BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,857,944	A→T	8.6%	S144T (TCA→ACA)	USA300HOU_RS09235 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,857,944	0	A	T	8.6%	714.9 / 3.5	290	S144T (TCA→ACA)	USA300HOU_RS09235	hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (127/127); new base T (20/13); total (149/141)
Fisher's exact test for biased strand distribution p-value = 2.72e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 291 total aligned reads displayed.

TGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCCTTTAATGCCGCT  >  USA300TCH1516_ALE/1857804‑1858083

  tttCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATa                                                                                                                                             >  1:1778222/1‑141 (MQ=255)

         ttGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGCTTCTTTATTTGATAAAGTcac                                                                                                                                      >  1:3834229/1‑141 (MQ=255)

           gtgCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCTCTGCTTCTTCTTCTTTATTTGTTACTGCcaatc                                                                                                                                    >  2:1769680/1‑138 (MQ=14)

           gtgCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTTCTACAGCTacac                                                                                                                                    >  2:3962035/1‑141 (MQ=255)

                 cttTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTTAATGCCACTGCTTTTTATTCTTTTTTTTTTACAGCCACATTTTTAt                                                                                                                              >  2:2306594/1‑141 (MQ=17)

                  ttttttATTTTCTTGTAGCTCCTGTGTCTCTTGTGATGTATCACTGTGTTTCTTTGTACTTGTTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCCATGCCATTACTATTAATGCTTTTGTTGATACAGCCACACTTTTATc                                                                                                                             <  2:4308698/141‑1 (MQ=9)

                  ttttttAGCTTCTTGAATCTCTTGTGCCTTTTGTGATGTATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATc                                                                                                                             <  2:342281/141‑1 (MQ=255)

                    ttttAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCg                                                                                                                           <  1:2914127/141‑1 (MQ=255)

                    ttttAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCg                                                                                                                           <  1:2619814/141‑1 (MQ=255)

                      ttggCTTCTTGATTCTCTTGTGCCTTTTGTGATATATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCt                                                                                                                         <  2:677157/138‑1 (MQ=14)

                      ttAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCt                                                                                                                         >  1:3142338/1‑141 (MQ=255)

                       tAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAGATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTCTATCCTCtt                                                                                                                        <  2:3629479/141‑1 (MQ=255)

                        aGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTc                                                                                                                       <  2:639206/141‑1 (MQ=255)

                        aGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCCACCTATTTGCACTTGATTCTTCATTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTCTTTGATACAGCCACACTTTTATCCGCTTc                                                                                                                       >  1:2212975/1‑141 (MQ=17)

                        aGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTc                                                                                                                       >  1:465229/1‑141 (MQ=255)

                        aGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTc                                                                                                                       <  1:3551464/141‑1 (MQ=255)

                        aGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTc                                                                                                                       >  1:1216759/1‑141 (MQ=255)

                          cttcttTAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTg                                                                                                                     <  2:3038367/141‑1 (MQ=255)

                           ttcttGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGc                                                                                                                    <  1:4058042/141‑1 (MQ=255)

                                    ctctTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGTTTGTGCTtc                                                                                                           >  1:87777/1‑141 (MQ=255)

                                       ttGTGTCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTctct                                                                                                        <  1:1015205/141‑1 (MQ=255)

                                       ttGTGCCTCTTGTGTTGTGTCACTCGAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGTTACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTctct                                                                                                        <  2:490917/141‑1 (MQ=255)

                                        tgtgCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGTTTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCtt                                                                                                       <  2:1683424/141‑1 (MQ=255)

                                         gtgCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTTAATGCCACTTCTTTTTATTCTTTTTTTGTTACATACACTCTTTTATCCTCTTTTGCTTTTGCTTTTCttt                                                                                                      >  2:544401/1‑141 (MQ=17)

                                         gtgCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTTTTTTATACAGCCACACTTTTCTCCTCTTCTGCTTGTGCTTCTCttt                                                                                                      >  1:1307857/1‑141 (MQ=255)

                                            ccTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTTCTTTTGATTCTTTATTTTATACATCCACTCCTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑ac                                                                                                  >  2:3547738/1‑140 (MQ=17)

                                               ctTGTGATGTATCACTAAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGctt                                                                                               <  1:377514/141‑1 (MQ=255)

                                                ttGTTATTTATTACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGcttc                                                                                              <  2:3099876/141‑1 (MQ=255)

                                                ttGTGATTTATCGCTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGTTACAGCTACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGcttc                                                                                              <  2:3451435/141‑1 (MQ=14)

                                                ttGTGATGTATCACTCAACTTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGTGCACATCCCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGcttc                                                                                              <  1:2082056/141‑1 (MQ=17)

                                                ttGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGcttc                                                                                              <  1:1956161/141‑1 (MQ=255)

                                                ttGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGcttc                                                                                              <  1:1516921/141‑1 (MQ=255)

                                                ttGTCATGTATCGCTCAAATTATTTTCACTTGCTTCTTCTTTTATCTCTGCTTGTTGTGCTTTCAATCCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGcttc                                                                                              <  2:564897/141‑1 (MQ=17)

                                                 tgtgATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTTTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGcttct                                                                                             <  1:3075311/141‑1 (MQ=255)

                                                 tgtgATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGcttct                                                                                             <  1:4246556/141‑1 (MQ=255)

                                                 tctcatctATCTCTCAATTTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCAATTGCTTTTGATTCTTTATTTGATACAGCCACACCTCTATCAGCTTTTGATTGTGATTCTCTTTT‑AGcttct                                                                                             <  2:2946859/134‑1 (MQ=17)

                                                  gtgATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGTTTCTTTATTTTATACAGCCACACTTTTATCCGCTTTTGCTTGTGCTTCCCTTTc‑ttcttctt                                                                                            >  2:2203743/1‑141 (MQ=17)

                                                    gATGTATTACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGa                                                                                          <  2:827012/141‑1 (MQ=255)

                                                      tGTATCTCTCATTTTATGTGCCCTTGCTTCTTGTGTTATAGCTTCTTCTTGTGCTTTCTTTGCCACTGCTTTTTATTCTTATTTTAATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAAt                                                                                        <  2:2694305/141‑1 (MQ=255)

                                                      tGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTTAATGCCACTTCTTTTTTTTTTTTTTTTTTTACAGCCACTCCTTTATCCTCTTCTGCTTGTGCTTCTCTTTT‑TTCTTCTTGagt                                                                                        >  2:1038390/1‑139 (MQ=17)

                                                      tGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATTCCACTGCTTTTGTTTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAAt                                                                                        <  2:289029/141‑1 (MQ=255)

                                                       gTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCCCTTGTTTTTATTTTTTATTGGTTACAGCTGCACTATTACCTTCTTCTGCTTATGCTTCTCTTTT‑AGCTTCTTGCAtt                                                                                       >  2:1212261/1‑140 (MQ=11)

                                                          tCACTCAAATTATGTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATctct                                                                                    <  1:237276/141‑1 (MQ=255)

                                                             cttagattattTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGCTTCTTTATTTGTTACAGCTACACTTTTATCCGCTTCTGCTCGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTtgt                                                                                 <  2:3904827/136‑1 (MQ=14)

                                                             cTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGCATCTCTtgt                                                                                 >  1:3311265/1‑141 (MQ=255)

                                                               taaaTTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGACATCTATTCCACTGCTTTTGATTCTTTATTTGATACAGCCGCACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGc                                                                               <  2:934388/140‑1 (MQ=14)

                                                               cAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGc                                                                               <  1:3627238/141‑1 (MQ=255)

                                                                aaaTTATTTGCACGTGCTTCTTCTTGTATCGCTGCTTGTTGTGCTTTGAATGCCACTGCTTTTCATTCTTTATTTGATACAGCCTCACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGct                                                                              <  2:2105380/141‑1 (MQ=14)

                                                                 aaTTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACCGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑CGCTTCTTGAATCTCTTGTGctt                                                                             <  1:649822/141‑1 (MQ=255)

                                                                  attattTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGcttc                                                                            <  1:2293437/141‑1 (MQ=255)

                                                                     attTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTtg                                                                         >  1:4138582/1‑141 (MQ=255)

                                                                     attTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTtg                                                                         >  1:1260129/1‑141 (MQ=255)

                                                                     attTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTCCTTCTtg                                                                         >  1:3257978/1‑141 (MQ=255)

                                                                       ttGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTTTTTCTTTATTTGTTAAAAATACACTTTTATCCGCTTCTGTTTTTGCTT‑TCTTTTCTGCTTTTTGTATTTCTTTTTtttcttttt                                                                       >  2:331986/1‑138 (MQ=2)

                                                                       ttGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTTCTTCTCTTTT‑AGCTTCTTTAATCTCTTCTGcttcttctt                                                                       >  1:3389686/1‑138 (MQ=255)

                                                                       ttGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTtgtg                                                                       >  1:793016/1‑141 (MQ=255)

                                                                        tGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGa                                                                      <  1:1390932/141‑1 (MQ=255)

                                                                         gCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAt                                                                     >  1:2706837/1‑141 (MQ=255)

                                                                         gCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAt                                                                     >  1:2014010/1‑141 (MQ=255)

                                                                           aCTTGCTTCTTCTTTTATAGCTGCTTGTTGTGCTTTCAATGCCTCTTCTTTTTATTTTTTATTTGATAAAAACACATTTTTATCCTCTTATGTTTGTTCTTCTCTTTT‑ATCATTTTGAATTTCTCATTCTTGTTGTCAttt                                                                   >  2:2243498/1‑139 (MQ=9)

                                                                               gCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTTATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCa                                                              >  2:3195641/1‑141 (MQ=255)

                                                                                  tcttcttTTATCGCTGCTTGTTGTGCTTTCAATGCCACTTCTTTTGATTCTTTATTTGATACAGACACACTTTTATCCGCTTCTGCTTTTGCTTCTGTTTT‑ATCTTCTTGCCTCTTTTGTTCTTCTTGTTTT‑TTCTCACtt                                                           >  2:1443210/1‑141 (MQ=14)

                                                                                  tcttcttTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTTTGCTTCTTGTGAT‑GTAtgcctt                                                           >  1:2655454/1‑136 (MQ=255)

                                                                                  tcttcttTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACtt                                                           <  1:1626756/141‑1 (MQ=255)

                                                                                   cttcttTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTa                                                          <  1:2976689/141‑1 (MQ=255)

                                                                                    ttcttTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCTACACTTTTATCCGCTTCTTTTTGTGCTTCTCTTTT‑AGCTTCTTGCATCTTTTTTGCTTCTTGTCTT‑TTATCACTTat                                                         >  2:3529248/1‑140 (MQ=14)

                                                                                    ttcttTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTaa                                                         >  1:3707139/1‑141 (MQ=255)

                                                                                     tcttTTGTTGCTGCTTGTTTTTTTTTTAATTCCACTGCTTTTGGTTTTTTATTTGTTGTTGATGTGTTTTTGTCTTCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTaaa                                                        <  2:1711032/141‑1 (MQ=2)

                                                                                     tcttTTATCGCTGTTTGTTGTGCTTTCAATGCCACTGCTTTTGTTTCTTTTTTTGATACAGCCACACTTTTATACGCTTCTGCTTGTGCTTTTTTTTT‑AGCTTCTTGAATTTCGTGTGCTTCTTGTGAT‑GTATCACTTaaa                                                        <  2:338324/141‑1 (MQ=14)

                                                                                     tcttTTATCGCTGTTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCTACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTaaa                                                        <  2:159514/141‑1 (MQ=255)

                                                                                          tATCGCTGCTTGTTGTGCTTTCCATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAattatt                                                   <  1:323000/141‑1 (MQ=255)

                                                                                             cGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGc                                                >  1:2478533/1‑141 (MQ=255)

                                                                                             cGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGc                                                >  1:3782569/1‑141 (MQ=255)

                                                                                              gctgctTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGcc                                               >  1:2129362/1‑140 (MQ=255)

                                                                                               ctgctTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCAc                                              <  1:348500/141‑1 (MQ=255)

                                                                                                tgctTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACt                                             <  1:4111744/141‑1 (MQ=255)

                                                                                                tgctTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACt                                             <  1:561136/141‑1 (MQ=255)

                                                                                                  tttgttgTTCTTTCTATCTCACTGCTTTTGATTCTTTATTTGATACAGCTACACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTg                                           <  2:2014902/140‑1 (MQ=11)

                                                                                                       tgtgCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGcttct                                      >  2:2517348/1‑141 (MQ=255)

                                                                                                          gCTTTCAGTGTCTCTGCGTTTGGTTCTTTATTTGTTTCTGCTGCACCGTTGTCCGCCTCTGTCTGTGCTTCTCTTTT‑CGCTTCTTCTCTCTCCTGCGCTTC‑TCCGATCTTATCACTTAAATTATTTGCACTTGcttcttct                                   <  2:2813598/141‑1 (MQ=9)

                                                                                                          gCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCTCACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGACTCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGcttcttct                                   <  1:2271456/141‑1 (MQ=255)

                                                                                                           cTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGcttcttctt                                  >  1:1452546/1‑141 (MQ=255)

                                                                                                                 aTGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGCATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCg                            >  2:172812/1‑141 (MQ=255)

                                                                                                                 aTGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAGATTATTTGCACTTGCTTCTTCTGTTATcc                            >  1:2510334/1‑140 (MQ=255)

                                                                                                                    ccACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCgctt                         >  1:4320261/1‑140 (MQ=255)

                                                                                                                    ccACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCgctg                         >  1:3090050/1‑141 (MQ=255)

                                                                                                                    ccACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCgctg                         >  1:2739797/1‑141 (MQ=255)

                                                                                                                      aCTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCgctgct                       >  1:9571/1‑141 (MQ=255)

                                                                                                                        tGCTTTTGATTCTTTATTTGATACAGCCACCCTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCttg                     <  1:725549/141‑1 (MQ=255)

                                                                                                                         gCTTTTGATTCTTTCTTTGATACAGCCACACTTTTCTCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTACATTATTTGCGATTAATTATTCTTTTATCGCTGCttgt                    <  1:1066950/141‑1 (MQ=17)

                                                                                                                         gCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCttgt                    >  1:3054145/1‑141 (MQ=255)

                                                                                                                         gCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAACTATTTGCACTTGCTTCTTCTTTTATCGCTGCttgt                    >  1:2795353/1‑141 (MQ=255)

                                                                                                                           ttttGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCttgttg                  >  1:1937031/1‑141 (MQ=255)

                                                                                                                           ttttGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGATGCttgttt                  >  2:4196561/1‑140 (MQ=255)

                                                                                                                             ttGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCATACCTGTT‑ATTTGCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTtgttgtt                >  1:3953020/1‑140 (MQ=18)

                                                                                                                                 ttCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCATTT‑AGCTTCTTGAATCTCGGTTTCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCCtt            >  1:1041789/1‑141 (MQ=18)

                                                                                                                                   cTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCCTTTa          >  1:3878931/1‑141 (MQ=255)

                                                                                                                                        tttGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCCTTTAATGcc     >  1:2050616/1‑141 (MQ=255)

                                                                                                                                         ttGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCCTTTAATGCCg    >  1:3566308/1‑141 (MQ=255)

                                                                                                                                          tGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCCTTTAATGCAGc   >  1:1889807/1‑141 (MQ=255)

TGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTT‑AGCTTCTTGAATCTCTTGTGCTTCTTGTGAT‑GTATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCCTTTAATGCCGCT  >  USA300TCH1516_ALE/1857804‑1858083

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: `‑`