Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	239,358	G→A	pseudogene (169/189 nt)	yafF →	putative uncharacterized protein YafF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	239,358	0	G	A	100.0%	200.9 / NA	61	pseudogene (169/189 nt)	yafF	putative uncharacterized protein YafF
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (37/24);  total (37/24)

GAAACGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGAC  >  NC_000913/239221‑239494                                                                                                                                          |                                                                                                                                         gAAACGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACg                                                                                                                                        >  2:770670/1‑140 (MQ=18)  aaaCGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTGAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACgg                                                                                                                                       >  2:1328886/1‑140 (MQ=18)                            tACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATAcccc                                                                                                             >  1:1160025/1‑140 (MQ=12)                                     ttGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTccc                                                                                                    <  1:257983/140‑1 (MQ=255)                                     ttGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCAGGCTTTCGTAGTAATACCCCGACTCTccc                                                                                                    <  1:634135/140‑1 (MQ=255)                                      tGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATAcc                                                                                                               <  2:1356577/128‑1 (MQ=14)                                      tGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATAcc                                                                                                               >  1:1356577/1‑128 (MQ=2)                                        cTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATAcccc                                                                                                             <  1:574920/128‑1 (MQ=18)                                        cTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATAcccc                                                                                                             >  2:574920/1‑128 (MQ=12)                                         tATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTc                                                                                                >  1:776144/1‑140 (MQ=255)                                           ttAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCt                                                                                              >  1:1440496/1‑140 (MQ=255)                                                  tttGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCg                                                                                                  >  1:710363/1‑129 (MQ=255)                                                  tttGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCg                                                                                                  <  2:710363/129‑1 (MQ=255)                                                  tttGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAacac                                                                                       >  1:1128921/1‑140 (MQ=255)                                                  tttGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAacac                                                                                       >  1:52273/1‑140 (MQ=255)                                                   ttGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCg                                                                                                  >  2:451689/1‑128 (MQ=255)                                                   ttGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCg                                                                                                  <  1:451689/128‑1 (MQ=255)                                                           tgataaGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAAccc                                                                                  >  2:793781/5‑136 (MQ=255)                                                           tGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAAccc                                                                                  <  1:793781/136‑1 (MQ=255)                                                                aGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcacc                                                                         <  2:1440496/140‑1 (MQ=255)                                                                 ggTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcacca                                                                        <  2:52273/140‑1 (MQ=255)                                                                    aTTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACaa                                                                     >  1:1432884/1‑140 (MQ=255)                                                                     ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAAc                                                                    >  1:509981/1‑140 (MQ=255)                                                                     ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAAc                                                                    >  1:827989/1‑140 (MQ=255)                                                                      tCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcacca                                                                        <  2:205589/135‑1 (MQ=255)                                                                      tCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcacca                                                                        >  1:205589/1‑135 (MQ=255)                                                                       cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcacc                                                                         >  1:641333/1‑133 (MQ=255)                                                                       cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcacc                                                                         <  2:641333/133‑1 (MQ=255)                                                                             aGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTc                                                            >  2:197160/1‑140 (MQ=255)                                                                             aGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTc                                                            >  2:948887/1‑140 (MQ=255)                                                                               ggTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCAt                                                          >  1:47487/1‑140 (MQ=255)                                                                                gTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATc                                                         >  1:590820/1‑140 (MQ=255)                                                                                   aaGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGc                                                      >  2:431486/1‑140 (MQ=255)                                                                                    aGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCAt                                                          <  1:1210553/135‑1 (MQ=255)                                                                                    aGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCAt                                                          >  2:1210553/1‑135 (MQ=255)                                                                                    aGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCa                                                     <  2:827989/140‑1 (MQ=255)                                                                                    aGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCa                                                     <  1:948887/140‑1 (MQ=255)                                                                                    aGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCa                                                     <  2:1128921/140‑1 (MQ=255)                                                                                         tAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATccgg                                                >  2:1403832/1‑138 (MQ=255)                                                                                         tAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTg                                                >  1:921301/1‑140 (MQ=255)                                                                                         tAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTg                                                <  2:509981/140‑1 (MQ=255)                                                                                         tAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTg                                                >  1:591284/1‑140 (MQ=255)                                                                                           aGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGcc                                              >  1:1324716/1‑140 (MQ=255)                                                                                                cGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGcc                                         >  2:607992/1‑140 (MQ=255)                                                                                                 gAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGTCg                                        >  1:430067/1‑140 (MQ=255)                                                                                                  aaaaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCgg                                       <  2:641617/140‑1 (MQ=255)                                                                                                   aaaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGa                                      <  1:197160/140‑1 (MQ=255)                                                                                                     agcagcCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGaaa                                    <  2:1432884/140‑1 (MQ=255)                                                                                                          ccATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCT‑CCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTtc                              >  2:162254/1‑140 (MQ=255)                                                                                                            aTGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTtct                             <  2:591284/140‑1 (MQ=255)                                                                                                             tGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTtctc                            <  2:921301/140‑1 (MQ=255)                                                                                                                         aCCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCa                <  2:776144/140‑1 (MQ=255)                                                                                                                          ccTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCaa               >  2:426272/1‑140 (MQ=255)                                                                                                                          ccTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCaa               >  1:1255030/1‑140 (MQ=255)                                                                                                                          ccTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCaa               >  2:1200705/1‑140 (MQ=255)                                                                                                                          ccTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCaa               >  1:748204/1‑140 (MQ=255)                                                                                                                            tGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAAtg             <  1:322854/140‑1 (MQ=255)                                                                                                                              gCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAAtgct           >  1:1292970/1‑140 (MQ=255)                                                                                                                              gCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAAtgct           >  1:416830/1‑140 (MQ=255)                                                                                                                                    gTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGcc        <  2:1224877/137‑1 (MQ=255)                                                                                                                                    gTCCTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGcc        >  1:1224877/1‑137 (MQ=255)                                                                                                                                       cTTACGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGAc  <  1:1200705/140‑1 (MQ=255)                                                                                                                                          |                                                                                                                                         GAAACGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGAC  >  NC_000913/239221‑239494

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: ‑