BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,455,698	2 bp→AT	coding (1216‑1217/1260 nt)	lyrA →	Lysostaphin resistance protein A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,455,698	0	C	A	90.7%	328.2 / 28.9	109	coding (1216/1260 nt)	lyrA	Lysostaphin resistance protein A
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (38/60); minor base . (7/3); total (46/63)
Fisher's exact test for biased strand distribution p-value = 8.97e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.96e-01
*	USA300TCH1516_ALE	2,455,699	0	A	T	97.2%	328.2 / ‑5.2	111	H406L (CAT→CTT)	lyrA	Lysostaphin resistance protein A
Reads supporting (aligned to +/- strand): ref base A (0/3); new base T (48/58); total (48/63)
Fisher's exact test for biased strand distribution p-value = 2.54e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 111 total aligned reads displayed.

CAGAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTG  >  USA300TCH1516_ALE/2455561‑2455837

||

cagAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGaaaaaa                                                                                                                                 >  2:1046591/1‑149 (MQ=255)

cagAAGCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGaaaaaa                                                                                                                                 >  2:470500/1‑149 (MQ=255)

        gTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTgaagaa                                                                                                                         <  1:601488/149‑1 (MQ=255)

        gTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTgaagaa                                                                                                                         >  1:999884/1‑149 (MQ=255)

        gTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTgaagaa                                                                                                                         >  1:114183/1‑149 (MQ=255)

            aaCAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAAt                                                                                                                     >  2:300347/1‑149 (MQ=255)

                aGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTc                                                                                                                 >  1:771148/1‑149 (MQ=255)

                  caccacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAg                                                                                                               <  2:325727/149‑1 (MQ=255)

                   accacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGa                                                                                                              <  1:160266/149‑1 (MQ=255)

                    ccacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGAt                                                                                                             <  1:778030/149‑1 (MQ=255)

                      acaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAAACTTCAACTTAGAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAAATAAAGAACAATCTTCAGATaa                                                                                                           >  2:512137/1‑149 (MQ=255)

                       caAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaaa                                                                                                          >  2:825128/1‑149 (MQ=255)

                        aaaGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaaaa                                                                                                         <  1:321418/149‑1 (MQ=255)

                         aaatGACGATTAAACAAACGAGCAAAATGAAGATGAAATAGAGAAATTATTAAAAGAACCTGCAACTTATAAAGAAGACAGATGTTCATTAGTTGAAAATGAAAAA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaaaaa                                                                                                        <  2:758738/146‑1 (MQ=255)

                         aaGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaaaaa                                                                                                        >  2:173061/1‑149 (MQ=255)

                         aaGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaaaaa                                                                                                        <  1:1008549/149‑1 (MQ=255)

                          aGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAAc                                                                                                       >  1:919701/1‑149 (MQ=255)

                          aGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaaaaaa                                                                                                       >  1:1008733/1‑148 (MQ=255)

                           gTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACa                                                                                                      >  1:901669/1‑149 (MQ=255)

                            tGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACaa                                                                                                     <  2:340341/149‑1 (MQ=255)

                             gACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCAGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACaaa                                                                                                    >  1:492783/1‑149 (MQ=255)

                             caCGATGTAACAAACGATTGAACAGCAGATGAAATAGCGCAATCATTAAAAGAACCTGCGACTCAGAAAGAAGACAGACGCTCAGCGGTCGCAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAATCaac                                                                                                    <  2:295212/148‑2 (MQ=255)

                                gATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGGAGAACAATCTTCAGATAAAAACAaataa                                                                                                 <  1:679733/149‑1 (MQ=255)

                                 aTTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGACAATGCGACTTATCAAGAAGCCAGACGTTCATCAGTTGTAATTGCTGCA‑AAAACATTCTAGAAAAACCTGACGAACCATCTAAAGATAAAAACAcataaa                                                                                                >  2:88633/1‑148 (MQ=255)

                                      aCAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACaa                                                                                           >  1:837293/1‑149 (MQ=255)

                                      aCAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACaa                                                                                           >  1:479971/1‑149 (MQ=255)

                                        aaaCGATTAAAAGGAAGATGAAATAGAGTAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAg                                                                                         <  1:278917/149‑1 (MQ=255)

                                         aaCGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAgc                                                                                        >  1:688750/1‑149 (MQ=255)

                                         aaCGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCATCAAATAAAAACAAATAATAACAAAga                                                                                        >  2:473230/1‑148 (MQ=255)

                                           cGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAATATTTGT‑GGCTTAACTGAAGTGGAAACTTTCGTAAAAAACAAATAATAACAAAgcgc                                                                                      >  1:254853/1‑149 (MQ=255)

                                              ttCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTg                                                                                   <  2:423613/149‑1 (MQ=255)

                                               tCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGc                                                                                  <  1:58141/149‑1 (MQ=255)

                                               tCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTGATAAAGAAGACAGACGTTAATGAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGAGCTTGc                                                                                  >  2:142868/1‑149 (MQ=255)

                                                  aaTGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGACAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTCGCTAg                                                                               >  2:411707/1‑149 (MQ=255)

                                                   actaaaaTGAAATAGAGCAATCATTAAAACAACCAGCGACTTATAAAGAAGACAGACGTTTATCAGTTGAAAAAAAAAAA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGt                                                                              <  2:925525/143‑1 (MQ=255)

                                                   aagaagaagaaATAGTGCAATCATGAAAAGAACCTGCAACATATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGGTAAAAACAAATAATAACAAAGCGCTTGCTAGt                                                                              <  2:76540/147‑1 (MQ=255)

                                                    agAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTa                                                                             <  1:1099968/148‑1 (MQ=255)

                                                    agAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTa                                                                             <  1:291361/148‑1 (MQ=255)

                                                      aaGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGAGGGGTGTTGACCAGTTGTAATTGCTGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAAAAAAGCGCTGGCTAGTAcc                                                                           >  2:442151/1‑149 (MQ=255)

                                                      aaGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTAcc                                                                           >  2:1005749/1‑149 (MQ=255)

                                                       aGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACct                                                                          <  1:48242/149‑1 (MQ=255)

                                                        gATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACTATCTTCAGATAAAAACAAGTATTAACAAAGCGCTTGCTAGTACctc                                                                         <  1:626131/149‑1 (MQ=255)

                                                        gATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctc                                                                         >  2:585515/1‑149 (MQ=255)

                                                        gATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctc                                                                         <  1:526066/149‑1 (MQ=255)

                                                        gATGAAATAGAGCAATCATTAAAAGAACCTGCGAATTATAAAGAAAACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAAATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctc                                                                         <  2:338781/149‑1 (MQ=255)

                                                           gAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTa                                                                      <  1:56556/149‑1 (MQ=255)

                                                           gAAAAAGAGCAATCATTAAAAGAACCTGCAACTTAGAAAGAAGACAGACGTTCATCAGTTGTAATCGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTa                                                                      <  2:6206/149‑1 (MQ=255)

                                                            aaaTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCATGCTAGTACCTCTTaa                                                                     >  1:681321/1‑149 (MQ=255)

                                                              aTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaa                                                                   <  2:341444/149‑1 (MQ=255)

                                                              aTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaa                                                                   <  1:290223/149‑1 (MQ=255)

                                                              aTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaa                                                                   >  2:227911/1‑149 (MQ=255)

                                                              aTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAAAAGATGAA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaa                                                                   <  2:931775/149‑1 (MQ=255)

                                                               tAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaaa                                                                  <  1:173061/149‑1 (MQ=255)

                                                                agagCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAg                                                                 >  1:965409/1‑149 (MQ=255)

                                                                   gCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatg                                                              <  1:823394/149‑1 (MQ=255)

                                                                    cAATCATTAAAAGAACCTTCGATGCATAAATAAGACATACGTTCATCCGTTGTAATTTAT‑CGAAAAAAATTATAGAAACATCTTAAGCACAATTTTCATATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatga                                                             <  2:342481/149‑1 (MQ=255)

                                                                    cAAGCATGAAAAGAGCCTGCGACGTATAAAGAAGACAGAGGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatga                                                             <  2:228198/149‑1 (MQ=255)

                                                                     aaTCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCTAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatgat                                                            >  1:154833/1‑149 (MQ=255)

                                                                      aTCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGatgatg                                                           <  1:656254/149‑1 (MQ=255)

                                                                       tCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGc                                                          >  2:648543/1‑149 (MQ=255)

                                                                        cATTAAAAGAACCTGTGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCt                                                         <  1:697889/149‑1 (MQ=255)

                                                                          ttAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAg                                                       >  1:339594/1‑149 (MQ=255)

                                                                            aaaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCa                                                     <  1:423965/149‑1 (MQ=255)

                                                                            aaaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAAATGATGCTAGCa                                                     >  1:18172/1‑149 (MQ=255)

                                                                            aaaaGAACCTGCGACTAATAAAGAAGACCGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCa                                                     <  1:324723/149‑1 (MQ=255)

                                                                              aaGAACCTGCGACTTATAAAGAAGACAGACGTTGAGCAGTTGTAATTGATGCA‑AAAAAATTATCGAAGAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAg                                                   >  2:580509/1‑149 (MQ=255)

                                                                              aaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAACAAAATGATGCTAGCAAg                                                   >  2:538083/1‑149 (MQ=255)

                                                                              aaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTGGCTAGTACCTCTTAAAAAGATGATGCTAGCAAg                                                   >  2:584554/1‑149 (MQ=255)

                                                                              aaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTCGCTAGTACCTCTTAAAAAGATGATGCTAGCAAg                                                   >  2:527920/1‑149 (MQ=255)

                                                                               aGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAACATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAACAGATGATGCTAGCAAgc                                                  >  1:1053007/1‑149 (MQ=255)

                                                                                gAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAACCAAACAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcg                                                 <  1:869937/149‑1 (MQ=255)

                                                                                aaaCCTGTGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcg                                                 <  2:857007/148‑1 (MQ=255)

                                                                                aaaCCTGCGACACACAAAAAAGAAAGACGCTCATCATTTGTAATTGATGCA‑AAAAAAAAAAAAAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcg                                                 <  2:634495/148‑1 (MQ=255)

                                                                                 acccTGCGACTGATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgc                                                <  2:326066/147‑1 (MQ=255)

                                                                                 aaCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgc                                                <  1:396670/149‑1 (MQ=255)

                                                                                 aaCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgc                                                <  2:114183/149‑1 (MQ=255)

                                                                                 aaCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgc                                                <  2:496848/149‑1 (MQ=255)

                                                                                 aaCCTGCGACTTAAAAAGAAGACAGACGTTCATCAGTTGTAATAGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTAACTCTTAAAAAGATGATGCTAGCAAgcgc                                                <  2:801551/149‑1 (MQ=255)

                                                                                     tGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCtttt                                            <  1:132100/149‑1 (MQ=255)

                                                                                      gCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTc                                           <  1:844897/149‑1 (MQ=255)

                                                                                         aattAAAAAGAAGACAGACGTTCATCAGTTGTAATTAATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctat                                        <  2:711002/147‑1 (MQ=255)

                                                                                         aCTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctat                                        <  1:993925/149‑1 (MQ=255)

                                                                                          cTTATAAAGAAGACAGACGTTCATCCGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctata                                       <  1:655978/149‑1 (MQ=255)

                                                                                          cTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctata                                       <  1:951594/149‑1 (MQ=255)

                                                                                           ttATAAAGAATACAGACGTTCATCAGGTGTAATTGATGCA‑AAAAAATTATCGATAAAACTGAAGAACAATCTTCGGATAAAAACGAATCATAACGGGGCACGTGTTAGGACCTCTTAAAAAGCTGATGCTAGCAAGCGCTTTTctatac                                      <  2:127183/149‑1 (MQ=255)

                                                                                               aaaGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatactata                                  <  2:153368/149‑1 (MQ=255)

                                                                                               aaaGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAACATGATGCTAGCAAGCGCTTTTctatactata                                  >  2:1000805/1‑149 (MQ=255)

                                                                                               aaaGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCATGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTGTTctatcctcta                                  >  2:365947/1‑149 (MQ=255)

                                                                                                 agaagaCAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatata                                >  1:239440/1‑149 (MQ=255)

                                                                                                   aagaCAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCAAGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTCTGCTATAtatt                              >  2:49030/1‑149 (MQ=255)

                                                                                                   aagaCAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAAGTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATAtatt                              <  2:911001/149‑1 (MQ=255)

                                                                                                     gacagacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATAtattat                            >  1:71629/1‑149 (MQ=255)

                                                                                                      acagacGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATattatt                           <  1:99106/149‑1 (MQ=255)

                                                                                                      acagacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCAAGCACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATattatt                           >  1:864345/1‑149 (MQ=255)

                                                                                                        agacGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAACAAGATGATGCTAGCAAGCGCTTTTCTACTCTATATATTAtttt                         >  1:629056/1‑149 (MQ=255)

                                                                                                                   aGTTGTTATTGATGCA‑AAAAAATTATCGAAAAAACTTAAGAACAATCTGCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAAtttt              <  1:403644/149‑1 (MQ=255)

                                                                                                                    gTTGTGATTGATGCA‑AAAAAAATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTa             <  2:954818/149‑1 (MQ=255)

                                                                                                                            tGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCctc     <  1:300347/149‑1 (MQ=255)

                                                                                                                               atgcaaaaaaaTTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCtt   >  2:717999/6‑149 (MQ=255)

                                                                                                                                tgcaaaaaaaTTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTg  >  2:524746/5‑149 (MQ=255)

||

CAGAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTG  >  USA300TCH1516_ALE/2455561‑2455837

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`