Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	239,378	G→A	pseudogene (273/273 nt)	yafF →	pseudogene, H repeat‑associated protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	239,378	0	G	A	100.0%	90.0 / NA	29	pseudogene (273/273 nt)	yafF	pseudogene, H repeat‑associated protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (14/15);  total (14/15)

GGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCGCAT  >  NC_000913/239245‑239504                                                                                                                                      |                                                                                                                               ggATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAataata                                                                                                                           >  2:797078/1‑139 (MQ=25)               gCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAACACCCCGACTCTcccc                                                                                                             <  2:621925/139‑1 (MQ=255)                         ttttGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAac                                                                                                   <  1:34146/139‑1 (MQ=255)                         ttttGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAac                                                                                                   <  1:879790/139‑1 (MQ=255)                          tttGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAaca                                                                                                  >  2:361562/1‑139 (MQ=255)                            tGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAAcaca                                                                                                >  2:769081/1‑139 (MQ=255)                                   tGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCa                                                                                         >  2:75664/1‑139 (MQ=255)                                    gagaAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCAc                                                                                        <  2:587254/139‑1 (MQ=255)                                     agaAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACt                                                                                       <  2:364778/139‑1 (MQ=255)                                            aTTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGTCTTTCGTAATAATACCCCGACTCTCCCCGCCCTTAAACACAACCCCCACTCACcaca                                                                                >  1:109901/1‑139 (MQ=255)                                             ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACaa                                                                               >  1:23325/1‑139 (MQ=255)                                             ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACaa                                                                               >  2:705279/1‑139 (MQ=255)                                              tCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAAc                                                                              >  2:740047/1‑139 (MQ=255)                                                    cAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAac                                                                                                   >  1:279625/1‑112 (MQ=255)                                                    cAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAac                                                                                                   <  2:279625/112‑1 (MQ=255)                                                       ggTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCa                                                                     >  2:140445/1‑139 (MQ=255)                                                             gACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCa                                                               <  1:769081/139‑1 (MQ=255)                                                                  aaGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTccc                                                                                                              <  2:1515/87‑1 (MQ=255)                                                                  aaGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTccc                                                                                                              >  1:1515/1‑87 (MQ=255)                                                                           aaaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCgg                                                 <  1:656099/139‑1 (MQ=255)                                                                                 gcCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTccc                                                                                                              >  2:551493/1‑72 (MQ=255)                                                                                 gcCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTccc                                                                                                              <  1:551493/72‑1 (MQ=255)                                                                                      ggACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTtctc                                      <  1:278903/139‑1 (MQ=255)                                                                                            aaaCTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATAtt                                >  2:130403/1‑139 (MQ=255)                                                                                            aaaCTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATAtt                                >  2:529429/1‑139 (MQ=255)                                                                                              aCTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTcc                              <  1:130403/139‑1 (MQ=255)                                                                                                     ggCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAAtg                       <  1:140445/139‑1 (MQ=255)                                                                                                                ttGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGAc            <  2:726466/139‑1 (MQ=255)                                                                                                                    ggggAGCGGGCGTTCGTAATAATACGCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCCAAACTCATCCGCAGGCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCt        <  2:248463/139‑1 (MQ=255)                                                                                                                         gCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCGCa   <  2:300876/139‑1 (MQ=255)                                                                                                                          cGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCGCAt  >  1:410137/1‑139 (MQ=255)                                                                                                                                      |                                                                                                                               GGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCGCAT  >  NC_000913/239245‑239504

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑