Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,258,987	T→C	T104A (ACC→GCC)	psuK ←	putative pseudouridine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,258,987	0	T	C	100.0%	223.3 / NA	64	T104A (ACC→GCC)	psuK	putative pseudouridine kinase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (39/25);  total (39/25)

TGCCTCTTCACTGATATTACAGTCCGCGACAATGACCTTTGCCCTCTGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGTATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAATCACTGCCTACGGCGCTCAGTAG  >  NC_000913/2258853‑2259122                                                                                                                                       |                                                                                                                                        tGCCTCTTCACTGATATTACAGTCCGCGACAATGACCTTTGCCCTCTGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGcattat                                                                                                                                    >  1:559739/1‑140 (MQ=255)     tctTCACTGATATTACAGTCCGCGACAATGACCTTTGCCCTCTGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAg                                                                                                                                <  2:398916/140‑1 (MQ=255)      ctTCACTGATATTACAGTCCGCGACAATGACCTTTGCCCTCTGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGt                                                                                                                               >  2:395212/1‑140 (MQ=255)       ttCACTGATATTACAGTCCGCGACAATGACCTTTGCCCTCTGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTa                                                                                                                              <  1:441747/140‑1 (MQ=255)                   aCAGTCCGCGACAATGACCTTTGCCCTCTGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAAc                                                                                                                  >  1:115652/1‑140 (MQ=255)                   aCAGTCCGCGACAATGACCTTTGCCCTCTGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAAc                                                                                                                  >  2:606667/1‑140 (MQ=255)                    cAGTCCGCGACAATGACCTTTGCCCTCTGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACt                                                                                                                 >  1:571192/1‑140 (MQ=255)                         cgcgACAATGACCTTTGCCCTCTGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTATTAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACg                                                                                                            >  2:225697/1‑140 (MQ=255)                         cgcgACAATGACCTTTGCCCTCTGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACg                                                                                                            >  1:156745/1‑140 (MQ=255)                         cgcgACAATGACCTTTGCCCTCTGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACg                                                                                                            >  2:210700/1‑140 (MQ=255)                         cgcgACAATGACCTTTGCCCTCTGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACg                                                                                                            >  1:36866/1‑140 (MQ=255)                            gACAATGACCTTTGCCCTCTGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTAt                                                                                                         >  1:117987/1‑140 (MQ=255)                            gACAATGACCTTTGCCCTCTGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTAt                                                                                                         >  2:540669/1‑140 (MQ=255)                              cAATGACCTTTGCCCTCTGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTAttt                                                                                                       <  2:559739/140‑1 (MQ=255)                                   aCCTTTGCCCTCTGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTcc                                                                                                  >  1:208606/1‑140 (MQ=255)                                        tGCCCTCTGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGca                                                                                             <  2:115652/140‑1 (MQ=255)                                            ctctGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAAt                                                                                         <  1:606667/140‑1 (MQ=255)                                               tGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAg                                                                                      <  2:156745/140‑1 (MQ=255)                                                gAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAgg                                                                                     <  1:789462/140‑1 (MQ=255)                                                        tCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATc                                                                             <  2:279743/140‑1 (MQ=255)                                                         cACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCa                                                                                       >  2:817807/1‑129 (MQ=255)                                                         cACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCa                                                                                       <  1:817807/129‑1 (MQ=255)                                                         cACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCg                                                                            >  1:402960/1‑140 (MQ=255)                                                           ccGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAAt                                                                                         <  1:473356/125‑1 (MQ=255)                                                           ccGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAAt                                                                                         >  2:473356/1‑125 (MQ=255)                                                           ccGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAgg                                                                                     >  1:857474/1‑129 (MQ=255)                                                           ccGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAgg                                                                                     <  2:857474/129‑1 (MQ=255)                                                           ccGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGAc                                                                          >  2:763796/1‑140 (MQ=255)                                                                  gtgCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACg                                                                   <  2:117987/140‑1 (MQ=255)                                                                             tCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAgattgatt                                                        >  2:701968/1‑140 (MQ=255)                                                                             tCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAgattgatt                                                        >  1:269679/1‑140 (MQ=255)                                                                               aGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTgg                                                      <  2:571192/140‑1 (MQ=255)                                                                                 cTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGtt                                                    <  1:210700/140‑1 (MQ=255)                                                                                    tAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGc                                                 >  1:637593/1‑140 (MQ=255)                                                                                    tAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGc                                                 >  2:517164/1‑140 (MQ=255)                                                                                      aTAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGt                                               >  1:659955/1‑140 (MQ=255)                                                                                           gTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTagca                                          >  2:357594/1‑140 (MQ=255)                                                                                           gTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTagc                                           <  2:585537/139‑1 (MQ=255)                                                                                           gTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTagc                                           >  1:585537/1‑139 (MQ=255)                                                                                            ttGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTagcag                                         >  2:751006/1‑140 (MQ=255)                                                                                              gCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCg                                       >  1:230705/1‑140 (MQ=255)                                                                                              gCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCg                                       >  2:36412/1‑140 (MQ=255)                                                                                               cTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGa                                      >  2:526323/1‑140 (MQ=255)                                                                                                     ttCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGAcc                                <  2:272795/140‑1 (MQ=255)                                                                                                     ttCATGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGAcc                                <  1:36412/140‑1 (MQ=255)                                                                                                         tGTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATaa                            >  2:315725/1‑140 (MQ=255)                                                                                                          gTCATTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATaaa                           >  1:685493/1‑140 (MQ=255)                                                                                                             aTTTATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAAt                        >  1:596102/1‑140 (MQ=255)                                                                                                               ttATAGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAATCa                      >  2:290204/1‑140 (MQ=255)                                                                                                                  taGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAATCACTg                   >  1:442832/1‑140 (MQ=255)                                                                                                                   aGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAATCACTGc                  >  2:205841/1‑140 (MQ=255)                                                                                                                   aGCAACCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAATCACTGc                  >  2:74122/1‑140 (MQ=255)                                                                                                                       aCCAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAATCACTGCCTAc              >  2:854760/1‑140 (MQ=255)                                                                                                                        ccAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGTTTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAATCACTGCCTACg             >  2:321579/1‑140 (MQ=255)                                                                                                                        ccAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAATCACTGCCTACg             >  2:401604/1‑140 (MQ=255)                                                                                                                        ccAGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAATCACTGCCTACg             >  2:747442/1‑140 (MQ=255)                                                                                                                          aGCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAATCACTGCCTACGgc           <  2:269679/140‑1 (MQ=255)                                                                                                                           gCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAATCACTGCCTACGgcg          <  2:230705/140‑1 (MQ=255)                                                                                                                           gCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAATCACTGCCTACGgcg          <  1:315725/140‑1 (MQ=255)                                                                                                                           gCATTTCACCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAATCACTGCCTACGgcg          <  2:157344/140‑1 (MQ=255)                                                                                                                                  aCCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAATCACTGCCTACGgc           >  1:266178/1‑132 (MQ=255)                                                                                                                                  aCCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAATCACTGCCTACGgc           <  2:266178/132‑1 (MQ=255)                                                                                                                                  aCCGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAATCACTGCCTACGGCGCTCAGTa   <  1:321579/140‑1 (MQ=255)                                                                                                                                   ccGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAATCACTGCCTACGGCGCTCAGTAg  <  1:357594/140‑1 (MQ=255)                                                                                                                                   ccGGCATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAATCACTGCCTACGGCGCTCAGTAg  <  1:395212/140‑1 (MQ=255)                                                                                                                                       |                                                                                                                                        TGCCTCTTCACTGATATTACAGTCCGCGACAATGACCTTTGCCCTCTGAATAAATTCACCGTGCTGTGCGAGATATTCAGCTGTAATAGCGTTGCTAATATTCATGTCATTTATAGCAACCAGCATTTCACCGGTATTATCGAGTAATGATAAATAACTCGACGTATTTTCTCCCGGCACAATCAGGCATTTATCGACATAAACGCCAGATTGATTGGTTTGCGTTAGCAGCGATTGACCATAAAAATCACTGCCTACGGCGCTCAGTAG  >  NC_000913/2258853‑2259122

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑