ggCAATCGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGccc                                                                                <  1:1183819/139‑1 (MQ=255)                                                gCAATCGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCg                                                                               >  1:387290/1‑139 (MQ=255)                                                     cGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGc                                                                                       <  1:141742/126‑1 (MQ=255)                                                     cGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGc                                                                                       >  2:141742/1‑126 (MQ=255)                                                      gATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCTCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCgg                                                                         >  2:874411/1‑139 (MQ=255)                                                       aTAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGt                                                                        <  2:480827/139‑1 (MQ=255)                                                       aTAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGt                                                                        <  1:874411/139‑1 (MQ=255)                                                          aaTCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAAc                                                                     <  1:770783/139‑1 (MQ=255)                                                                          gtATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGt                                                                        >  2:310504/1‑120 (MQ=255)                                                                          gtATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGt                                                                        <  1:310504/120‑1 (MQ=255)                                                                          gtATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGtt                                                     >  2:164075/1‑139 (MQ=255)                                                                            aTTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGtttt                                                   >  1:163782/1‑139 (MQ=255)                                                                             ttCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTg                                                  >  2:495854/1‑139 (MQ=255)                                                                               cacaGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGAt                                                <  1:736809/139‑1 (MQ=255)                                                                               cacaGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGAt                                                <  1:66563/139‑1 (MQ=255)                                                                                   ggAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGgc                                            >  2:557440/1‑139 (MQ=255)                                                                                    gagaGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGgcg                                           <  2:387290/139‑1 (MQ=255)                                                                                     agagCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGcc                                                                                 >  2:1403586/1‑100 (MQ=255)                                                                                     agagCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGcc                                                                                 <  1:1403586/100‑1 (MQ=255)                                                                                       agCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCcatc                                                                                            >  2:440790/1‑87 (MQ=255)                                                                                       agCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCcatc                                                                                            <  1:440790/87‑1 (MQ=255)                                                                                       agCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGcc                                                                                 <  2:1422804/98‑1 (MQ=255)                                                                                       agCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGcc                                                                                 >  1:1422804/1‑98 (MQ=255)                                                                                       agCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGgcg                                           >  2:418418/1‑136 (MQ=255)                                                                                       agCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGgcg                                           <  1:418418/136‑1 (MQ=255)                                                                                       agCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGGCGCAg                                        >  2:452644/1‑139 (MQ=255)                                                                                         cgcCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTa                                                                       >  2:282306/1‑106 (MQ=255)                                                                                         cgcCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTa                                                                       <  1:282306/106‑1 (MQ=255)                                                                                         cgcCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGGCGCAGAc                                      >  2:578928/1‑139 (MQ=255)                                                                                         cgcCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGGCGCAGAc                                      >  1:974556/1‑139 (MQ=255)                                                                                           ccATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGGCGCAGACCa                                    <  2:1379513/139‑1 (MQ=255)                                                                                              ttGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGc                                                                                       >  2:101376/1‑85 (MQ=255)                                                                                              ttGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGc                                                                                       <  1:101376/85‑1 (MQ=255)                                                                                               tGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGt                                                                        <  2:803495/99‑1 (MQ=255)                                                                                               tGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGAATCGCCCGCTCCGGt                                                                        >  1:803495/1‑99 (MQ=255)                                                                                                      cATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGt                                                                        <  1:637216/92‑1 (MQ=255)                                                                                                      cATCCCTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGt                                                                        >  2:637216/1‑92 (MQ=255)                                                                                                         cccTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGAt                                                <  2:1335870/113‑1 (MQ=255)                                                                                                         cccTGTGCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGAt                                                >  1:1335870/1‑113 (MQ=255)                                                                                                            tgtgCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGT‑ACATTAATAACATTGGTTTTGATCGGCGCAGACCAGCCACTTTCACCGCTGat                  >  1:918464/1‑139 (MQ=255)                                                                                                             gtgCGAAACGAACAGCTTCGTCAAACGACACGCCGTCTACCCAACACGAAGCAAGCCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGGCGCAGACCAGCCACTTTCACCGCTGat                  <  2:704428/139‑1 (MQ=255)                                                                                                              tgCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGGCGCAGAc                                      <  2:1487303/118‑1 (MQ=255)                                                                                                              tgCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGGCGCAGAc                                      >  1:1487303/1‑118 (MQ=255)                                                                                                              tgCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGGCGCAGACCAGCCACTTTCACCGCTGata                 >  1:1421513/1‑139 (MQ=255)                                                                                                              tgCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGCCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGgcgc                                          >  1:649859/1‑114 (MQ=255)                                                                                                              tgCGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGCCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGgcgc                                          <  2:649859/114‑1 (MQ=255)                                                                                                                cGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTaa                                                                      >  1:1218886/1‑84 (MQ=255)                                                                                                                cGAAACGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTaa                                                                      <  2:1218886/84‑1 (MQ=255)                                                                                                                   aaCGAACAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGGCGCAGACCAGCCACTTTCACCGCTGATATCGCt            >  1:1110187/1‑139 (MQ=255)                                                                                                                        aCAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGGCGCAGACCAGCCACTTTCACCGCTGATATCg              <  2:626482/132‑1 (MQ=255)                                                                                                                        aCAGATTCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGGCGCAGACCAGCCACTTTCACCGCTGATATCg              >  1:626482/1‑132 (MQ=255)                                                                                                                             ttCGGCAAACGACATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGGCGCAGACCAGCCACTTTCACCGCTGATATCGCTGTAATAAACg  <  1:557440/139‑1 (MQ=255)                                                                                                                                        |                                                                                                                                ATTTTTAATTCAGACATTCTGCGTTCTCCACTAACGATATAACGTTGGCAATCGATAAATCGGGGTTATTGGTGTATTCACAGGAGAGCGCCATTGACGAACATCCCTGTGCGAAACGAACAGATTCGGCAAACGGCATTCCGTCTACCCAACACGAAGCAAGTCCCGCCATCATGGCATCGCCCGCTCCGGTAACATTAATAACATTGGTTTTGATCGGCGCAGACCAGCCACTTTCACCGCTGATATCGCTGTAATAAACG  >  NC_000913/2258351‑2258613

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: ‑