BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,455,698	2 bp→AT	100%	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	91.3%	306.3 / 24.5	104	coding (1216/1260 nt)	lyrA	Lysostaphin resistance protein A
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (42/51); minor base . (7/2); total (50/54)
Fisher's exact test for biased strand distribution p-value = 8.39e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.
*	USA300TCH1516_ALE	2,455,699	0	A	T	98.0%	294.2 / ‑5.3	104	H406L (CAT→CTT)	lyrA	Lysostaphin resistance protein A
Reads supporting (aligned to +/- strand): ref base A (1/3); new base T (48/50); total (50/54)
Fisher's exact test for biased strand distribution p-value = 6.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

Only 100 of 104 total aligned reads displayed.

AGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTT  >  USA300TCH1516_ALE/2455568‑2455825

||

aGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑Gaaaaa                                                                                                                       >  1:326947/1‑141 (MQ=255)

      aCAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGCGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTgaa                                                                                                                >  1:319968/1‑141 (MQ=255)

       cAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTgaag                                                                                                               <  1:51484/141‑1 (MQ=255)

       cAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTgaag                                                                                                               <  1:704739/141‑1 (MQ=255)

       cAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACCTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATC‑GAAAAA‑ACTgaag                                                                                                               >  1:613118/1‑141 (MQ=255)

       cAAGAAGCATAAAGTGACGATATAACAAAAAATACAAATGAAAATGAAATCGAGCAATCAGTAAAAGAACCTGCGACTTACAAAGACGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAAAAAAA‑AAAAAA‑ACTgaag                                                                                                               <  2:632848/141‑1 (MQ=255)

        aaGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATC‑GAAAAA‑ACTgaaga                                                                                                              <  2:504721/141‑1 (MQ=255)

        aaGCACCACAAAGTGACGATTAAAAAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAAATATA‑GAAAAA‑ACTgaaga                                                                                                              <  2:10007/141‑1 (MQ=255)

          gCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTgaagaaa                                                                                                            >  2:349835/1‑140 (MQ=255)

          gCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAAc                                                                                                            >  1:713806/1‑141 (MQ=255)

          gCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAAc                                                                                                            <  1:843822/141‑1 (MQ=255)

           caccacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCACTAAAAGCACCTGCGACGTAGAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACa                                                                                                           >  1:180670/1‑141 (MQ=255)

               acaAAGTGACGATTTAACAAACTATTCAAATGAAGATAAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCt                                                                                                       <  1:176841/141‑1 (MQ=255)

               acaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAA‑ATTTCAGAAAAA‑ACTGAAGGACAATCt                                                                                                       >  1:18077/1‑141 (MQ=255)

                   attGACGAGCTAACAAACGGTGCAGATGAAAATGAAATTGAGCAATGATTAAAAGAACCTGCGACTTATAAAGAATACAGACTTTCACCAGTTTTAATTGATGCA‑AAAAAATGATC‑GAAAAA‑ACTGAAGAACAATCTTCAg                                                                                                   <  2:25743/139‑1 (MQ=255)

                   aGTGACGAATTAACAAAAGATTAAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGAAAAAAAAAAA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAg                                                                                                   <  2:462890/141‑1 (MQ=255)

                    gTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGa                                                                                                  <  1:489446/141‑1 (MQ=255)

                     tGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGAt                                                                                                 <  1:346334/141‑1 (MQ=255)

                      caCGATTAAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATa                                                                                                <  1:890175/140‑1 (MQ=255)

                        cGATTTAACAAACGATTGAAGTGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATaaa                                                                                              <  2:825574/141‑1 (MQ=255)

                             tAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTAAGATAAAAACaa                                                                                         >  2:437739/1‑141 (MQ=255)

                                  aaCGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAaataat                                                                                    >  2:708698/1‑141 (MQ=255)

                                   aCGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAataata                                                                                   <  2:669186/141‑1 (MQ=255)

                                     gATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACATATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAAc                                                                                 <  2:897316/141‑1 (MQ=255)

                                      aTTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACa                                                                                <  1:332517/141‑1 (MQ=255)

                                       ttCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACaa                                                                               <  1:501733/141‑1 (MQ=255)

                                       atgaaaTGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACaa                                                                               <  2:785216/138‑1 (MQ=255)

                                          aaaaGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAgc                                                                            <  1:723532/141‑1 (MQ=255)

                                          aaaTGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATAAGTTGTTATTGATGCA‑AAACATCT‑TC‑GAAAAATACTGAAGACAAATCTTGCGGGTAAAACAAATAATAAAAAAgc                                                                            >  1:658115/1‑141 (MQ=255)

                                           aaTGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACACAgcg                                                                           >  2:394998/1‑141 (MQ=255)

                                           aaTGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTAGAAAGAATACAGACGTTCATCATTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACGGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAgcg                                                                           <  2:444748/141‑1 (MQ=255)

                                                aGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGc                                                                      <  2:13796/141‑1 (MQ=255)

                                                  aTGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTa                                                                    <  1:421932/141‑1 (MQ=255)

                                                   tGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAg                                                                   >  1:279364/1‑141 (MQ=255)

                                                    gAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGt                                                                  >  1:525681/1‑141 (MQ=255)

                                                      aaTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGCTCATCAGTTGTAATTGATGCAAAAAAA‑TTATC‑GAAAAA‑ACTGAAGAACCATCTCCAGATAAGAACAAATAATAACAAAGCGCTAGCTAGCAc                                                                >  1:111734/1‑141 (MQ=255)

                                                       aTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTAcc                                                               >  1:423226/1‑141 (MQ=255)

                                                         agagCAAACATTAAAAGAACCTACGAGTTATACAGAAGACAGACGTTCATGAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAGCAAAGCGCTTGCTAGTACctc                                                             <  2:865797/141‑1 (MQ=255)

                                                          agggaaacATTAAAAAAACATACGACTTATAAAGAAGACAGACGTTCATTAGTTGTAATTGATGCAAAAAAATA‑ATA‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctct                                                            <  2:6960/134‑1 (MQ=255)

                                                           agCAATCATTAAAAGAACCTGCGACTTGTAAACAAAACAGACGTGCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTAAGATAAAAAAAAATAAAAACAAAGCGCTTGCTAGTACCTCtt                                                           >  2:52352/1‑141 (MQ=255)

                                                           agCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCtt                                                           >  2:782480/1‑141 (MQ=255)

                                                           agCAATCATTAAAAGAACCGGCGACTTATAAAGAGGACAGACGTTCATTAGTTGTAATTGAGGC‑GAAGAAATAAGC‑GAAAAA‑AGTGAAGAGCAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCGAGTACCTCtt                                                           >  1:680993/1‑141 (MQ=255)

                                                             cAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATC‑GAAAAA‑ACTGAAGAGCAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaa                                                         >  2:277828/1‑141 (MQ=255)

                                                              aaacATTAAAAGAACCTGCGACTTATAAAGAAAACAGCCATTAATACATAGTCATTGGTAC‑GATAAAACTATC‑GAAAAA‑ATCGAAGTACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaa                                                        <  2:191623/138‑1 (MQ=255)

                                                              aaacATTAAAAGAACCTGCGACTTACAAAGAAGACAGACGTACATCAGTTGTAATAGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAACAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaa                                                        <  1:254408/138‑1 (MQ=255)

                                                              aaTCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaa                                                        <  2:302616/141‑1 (MQ=255)

                                                              aaTCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaa                                                        <  1:513771/141‑1 (MQ=255)

                                                               aTCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaa                                                       <  1:166715/141‑1 (MQ=255)

                                                               aTCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAAGTAATGGA‑ACAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTGCAGATAAAAACAAATAATAACAAAGCGCTTGATATGACCTCTTaaga                                                       >  1:253965/1‑139 (MQ=255)

                                                                tCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaaa                                                      >  1:817113/1‑141 (MQ=255)

                                                                 cATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAg                                                     <  2:14945/141‑1 (MQ=255)

                                                                  aTTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACCTCTTAAAAAga                                                    >  2:168243/1‑141 (MQ=255)

                                                                   ttAAGAGAACCTGCGACTTATAAAGAAGACCGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGATTGCTAGTAACTCTTAAAAAgac                                                   >  2:554784/1‑140 (MQ=255)

                                                                   ttAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAGCAAACTTCAGATAAAAACGAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgat                                                   <  2:818051/141‑1 (MQ=255)

                                                                     aaaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGC‑GAAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTACAAAgatga                                                 >  1:395517/1‑141 (MQ=255)

                                                                       aaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATGGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGatgatg                                               <  2:180670/141‑1 (MQ=255)

                                                                         gAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCt                                             <  1:379274/141‑1 (MQ=255)

                                                                          aaCCTACAACATATAAAGAAGACAGACGTTCATCAGTAGAAAAAAAAAAA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTa                                            <  2:609547/141‑1 (MQ=255)

                                                                           aCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGAGGCTGCTAg                                           >  2:859343/1‑141 (MQ=255)

                                                                            ccTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTGGc                                          >  2:749491/1‑141 (MQ=255)

                                                                            ccTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGc                                          >  2:742796/1‑141 (MQ=255)

                                                                              tGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGcca                                        >  1:398279/1‑139 (MQ=255)

                                                                              tGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa                                        <  2:644744/141‑1 (MQ=255)

                                                                               gCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAg                                       <  2:768309/141‑1 (MQ=255)

                                                                                cGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgc                                      >  1:648315/1‑141 (MQ=255)

                                                                                cGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgc                                      >  1:845056/1‑141 (MQ=255)

                                                                                cGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgc                                      <  1:273517/141‑1 (MQ=255)

                                                                                cGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgc                                      >  1:712516/1‑141 (MQ=255)

                                                                                  aCTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGCTATTAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgc                                    <  1:394998/141‑1 (MQ=255)

                                                                                  aCTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgc                                    >  2:701018/1‑141 (MQ=255)

                                                                                  aCTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgc                                    >  2:815026/1‑141 (MQ=255)

                                                                                  aCTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTACCAAgcgc                                    >  1:73446/1‑141 (MQ=255)

                                                                                   cTTCTAAAGAAGACAGACGTTCAGCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCt                                   <  1:764243/141‑1 (MQ=255)

                                                                                      ataAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCtttt                                <  1:741196/141‑1 (MQ=255)

                                                                                      ataAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCtttt                                <  1:752178/141‑1 (MQ=255)

                                                                                      ataAAGAAGACAGACGTTCATCAGTTGTAATAGATACA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCGAGCGCtttt                                <  2:221500/141‑1 (MQ=255)

                                                                                       taAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTc                               >  2:168651/1‑141 (MQ=255)

                                                                                       taAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTc                               >  1:455535/1‑141 (MQ=255)

                                                                                       aaaaGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAACAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTc                               <  2:722937/140‑1 (MQ=255)

                                                                                          agaagaCAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCTAGCGCGTTTctat                            >  1:286962/1‑141 (MQ=255)

                                                                                           gaagaCAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctata                           >  2:803081/1‑141 (MQ=255)

                                                                                            aagaCAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATGTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTATCAGGGGCttttttctat                          >  2:78996/1‑135 (MQ=255)

                                                                                            aagaCAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTCAAAAGATGATGCTAGCAAGCGCGTTTctatac                          >  2:629861/1‑141 (MQ=255)

                                                                                                 agagGTTCATCACTTGTAATTCATGCA‑AAAAAATTATC‑AAAAAA‑ACTTAATAACAATCTTCAGATAAAAACAAATAACAACAAAGCGCTTGCTAGTACCTCTTAAATAGATGATGCTAGCAAGCGCTTTTCTATACtatat                     <  2:387410/141‑1 (MQ=255)

                                                                                                 agacGTTTATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACAGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatat                     <  1:2522/141‑1 (MQ=255)

                                                                                                 agacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatat                     <  2:515001/141‑1 (MQ=255)

                                                                                                 agacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatat                     >  2:212396/1‑141 (MQ=255)

                                                                                                  gacGTTCATCAGTTGTGAGTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCGAGCGCTTTTCTATACtatata                    <  2:365630/141‑1 (MQ=255)

                                                                                                  gacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACTAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatatt                    >  2:653355/1‑140 (MQ=255)

                                                                                                  gacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTAGCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACcatata                    >  2:467448/1‑141 (MQ=255)

                                                                                                  gacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCACGCGCTTTTCTATACtatata                    >  2:520137/1‑141 (MQ=255)

                                                                                                    cGTTCATCAGTTGTAATTGATGCA‑AAAAAATTGTC‑GAAAAA‑ACTGACGAACAGTCTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTGCCGGTGAAAAAGCAGATGCTAGCAGCCCCTCTTgtatacaatggatt                  >  2:475553/1‑136 (MQ=255)

                                                                                                    cGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTTTATACTATAtttt                  >  1:417650/1‑141 (MQ=255)

                                                                                                    cGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTAAAtatt                  >  2:161574/1‑141 (MQ=255)

                                                                                                       tcatcaGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATattatt               <  2:606687/141‑1 (MQ=255)

                                                                                                         atcaGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAtttt             <  1:708698/141‑1 (MQ=255)

                                                                                                           caGTTGTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTc           <  1:834976/141‑1 (MQ=255)

                                                                                                            aGTTGTAATTGATGCAAAAAAA‑TTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCCCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTCTATATTATTTTTCt          >  2:516928/1‑141 (MQ=255)

                                                                                                                gTAATTGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTaaaa      <  2:720161/141‑1 (MQ=255)

                                                                                                                    ttGATGCA‑AAAAAATTATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAAtttt  <  1:152395/141‑1 (MQ=255)

||

AGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATC‑GAAAAA‑ACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTT  >  USA300TCH1516_ALE/2455568‑2455825

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: `‑`