BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,307,294	A→T	12.3%	L169Q (CTG→CAG)	alsK ←	D‑allose kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,307,294	0	A	T	12.3%	85.5 / 5.0	42	L169Q (CTG→CAG)	alsK	D‑allose kinase
Reads supporting (aligned to +/- strand): ref base A (18/17); new base T (2/3); total (21/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.61e-01

GCGTTTTCCGCATGGACGAAAAGATCGCGCAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAGAACCAGTTGTTGCGTAAGGCGGTTTTCTACTA  >  NC_000913/4307153‑4307429

gCGTTTTCCGCCTGAAAGAAACGATCGCGCATTGGTTAATTTCGGGGCTGTTGTGCGTACCAGCGTCTTAGCGCCATTCGAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAg                                                                                                                                        <  2:92701/143‑1 (MQ=255)

gCGTTTTCCGCATGGACGAAAAGATCGCGCAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGGTTGCCGCACGCGCAGTGTTGGGTCATCTCTCGCAg                                                                                                                                        >  1:137220/1‑143 (MQ=255)

 cGTTTTCCGCATGGACGAAAAGATCGCGCAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCAAGGCACCCAGGATTGCCACACGCGCAGTGTTGGCTCATATCTCCCAgg                                                                                                                                       >  1:557304/1‑143 (MQ=255)

  gTTTTTCGCTTGGACGATAAGATCGCGCAATGGGTAAGTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGGGGCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAggg                                                                                                                                      <  1:736839/143‑1 (MQ=255)

  gTTTTCCGCATGGACGGACAGATCGCGGAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAggg                                                                                                                                      <  1:402505/143‑1 (MQ=255)

    ttgccGCATGGACGAAACGCTCGCGCAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGCATTAGCGCCATGCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAggggg                                                                                                                                    <  2:763791/140‑1 (MQ=255)

         gCATGGACGAAAAGATCGCGCAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGCCATCTCTCCGAGGGGGATATg                                                                                                                               >  1:647499/1‑143 (MQ=255)

         gCATGGACGAAAAGATCGCGCAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGAACATATCTCCCAggggggcatg                                                                                                                               >  2:639911/1‑138 (MQ=255)

          cATGGACGAAAAGATCGCGCAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCCCCCTGGGAGATATGa                                                                                                                              <  1:85535/143‑1 (MQ=255)

           aTGGACGAAAAGATCGCGCAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCCCTCTGGGAGATATGAc                                                                                                                             <  1:943512/143‑1 (MQ=255)

            tGGACGAAAAGATCGCGCAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGAcc                                                                                                                            >  1:669170/1‑143 (MQ=255)

                      gcgcgccCAATGGGTCTTTTCGGGGCTGTCGCTCGTACCAGCGTCTTAGCGCCCTTCCAGAGCAATTGGTTTCGAGGCACCCAGGATAGCCACACGCGCAGTTTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCt                                                                                                                  <  2:248153/140‑1 (MQ=255)

                           cgcAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCAAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTTCTATGTCCCAGGTGGATATGACCCACTTCGCGTGCcac                                                                                                             >  2:600611/1‑143 (MQ=255)

                                     caTTGCGCGGCTGTTGTTCGTACGAGTGTCTTAGCGCCATTTCAGGGCAATTGGTTGCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGGCATATCTCCCAGGGGGGTATGACCCAGTTCGCCTGCCACACCGTGTGCa                                                                                                   <  2:262222/142‑1 (MQ=255)

                                        ttCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCGGGGGGATATGACCCAGTTGGCCTGCCACACCGCGTCCGccc                                                                                                >  1:29216/1‑143 (MQ=255)

                                                                   ttAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACt                                                                     <  1:135047/143‑1 (MQ=255)

                                                                    tAGCGCCATCCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTGGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTg                                                                    <  2:434873/143‑1 (MQ=255)

                                                                      ccgcCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCg                                                                  <  1:566000/142‑1 (MQ=255)

                                                                                 gatcAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATccc                                                       <  1:142369/140‑1 (MQ=255)

                                                                                    gagttGGTTTCCAGGCACCCAGGAGTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGt                                                    <  2:820602/140‑1 (MQ=255)

                                                                                     agtgtgTTGCCTGGCTCTCAGCATTGCCTCACGCGCAGTGTTGGGTCATATCTCCCTGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTa                                                   <  1:386745/138‑1 (MQ=255)

                                                                                        tGGTTTCCAGGCCCCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCg                                                <  1:549087/143‑1 (MQ=255)

                                                                                          gTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCGGCCACACCGTGTGCGCCCGTCCACGGCGCGCCGTTCATCTCCACTGCGACCCCCGTCGCCGtcgcgtg                                              >  1:126820/1‑137 (MQ=255)

                                                                                                aGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACGGCGAACCCCATCCCCGTACCGAGATAGgc                                        >  1:345321/1‑143 (MQ=255)

                                                                                                aGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATAGGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCAGCCACACTGCGAACCCCGTACCCGTCACGAGATAGgc                                        >  1:827188/1‑143 (MQ=255)

                                                                                                 ggCCCCCAGGAGTGCCACACGCGCAGTGTTGGGTCATAGCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGGCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGgcc                                       <  1:217380/143‑1 (MQ=255)

                                                                                                 ggCACCCAGGATTGCCACACGCGCAGTGTTGGGACATATCTCCCAGGGGGATATGACCCAGTTCGCCCACCGCCCCGTGTGCACCCGGCCACGGCGCACCGCTCATCCACCGTGCGAACCCCATCCCCCTACCGCGACCGgcc                                       >  2:765262/1‑143 (MQ=255)

                                                                                                  gCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTACACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGGACCGGGATAGgccg                                      >  1:850634/1‑143 (MQ=255)

                                                                                                      ccAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAg                                  >  1:918923/1‑143 (MQ=255)

                                                                                                       cAGGATTGCCACACGCGCAGGGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATc                                                                           >  1:388236/1‑101 (MQ=255)

                                                                                                       cAGGATTGCCACACGCGCAGGGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATc                                                                           <  2:388236/101‑1 (MQ=255)

                                                                                                        aGGATTGCCACAGGCGCAGTTTTGGGTCATACCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTTTGCACCCGTCCACGCCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAGaa                                <  2:482306/143‑1 (MQ=255)

                                                                                                         ggATTGCCACACGCGCAGTGTTGAGTCATCTCTCACACACACATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAGAAc                               <  1:390799/143‑1 (MQ=255)

                                                                                                                   tcgtgcAGTGTTGTGTCATATCTCCCAGTGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCTCATCCCCGTACCGAGATAGGCCGCCAGAACCAGTTGTTGc                     <  1:88703/139‑1 (MQ=255)

                                                                                                                   acGCGCAGTGTTGGGTCATATCTCCCAGGGGGCTATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACCCTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAGAACCAGGTGTTGc                     >  1:645939/1‑143 (MQ=255)

                                                                                                                           tgtTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCGCCCGTCCACGGCGCACCGTTCATCCACACTGCGCACCCCATCCCCGTACCGAGATAGGCCGCCAGAACCAGTTGTTGCGTAAGGcc             >  1:415405/1‑142 (MQ=255)

                                                                                                                             ttGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAGAACCAGTTGTTGCGTAAGGCGGt           >  1:762727/1‑143 (MQ=255)

                                                                                                                             ttGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAGAACCAGTAGTTGCGTAAGGCGGt           >  1:245071/1‑143 (MQ=255)

                                                                                                                                ggTCATATCCCCCTGGGAGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCCGAACCAGTTGTTGCGTAAGGCGGttta        >  1:778742/1‑142 (MQ=255)

                                                                                                                                 gTCTTATCGCCCGGTGTGAGATGCCCCCGTCCGCCGCCCACACCGTGTGCACCCGACCCCGGCGCCACGGTGATCTACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAGAACCAGTTGTTGCGTAAGGCGGTTTTc       <  2:173793/143‑1 (MQ=255)

                                                                                                                                  tCATATCCCCCTGGGAGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAGAACCAGTTGTTGCGTAAGGCGGTTTTct      >  1:533628/1‑143 (MQ=255)

                                                                                                                                      atCTCCCAGGGGGATATGACCCAGTTCTCCTGCCACACCCTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTCCGAACCCCATCCCCGTACCGAGATAGGCCCCCAGAACACGTTATTGCGAAAGGCGGTTTTatccta  >  2:368879/1‑143 (MQ=255)

GCGTTTTCCGCATGGACGAAAAGATCGCGCAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAGAACCAGTTGTTGCGTAAGGCGGTTTTCTACTA  >  NC_000913/4307153‑4307429

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: `‑`