Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,520,500	Δ1 bp	8.0%	intergenic (‑176/+171)	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	4,520,500	0	A	.	8.0%	134.3 / 7.0	50	intergenic (‑176/+171)	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 A (20/26);  new base . (2/2);  total (22/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.06e-01

TCTTAACCCTGTTTACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATGGGGGACA  >  NC_000913/4520360‑4520635                                                                                                                                              |                                                                                                                                         tCTTAACCCTGTTTACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACa                                                                                                                                        >  1:607390/1‑143 (MQ=255)        ccTGTTTACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACGATTTGAGCGATCGCCCGCTGTTCCCCCACACTG‑AACGCACGGCGACAtc‑ctccc                                                                                                                                >  2:4694/1‑142 (MQ=255)        ccTGTTTACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CCCCg                                                                                                                                >  2:686923/1‑143 (MQ=255)         gtGTTTACCCGGAGAGTGGAGGCAGGTTTCCACTGGCCTGGGTTTGTGCGGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAG‑CATGTCTCCgg                                                                                                                               <  2:280978/142‑1 (MQ=255)         cTGTTTACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTTCgg                                                                                                                               >  1:457917/1‑143 (MQ=255)         cTGTTTACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCgg                                                                                                                               >  1:435686/1‑143 (MQ=255)            tttCCCGGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGTGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCtt                                                                                                                            <  1:510325/143‑1 (MQ=255)            tttACCCGGAGAGTTGATGCAGATTGCAAGTGGCACGAGTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCtt                                                                                                                            <  2:357076/143‑1 (MQ=255)              tACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCTCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTa                                                                                                                          <  1:527276/143‑1 (MQ=255)              tACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTa                                                                                                                          <  1:532622/143‑1 (MQ=255)                 ccGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAg                                                                                                                       >  1:428559/1‑143 (MQ=255)                 ccGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CCCCGGCTTTACAg                                                                                                                       >  2:763022/1‑143 (MQ=255)                  cGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGt                                                                                                                      <  2:717343/143‑1 (MQ=255)                   ggAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCTGGCTTTACAGTa                                                                                                                     >  1:246436/1‑143 (MQ=255)                      gagTTGATGCAGATTGCCAGTGGCATGATTTTAGACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAG‑CATGTCTCCGGCTTTACAGTAtgg                                                                                                                  <  1:139573/143‑3 (MQ=38)                          tGATGCATATTGCCAGCGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCTTACCATTTGAGCGATCGCCCGCTGTCCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTga                                                                                                              <  2:781823/143‑1 (MQ=255)                             tGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGaa                                                                                                           <  1:125559/143‑1 (MQ=255)                              gCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTGACAGTATTACTGAGAAt                                                                                                          >  2:182209/1‑143 (MQ=255)                               cAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGCGACGTG‑CTCCGGCTTTACAGGAGTAGTGAGAATa                                                                                                         >  1:398224/1‑143 (MQ=255)                                aGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACCTC‑CTCCGCCTCTACAGTATTACTCAGAAtcc                                                                                                        >  2:342831/1‑141 (MQ=255)                                 gATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATaca                                                                                                       <  1:51864/143‑1 (MQ=255)                                  aTTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTTCCCGCTACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATacac                                                                                                      >  1:593023/1‑143 (MQ=255)                                  aTTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATacac                                                                                                      >  1:521884/1‑143 (MQ=255)                                       cAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACCGTATTACTGAGACTACACCCATc                                                                                                 >  1:439402/1‑143 (MQ=255)                                          tGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAg                                                                                              <  1:716554/143‑1 (MQ=255)                                                      ataCAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAgg                                                                                  <  1:673497/143‑1 (MQ=255)                                                          aGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCa                                                                              <  1:323973/143‑1 (MQ=255)                                                          aGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCAATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAAAATAGACCCATCAAGCATAATCGAAGGTTcc                                                                              >  2:118903/1‑142 (MQ=255)                                                                tttATTCTTTTACATGAAATAAACCCTCGGGGCATTGGAGCGATCGCCCGCTGTGCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCg                                                                        <  2:199881/143‑1 (MQ=255)                                                                       ttttGCATGAAATAAACCAGCATACCATTTGAGCGACCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGCACACATG‑CTCCGGTTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCttt                                                                 <  2:252693/143‑1 (MQ=255)                                                                       ttttACATAAAATAAACCAGAATAACAAGGGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGGGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCttt                                                                 <  1:48009/143‑1 (MQ=255)                                                                         tgacacGAACTAAGCCGGCATCCCATTTGAGCGGTCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCttttt                                                               <  2:527039/141‑1 (MQ=255)                                                                             ctGAAATACACCAGCATCCCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAACTGTATTTAAGGTTCAATATGGTCCCTTTTTGATc                                                           <  2:758625/142‑1 (MQ=255)                                                                                    aaaCCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACGGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCg                                                    <  1:57451/143‑1 (MQ=255)                                                                                                 aTTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTg                                       <  1:293539/143‑1 (MQ=255)                                                                                                  tgtGAGCGACCTGCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGc                                      <  2:262734/141‑1 (MQ=255)                                                                                                            cGCCCGCTGGCCCCCCATACGGTAAAGC‑CGGAGACATG‑CGCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCTTACTCGAAGGTTTAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGc                            <  1:342831/143‑1 (MQ=255)                                                                                                             gCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTAGTCACCGTGCGGCCGGGTGcc                           >  1:625698/1‑143 (MQ=255)                                                                                                              cccGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCATGCAGACGGTTGCCg                          <  2:435686/143‑1 (MQ=255)                                                                                                                    gTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGtcactc                    <  1:445826/143‑1 (MQ=255)                                                                                                                     ttCCCCCCCACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAACCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGtcactca                   <  1:264247/143‑1 (MQ=255)                                                                                                                        ccccATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTa                >  1:63921/1‑143 (MQ=255)                                                                                                                        ccccATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGGTGCCGTCACTCACTa                >  1:516798/1‑143 (MQ=255)                                                                                                                                tGTAACGC‑CGGAGACATA‑CTCCTGCTTTACAGTATTACTGACAATTCACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATgg        <  1:221476/143‑1 (MQ=255)                                                                                                                                tGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAAGACACCCATCAAGCATAATCGAAGGTTCACTACCGGCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATgg        <  1:114715/143‑1 (MQ=255)                                                                                                                                 gTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCCTTTTGATCACCAGCGACTCGTCACCGTTCAGCCGGTTGCCGTCACACACTAAATTAAggc       >  2:735048/1‑142 (MQ=255)                                                                                                                                     aGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTCGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATGGGGGAc   >  2:242461/1‑143 (MQ=255)                                                                                                                                     aGC‑CGGAG‑CATGTCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGCTTCGTCACCGCGCAGACGGTTGCCGTCACGCACTAACTTAttgcggcc   >  2:32875/1‑136 (MQ=255)                                                                                                                                     aGC‑CGGAG‑CATGTCTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATGGGGGAc   >  2:327573/1‑143 (MQ=255)                                                                                                                                      gC‑CGGAGACAGG‑CTCCGGCTTTACAGTATTACCGAGAATGCACCCATCAAGCATAATCGAAGGTTCAAGATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATGGGGGACa  <  2:188459/143‑1 (MQ=255)                                                                                                                                              |                                                                                                                                         TCTTAACCCTGTTTACCCGGAGAGTTGATGCAGATTGCCAGTGGCATGATTTTATACAGATATTTTATTCTTTTACATGAAATAAACCAGCATACCATTTGAGCGATCGCCCGCTGTTCCCCCATACTGTAAAGC‑CGGAGACATG‑CTCCGGCTTTACAGTATTACTGAGAATACACCCATCAAGCATAATCGAAGGTTCAATATCGCCCCTTTTTGATCGCCAGCGATTCGTCACCGTGCAGACGGTTGCCGTCACTCACTAAATTATGGGGGACA  >  NC_000913/4520360‑4520635

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑