Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,520,503	T→C	intergenic (‑179/+168)	yjhU ← / ← yjhF	KpLE2 phage‑like element; putative DNA‑binding transcriptional regulator YjhU/KpLE2 phage‑like element; putative transporter YjhF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,520,503	0	T	C	100.0%	181.8 / NA	52	intergenic (‑179/+168)	yjhU/yjhF	KpLE2 phage‑like element; putative DNA‑binding transcriptional regulator YjhU/KpLE2 phage‑like element; putative transporter YjhF
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (25/27);  total (25/27)

CTGTTTACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACATGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATGGGGGACAGTG  >  NC_000913/4520368‑4520638                                                                                                                                        |                                                                                                                                        cTGTTTACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTc                                                                                                                                     <  2:776608/140‑1 (MQ=255) cTGTTTACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTc                                                                                                                                     <  1:822922/140‑1 (MQ=255) cTGTTTACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTc                                                                                                                                     <  2:663967/140‑1 (MQ=255) cTGTTTACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTc                                                                                                                                     <  2:208161/140‑1 (MQ=255)    tttACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGGATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCgg                                                                                                                                  >  2:775591/1‑140 (MQ=255)    tttACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCgg                                                                                                                                  >  2:430262/1‑140 (MQ=255)    tttACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCgg                                                                                                                                  >  2:433672/1‑140 (MQ=255)    tttACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCgg                                                                                                                                  >  1:201399/1‑140 (MQ=255)    tttACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCgg                                                                                                                                  >  2:249332/1‑140 (MQ=255)       aCCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCtt                                                                                                                               <  2:330808/140‑1 (MQ=255)         ccGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTa                                                                                                                             <  2:651422/140‑1 (MQ=255)         ccGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTa                                                                                                                             <  1:596094/140‑1 (MQ=255)           ggAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACa                                                                                                                           <  2:612446/140‑1 (MQ=255)           ggAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACa                                                                                                                           <  1:775591/140‑1 (MQ=255)            gagaGTTGATGCAGATTGCCAGTGGCATGA‑TTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGt                                                                                                                         >  1:272756/1‑140 (MQ=255)             agagTTGATGCAGATTGCCAGTGGCATGA‑TTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTa                                                                                                                        <  2:272756/140‑1 (MQ=255)              gagTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTa                                                                                                                        >  1:760492/1‑140 (MQ=255)              gagTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTa                                                                                                                        >  1:679432/1‑140 (MQ=255)                  tGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTAc                                                                                                                    >  1:101903/1‑140 (MQ=255)                   gATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACt                                                                                                                   <  1:749105/140‑1 (MQ=255)                     tGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTga                                                                                                                 <  2:679432/140‑1 (MQ=255)                              ccAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACAcc                                                                                                        <  2:352473/140‑1 (MQ=255)                                       tGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCa                                                                                               <  1:134657/140‑1 (MQ=255)                                              ataCAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGa                                                                                        <  2:431598/140‑1 (MQ=255)                                               taCAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGaa                                                                                       >  2:232359/1‑140 (MQ=255)                                                            ttCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGc                                                                          >  2:16247/1‑140 (MQ=255)                                                              cTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGa                                                                                        >  2:469814/1‑124 (MQ=255)                                                              cTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGa                                                                                        <  1:469814/124‑1 (MQ=255)                                                                 ttACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCtt                                                                     >  2:329471/1‑140 (MQ=255)                                                                                       ccATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCa                                               <  1:713742/140‑1 (MQ=255)                                                                                       ccATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAAGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCa                                               <  1:565235/140‑1 (MQ=255)                                                                                        cATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCAc                                              <  2:370712/140‑1 (MQ=255)                                                                                        cATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCAc                                              >  2:361339/1‑140 (MQ=255)                                                                                             gAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGc                                         >  2:98253/1‑140 (MQ=255)                                                                                              aGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCa                                        <  1:361339/140‑1 (MQ=255)                                                                                                 gATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGAc                                     >  2:764692/1‑140 (MQ=255)                                                                                                   tCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACgg                                   <  1:16247/140‑1 (MQ=255)                                                                                                             ttCCCCCATACTGTAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGtcac                         >  1:810985/1‑140 (MQ=255)                                                                                                                          tAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATg            >  2:142049/1‑140 (MQ=255)                                                                                                                          tAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATg            <  1:249332/140‑1 (MQ=255)                                                                                                                          tAAAGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATg            >  1:595946/1‑140 (MQ=255)                                                                                                                            aaGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATggg          >  1:30068/1‑140 (MQ=255)                                                                                                                            aaGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATggg          >  2:567517/1‑140 (MQ=255)                                                                                                                            aaGCCGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATggg          <  1:345293/140‑1 (MQ=255)                                                                                                                               ccGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATGGGGGa       <  1:98253/140‑1 (MQ=255)                                                                                                                               ccGGAGACACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATGGGGGa       >  1:480224/1‑140 (MQ=255)                                                                                                                                  gagaCACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATGGGGGa       >  2:658965/1‑137 (MQ=255)                                                                                                                                  gagaCACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATGGGGGa       <  1:393678/137‑1 (MQ=255)                                                                                                                                  gagaCACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATGGGGGa       <  1:658965/137‑1 (MQ=255)                                                                                                                                  gagaCACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATGGGGGa       >  2:393678/1‑137 (MQ=255)                                                                                                                                  gagaCACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATGGGGGACAg    >  1:731246/1‑140 (MQ=255)                                                                                                                                    gaCACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATGGGGGACAGTg  >  1:386923/1‑140 (MQ=255)                                                                                                                                    gaCACGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATGGGGGACAGTg  <  2:598285/140‑1 (MQ=255)                                                                                                                                        |                                                                                                                                        CTGTTTACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGCCGGAGACATGCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATGGGGGACAGTG  >  NC_000913/4520368‑4520638

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: ‑