BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,614,185	T→C	15.4%	D129D (GAT→GAC)	USA300HOU_RS08000 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,614,185	0	T	C	15.4%	52.4 / 3.8	30	D129D (GAT→GAC)	USA300HOU_RS08000	hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (11/13); new base C (2/2); total (14/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.58e-01

TTATCAGTTGTTAATTGAGCAACAGATTGCAAAATTGAATGCAGCAAAGCCTTTTTCATCTGTTATATTACCAATAACTCCAGTCTTTGAACGCATCATCAAGGCCAACTATCCAGACTATGATTATAATCAGGAAACAGCAACAGATCCTTTTATTGTAGACCATCACATGCGCCGTGATCGTTCAGAAGTGATTGCAGCAAAAGAAGAAGCGATTCAATTAAGAAAACATAGACGTAATTAATCAACCAATTTAAAAA  >  USA300TCH1516_ALE/1614062‑1614321

ttagtaGTTGTTAGTTGAGCAATGGATTGAAAAATTGAATGCAGCAAAGCCTTATTTATCTGTTATATTACCAATATCTACAGTCTTTGAACACATCATCAAGGCTAACTATCCAGACTATGATTATAATCAGGAAACAGc                                                                                                                         <  2:84583/136‑1 (MQ=255)

       ttgttAATTGAGCAACAGATTGCAAAATTGAATGCAGCAAAGCCTTTTTCATCTGTTATATTACCAATAACTCCAGTCTTTGAACGCATCATCAAGGCCAACTATCCAGACTATGATTATAATCAGGAAACAGCAACAGAt                                                                                                                  <  2:105615/141‑1 (MQ=255)

           tAATTGAGCAACAGATTGCAAAATTGAATGCAGCAAAGCCTTTTTCATCTGTTATATTACCAATAACTCCAGTCTTTGAACGCATCATCAAGGCCAACTATCCAGACTATGATTATAATCAGGAAACAGCAACAGATCCtt                                                                                                              <  1:170603/141‑1 (MQ=255)

            aaTTGAGCAATAGATTGCAAAATTGAATGCAGCAAAGCCTTTTTCATCTGTTATATTACCAATAACTCCAGTCTTTGAACGCATCATCAAGGCCAACTATCCAGACTATGATTATAATCAGGAAACAGCAACAGATCCttt                                                                                                             <  2:294893/141‑1 (MQ=255)

            aaTTGAGCAACAGATTGCAAAATTGAATGCAGCAAAGCCTTTTTCATCTGTTATATTACCAATAACTCCAGTCTTTGAACGCATCATCAAGGCCAACTATCCAGACTATGATTATAATCAGGAAACAGCAACAGCTCCttt                                                                                                             >  1:299598/1‑141 (MQ=255)

                gAGCAACAGATTGCAAAATTGAATGCAGCAAAGCCTTTTTCATCTGTTATATTACCAATAACTCCAGTCTTTGAACGCATCATCAAGGCCAACTATCCAGACTATGATTATAATCAGGAAACAGCAACAGATCCTTTTAtt                                                                                                         >  1:341051/1‑141 (MQ=255)

                 aGCAACAGATTGCAAAATTGAATGCAGCAAAGCCTTTTTCATCTGTTATATTACCAATAACTCCAGTCTTTGAACGCATCATCAAGGCCAACTATCCAGACTATGATTATAATCAGGAAACAGCAACAGATCCTTTTATTg                                                                                                        >  1:48416/1‑141 (MQ=255)

                  gCAACAGATTGCAAAATTGAATGCAGCAAAGCCTTTTTCATCTGTTATATTACCAATAACTCCAGTCTTTGAACGCATCATCAAGGCCAACTATCAAGACTATGATTATAATCAGGACACAGAAACAGATCCTTTTACTGt                                                                                                       >  2:282718/1‑141 (MQ=255)

                       aGATTGCAAAATTGAATGCAGCAAAGCCTTTTTCATCTGTTATATTACCAATAACTCCAGTCTTTGAACGCAGGATCAAGGCCAACTATCCAGACTATGATTATAATCAGGAAACAGCAACAGATCCTTTTATTGTAGAcc                                                                                                  >  1:289829/1‑141 (MQ=255)

                         aTTGCAAAATTGAATGCAGCAAAGCCTTTTTCATCTGTTATATTACCAATAACTCCAGTCTTTGAACGCATCATCAAGGCCAACTATCCAGACTATGATTATCATCAGGAAACAGGAACAGATCCTTTTATTGTAGACCAt                                                                                                >  1:154462/1‑141 (MQ=255)

                                      aTGCAGCAAAGCCTTTTTCATCTGTTATATTACCAATAACTCCAGTCTTTGAACGCATCATCAAGGCCAACTATCCAGACTATGATTATAATCAGGAAACAGCAACAGATCCTTTTATTGTAGACCATCACATGCGCCGTg                                                                                   <  2:10244/141‑1 (MQ=255)

                                            caAAGCGTTTTTCATGTGTTATATTACCAATAACGCGAGTCTTTGAACGCATCATCAAGGCCAACTATCCAGACTATGATTATAATCAGGAAACAGCAACAGATCCTTTTATTGTAGACCATCACATGCGCCGTGATCGtt                                                                             <  2:407855/141‑1 (MQ=255)

                                                  cTTTGTCATCTGTTATATTACCAATAACTCCAGTCTTTGAACGCATCATCAAGGCCAACTATCCAGACTATGATTATAATCAGGAAACAGCAACAGATCCTTTTATTGTAGACCATCACATGCGCCGTGATCGTTCAGAAg                                                                       <  2:163331/141‑1 (MQ=255)

                                                     tttCATCTGTTATATTACCAATAACTCCAGTCTTTGAACGCATCACCAAGGCCAACTATCCAGCCTATGATTATAATCACGAAACACCAACAGATCCTCTTACTGTAGACCATCACATGCGCCGCCGTCGTTCCGAAGTGa                                                                    >  2:134722/1‑141 (MQ=255)

                                                        cATCTGTTATATTACCAATAACTCCAGTCTTTGAACGCATCATCAAGGCCAACTATCCAGACTATGATTATAATCAGGAAACAGCAACAGATCCTTTTATTGTAGACCATCACATGCGCCGTGATCGTTCAAAAGTGAttc                                                                 >  2:79642/1‑140 (MQ=255)

                                                                     aCCAATAACTCCAGTCTTTGAACGCATCATCAAGGCCAACTATCCAGACTATGACTATAATCAGGAAACAGCAACAGATCCTTTTATTGTAGACCATCACATGCGCCGTGATCGTTCAGAAGTGATTGCAGCAAaagaaga                                                    >  2:265148/1‑141 (MQ=255)

                                                                     aCCAATAACTCCAGTCTTTGAACGCATCATCAAGGCCAACTATCCAGACTATGACTATAATCAGGAAACAGCAACAGATCCTTTTATTGTAGACCATCACATGCGCCGTGATCGTTCAGAAGTGATTGCAGCAAaagaaga                                                    >  2:60847/1‑141 (MQ=255)

                                                                               ccAGTCTTTGAACGCATCATCAAGGCAAACTATCAAGACTATGAAGATAATCAGGAAACAGCAACAGATCCTTTTATTGTAGACCATCACATGCGCCGTGATCGTTCAGAAGTGATTGCAGCAAAAGAAGAAGCGATTCaa                                          >  1:332231/1‑141 (MQ=255)

                                                                                  gTCTTTGAACGCATCATCAAGGCCAACTATCCAGACTATGATTATAATCAGGAAACAGAAACACAGCCTTTTATTGTAGACCATCACATGCGCCGTGATCGTTCAGAAGTGATTGCAGCAACAGAAGACGCGATTCACttc                                       >  2:258512/1‑140 (MQ=255)

                                                                                     tttGAACGCATCATCAAGGCCAACTATCCAGACTATGATTATAATCAGGAAACAGCAACAGATCCTTTTATTGTAGACCATCACATGCGCCGTGATCGTTCAGAAGTGATTGCAGCAAAAGAAGAAGCGATTCAATTAAGa                                    <  1:411/141‑1 (MQ=255)

                                                                                        gAACGCATCATCAAGGCCAACTATCCAGACTATGATTATAATCAGGAAACAGCAACAGATCCTTTTATTGTAGACCATCACATGCGCCGTGATCGTTCAGAAGTGATTGCAGCAAAAGAAGAAGCGATTCAATTAAGaaaa                                 <  1:149833/141‑1 (MQ=255)

                                                                                                   caAGGCCGACTATCCAGACTATGAATATAAGCAGGAAAGGGCAACAGATCCTTTTATTGGAGACCATCACATGCGCCGTGATCGTTCAGAAGTGATTGCAGCAAAAGAAGAAGCGATTCAAATCAGGTACCAGAGACGtaa                      <  2:154462/141‑1 (MQ=255)

                                                                                                       gacAACTATCCAGATTATGATTATAATCAGGAAACGTGAACAGATACTTCGATGGTGTACCATCACATGCGCCGTGAGCGTTCAGAAGTGATTGCAGCAAAAGAAGAAGCGATTCAATTAAGAAAACATAGACGtaattaa                  <  2:148683/139‑1 (MQ=255)

                                                                                                        ccAACTATCCAGACTATGATTATAATCAGGAAACAGCAACAGATCTTTTTATTGTAGACCATCACATGCGCCGTGATCGTTCAGAAGTGATTGCAGCACAAGAAGAAGCGATTCAATAAAGAAACCATAGACGtaattaat                 >  2:42605/1‑141 (MQ=255)

                                                                                                          aaCTATCCAGACTATGATTATAATCAGGAAACAGCAACAGATCCTTTTATTGTAGACCATCACATGCGCCGTGATCGTTCAGAAGTGATTGCAGCAAAAGAAGAAGCGATTCAATTAAGAAAACATAGACGTAATTAATCa               >  1:245135/1‑141 (MQ=255)

                                                                                                               tCCAGACTATGACTATAATCAGGAAACAGCAACAGATCCTTTTATTGTAGACCATCACATGCGCCGTGATCGTTCAGACAAGATTTCAGCAAAAGAAGAAGCGATTCAATTAAGAAAACATAGACGTAATTAATCAACCaa          <  1:60847/141‑1 (MQ=255)

                                                                                                               tCCAGACTATGACTATAATCAGGAAACAGCAACAGATCCTTTTATTGTAGACCATCACATGCGCCGTGATCGTTCAGAAGTGATTGCAGCAAAAGAAGAAGCGATTCAATTAAGAAAACATAGACGTAATTAATCAACCaa          <  1:265148/141‑1 (MQ=255)

                                                                                                                 cAGACTATGATTATAATCAGGAAACAGCAACAGATCCTTTTATTGTAGACCATCACATGCGCCGTGATCGTTCAGAAGTGATTGCAGCAAAAGAAGAAGCGATTCAATTAAGAAAACATAGACGTAATTAATCAACCAAtt        <  1:234188/141‑1 (MQ=255)

                                                                                                                  aGAATATGATTATAATCAGGAAACAGCAACAGATACTTTTAGTGTAGACCATCAGATGCGGCGTGATCGTTCAGAAGTGATTGCAGCAAAAGAAGAAGCGATTCAATTAAGAAAACATAGACGTAATTAATCAACCAAttt       <  2:163478/141‑1 (MQ=255)

                                                                                                                       aTGATTATAATCAGGAAACAGCAACAGATCCTTTTATTGTAGACCATCACATGCGCCGTGATCGTTCAGAAGTGATTGCAGCAAAAGAAGAAGCGATTCAATTAAGAAAACATAGACGTAATTAATCAACCAATTTaaaaa  <  1:52570/141‑1 (MQ=255)

TTATCAGTTGTTAATTGAGCAACAGATTGCAAAATTGAATGCAGCAAAGCCTTTTTCATCTGTTATATTACCAATAACTCCAGTCTTTGAACGCATCATCAAGGCCAACTATCCAGACTATGATTATAATCAGGAAACAGCAACAGATCCTTTTATTGTAGACCATCACATGCGCCGTGATCGTTCAGAAGTGATTGCAGCAAAAGAAGAAGCGATTCAATTAAGAAAACATAGACGTAATTAATCAACCAATTTAAAAA  >  USA300TCH1516_ALE/1614062‑1614321

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`