BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	3,839,567	G→C	10.9%	L143V (CTT→GTT)	nlpA ←	lipoprotein‑28

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,839,567	0	G	C	10.9%	73.9 / 4.0	35	L143V (CTT→GTT)	nlpA	lipoprotein‑28
Reads supporting (aligned to +/- strand): ref base G (16/15); new base C (2/2); total (18/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.11e-01

CTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGTAATAACCCTTTTCCCTCTT‑TCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGATTTTTTTGGAATAACCCGCCATAGGGAAGACAAACGTATTTCCCACCGCTACCAGTTTATAACCATGCGCCTGA  >  NC_000913/3839433‑3839703

cTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGTAATAACCCTTTTCCCTCTT‑TCAGAGTAATTAGCTTCTCTTTTTGCGACTGTCAAATTGCGCGACCTTGGTTgttgg                                                                                                                                  >  1:300307/1‑139 (MQ=255)

 tGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGTAATAACCCTTTTCCCTCTT‑TCAGCGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTggtcgg                                                                                                                                 >  2:288001/1‑143 (MQ=255)

  gcgcCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATAGCCAGCGCGGTAGGTAATAACCCTTTTCCCTCTT‑TCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAACCTTggtcgcg                                                                                                                                <  2:162435/143‑3 (MQ=255)

   cgcCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGTAATAACCCTTTTCCCTCTT‑TCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTggtcgggt                                                                                                                               >  1:470879/1‑143 (MQ=255)

        ccTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGTAATAACCCTTTTCCCTCTT‑TCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTg                                                                                                                          >  1:348344/1‑143 (MQ=255)

                         tGCAAGTGACGAGGACAATCCGTTATACCCATCGAGGTAGGTAATAACCCTTTTCCCTCTT‑TCAGAGTTATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTcgc                                                                                                         <  2:3016/143‑1 (MQ=255)

                         tGCAAATTACGGGGATTATCTGTTATATCCAGCGCGGTAGTTAATAACACTTTTCGCTCTT‑TCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTcgc                                                                                                         <  2:149468/143‑1 (MQ=255)

                                   gAGGATTATCGGTTATATCCAGCGCGGTAGGTAATAACCCTTTTCCCTCTT‑TCAGAGTAATGAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCTACTGTCGAGCCTCCtttt                                                                                               >  2:283205/1‑143 (MQ=255)

                                          aTCGGTTATATCCAGCGCGGTAGGTAATAACCCTTTTCCCTCTT‑TCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTgcg                                                                                        <  1:445626/143‑1 (MQ=255)

                                           tCGGTTATATCCAGCGCGGTAGGTAATAACCATTTTCCCTCTT‑TCAGGTGAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTgcgc                                                                                       >  1:241797/1‑143 (MQ=255)

                                               ttATATCCAGCGCGGTAGGTAATAACCCTTTTCCCTCTT‑TCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAGAAATGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTCCTTTTATTTgcgcggcg                                                                                   >  2:171006/1‑139 (MQ=255)

                                               ttATATCCAGCGCGGTAGGTAATAACCCTTTTCCCTCTT‑TCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGGCACg                                                                                   >  1:290035/1‑143 (MQ=255)

                                                  tatCCAGCGCGGTAGGTAATACCCCTTTTTCCTCTT‑TCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGTTCGTTGTGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGtt                                                                                <  2:224778/143‑1 (MQ=255)

                                                    tCCAGCGCGGTAGGTAATAACCCTTTTCCCTCTT‑TCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGtttt                                                                              <  1:168337/143‑1 (MQ=255)

                                                              tatgtaATAACCCTTTTCCCTCTTCTCTG‑GTAATTATCTTCTCTTCTTTCCACTGTAAAAGTTCCCGACCAAGGTTGCTCGGGTCGTTGTGTATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGATTTTTTTg                                                                    <  2:297855/140‑1 (MQ=255)

                                                              taggtaATAACCCTTTTACCTCTT‑TCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAGGGTTGGTGGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGACACGGTTTTGATTTTTTTg                                                                    >  1:239346/1‑143 (MQ=255)

                                                               agttaataaCCCTTGTCCCTCGT‑TCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGATTTTTTTgg                                                                   <  1:83027/140‑1 (MQ=255)

                                                               aggtaATAACCCTTTTCCCTCTT‑TCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGAGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGATTTTTTTgg                                                                   <  1:267399/143‑1 (MQ=255)

                                                                 gtaATAACCCTTTTCCCTCTT‑TCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGCTTTTTTTGGaa                                                                 >  2:156609/1‑143 (MQ=255)

                                                                 gtaATAACCCTTTTCCCTCTT‑TCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGATTTTTTTGGaa                                                                 <  1:44867/143‑1 (MQ=255)

                                                                   aatatCCCTTTTCCTTTTT‑TCTGAGTAATTAGTTTCTCTTTTTGCAACAGTAAAAGTGCGCGACTAAGTTTGGTCGGGTTGTTGGGGATCGCTACTGTTGCGTATTCTTTTATTTGCGTCATGGTTTTGATTTTTTTGGAATa                                                               <  2:267035/143‑1 (MQ=255)

                                                                             ttCCCTTTT‑TCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGTATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGATTTTTTTGGAATAACCCGCCATa                                                     <  2:179565/143‑1 (MQ=255)

                                                                                    tt‑tCAGAGTAATTAGCTTCTCTTTTTGCAACCGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCGACTGTCGCGCCTTCTTTTGTTTGCGCCACGGTGTTCATTTTCTTCGTATAACCGGCCAGACCGAAGa                                              >  2:364872/1‑143 (MQ=255)

                                                                                               aTTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGA‑TTTTTTGGAATAACCCGCCATAGGGAAGACAAACGTAttt                                   <  1:40601/143‑1 (MQ=255)

                                                                                                   gCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCCTTTATTTGCGGCACGGGTTTGATTCTTTTGGAATATTCCGTCTTAGGTACGTCAAACGTATTTtcc                                >  2:54996/1‑143 (MQ=255)

                                                                                                     ttCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGATTTTTTTGGCATAACGCGCCATAGGGAAGACAAGCGTAttctctag                              >  2:247233/1‑137 (MQ=255)

                                                                                                                    aGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGATTTTTTTGGACTAACACGCCATATCTATGACACACATATTTCCCACAGCTACCAGTTtatc               >  2:162053/1‑142 (MQ=255)

                                                                                                                    aGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGATTTTTTTGGAATAACCCGCCATAGGGAAGACACACGTATTTCCCACCGCTACCCGCTtaga               >  1:388897/1‑141 (MQ=255)

                                                                                                                       aaaaGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTCTTTGCGCCACGGTTTTGATTTTTTTGGCATAACCCACCATAGGGAAGACAAACGTATTTCCCACCGCTACCAGTGCATAAcc            >  1:93198/1‑143 (MQ=255)

                                                                                                                         gagggcgcGACCAAGGGTGGGCGGGTCGGTGGGGATCGCCACGGGCGCGCCTTCTTTTATTTGCGCCCCGGTTTGGATCTTTTTGGAATAACCCGCCATAGGGAAGACAAACGTATTTCCCACCGCTACCAGTTTATAACCAt          <  1:144895/139‑1 (MQ=255)

                                                                                                                            tGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGATTTTTTTGGAATAACCCGCCATAGGGAAGACAAACGTATTTCCCACCGCTACCAGTTTATAACCATgcg       <  1:271871/143‑1 (MQ=255)

                                                                                                                              cccgACCAACCTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGATTTTTTTGGCATCTCCCGCCATCGGGAAGACAAACGTATTTAACACCAATACCAGTTTATAACAATGCGcc     >  1:25301/3‑143 (MQ=255)

                                                                                                                               gcgGCCGAGGTTGGGCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCGCGGTTTTGATTTTTTTGGAATAACCCGCCATAGGGAAGACAAACGTTTTTCGTCCTGCTAGCAGTTTATAACCATGCGCCt    <  2:286085/143‑1 (MQ=255)

                                                                                                                               ccgACCAACCTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGATTTGATTTTTTTGGAGTAACCCGCCATAGTGCAGACAAACGTATCTCCCCCTCCTACCAGTTTATAACCATGCGCCt    >  2:308229/2‑143 (MQ=255)

                                                                                                                                 gcgcAACGTTTGTCGGGTCGTTGGGGCTCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGATTTTTTTGGAATAACCCGCCATAGGGAAGACAAACGTATTTCCCACCGCTACCAGTTTATAACCATGCGCCTGa  <  1:399522/140‑1 (MQ=255)

CTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGTAATAACCCTTTTCCCTCTT‑TCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGATTTTTTTGGAATAACCCGCCATAGGGAAGACAAACGTATTTCCCACCGCTACCAGTTTATAACCATGCGCCTGA  >  NC_000913/3839433‑3839703

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`