BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,774,975	A→G	6.1%	D737D (GAT→GAC)	clfB ←	Clumping factor B

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,774,975	0	A	G	6.1%	663.3 / 7.3	230	D737D (GAT→GAC)	clfB	Clumping factor B
Reads supporting (aligned to +/- strand): ref base A (90/120); new base G (12/5); total (103/127)
Fisher's exact test for biased strand distribution p-value = 4.04e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 272 total aligned reads displayed.

ATCCGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTG  >  USA300TCH1516_ALE/2774885‑2775065

aTCCGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTa                                                                                            <  1:3472972/91‑1 (MQ=255)

 tCCGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTat                                                                                           >  1:4957647/1‑91 (MQ=255)

  ccGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTatc                                                                                          >  2:2310588/1‑91 (MQ=40)

    gAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTatctg                                                                                        <  1:4519225/91‑1 (MQ=38)

      gTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTatctgaa                                                                                      <  1:4438423/91‑1 (MQ=39)

       tCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTgtctgaat                                                                                     >  2:4869211/1‑91 (MQ=11)

       tCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTgtctgaat                                                                                     >  2:23748/1‑91 (MQ=255)

       tCTGAGTCGCTGTCTGAATCTGAATCACTGTCTGAGTCCGAGTCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTgtctgagt                                                                                     >  2:5202685/1‑89 (MQ=1)

         tGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTatctgaatct                                                                                   <  1:189977/91‑1 (MQ=37)

            gTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAg                                                                                >  2:4426653/1‑91 (MQ=39)

            gTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAg                                                                                <  1:4839776/91‑1 (MQ=39)

            gTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAg                                                                                <  1:1588145/91‑1 (MQ=39)

             tCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGt                                                                               <  2:2086653/91‑1 (MQ=38)

              cGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTc                                                                              <  1:3138841/91‑1 (MQ=39)

              cGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTc                                                                              <  1:4110658/91‑1 (MQ=39)

                  gTCTGAATCTGAATCGCTGTCTGAGTCCGAGTCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTa                                                                          <  2:119950/91‑1 (MQ=21)

                  gTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCtg                                                                          >  2:2657587/1‑90 (MQ=255)

                  gTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTa                                                                          >  1:2619764/1‑91 (MQ=35)

                      gaatctgaatcGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctg                                                                      <  2:1506570/91‑1 (MQ=33)

                      gaatctgaatcGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctg                                                                      <  1:2183022/91‑1 (MQ=33)

                      gaatctgaatcGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctg                                                                      <  2:157955/91‑1 (MQ=33)

                       aatctgaatcGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctga                                                                     <  1:4285810/91‑1 (MQ=32)

                       aatctgaagcGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctga                                                                     <  1:15302/91‑1 (MQ=17)

                        atctgaatcGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGtctgag                                                                    >  2:4464041/1‑91 (MQ=14)

                        atctgaatcGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgag                                                                    <  2:1147918/91‑1 (MQ=31)

                        atctgaatcGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgag                                                                    <  1:518396/91‑1 (MQ=31)

                              atcGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAAtcgctgtctgagtctgagtcgctgtctgagtctgag                                                              >  2:3182720/1‑91 (MQ=255)

                                cGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtc                                                            <  1:5290193/91‑1 (MQ=33)

                                cGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtc                                                            >  1:5655460/1‑91 (MQ=33)

                                    gTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctg                                                        <  1:244928/91‑1 (MQ=34)

                                     tatGAGTCCGAATCGCTATCTGAATATGAGTCGCAGTCTGAGTCTGCATCGCTATACGAATCTGAGTCGCAAtctgagtctgagtcgccgt                                                       >  2:4720090/3‑91 (MQ=11)

                                     tCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgt                                                       <  2:3361200/91‑1 (MQ=34)

                                      cTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTCTCTGAATCTGAGTCGCTGtctgagtctgagtcgctgtc                                                      >  2:322750/1‑91 (MQ=16)

                                        gAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctg                                                    >  2:1433357/1‑91 (MQ=35)

                                        gAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtccg                                                    >  2:3911488/1‑89 (MQ=14)

                                          gTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgag                                                  <  1:5390376/91‑1 (MQ=39)

                                           tCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagt                                                 >  1:3494393/1‑91 (MQ=40)

                                           tCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagt                                                 <  2:2391010/91‑1 (MQ=40)

                                            ccGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtc                                                <  2:1328747/91‑1 (MQ=40)

                                             cGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtct                                               <  1:4003072/91‑1 (MQ=255)

                                             cGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtct                                               <  1:2990544/91‑1 (MQ=255)

                                              gAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtctg                                              >  1:3583572/1‑91 (MQ=255)

                                              gAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgaatctg                                              >  2:656526/1‑91 (MQ=21)

                                               actCGCTATCTGAATCTGAGTCGCTGTCTGACTCTGAATCGCTCTCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtctga                                             <  2:2533187/89‑1 (MQ=255)

                                               aaTCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtctga                                             <  2:3288515/91‑1 (MQ=255)

                                               aaTCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtctga                                             <  2:4960702/91‑1 (MQ=255)

                                               aaTCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtctga                                             <  1:3861375/91‑1 (MQ=255)

                                               aaTCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtctga                                             <  1:3931363/91‑1 (MQ=255)

                                                aTCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtctgag                                            <  1:1103450/91‑1 (MQ=255)

                                                 tCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtctgagt                                           >  1:4960864/1‑91 (MQ=255)

                                                 tCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtctgagt                                           >  1:1230552/1‑91 (MQ=255)

                                                  cGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtctgagtc                                          >  2:4982128/1‑91 (MQ=255)

                                                    cTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtctgagtcgc                                        >  1:4061082/1‑91 (MQ=255)

                                                    cTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtctgagtcgc                                        >  1:2561579/1‑91 (MQ=255)

                                                     tATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtctgagtcgct                                       >  1:3685637/1‑91 (MQ=255)

                                                      atctgaatctgaGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtctgagtcgctg                                      <  2:5321474/91‑1 (MQ=255)

                                                      atctgaatctgaGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtctgagtcgctg                                      >  1:2329464/1‑91 (MQ=255)

                                                          gaatctgaGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGagtctgagtcgctgtctgagtctgagtcgctgtctg                                  >  1:4766988/1‑91 (MQ=255)

                                                          gaatctgaGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGagtcggagtcgctgtctgagtctgagtcgcagtctg                                  >  1:71383/1‑91 (MQ=255)

                                                          gaatctgaATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTATCTGagtctgagtcgctgtctgaatctgagtcgctgtctg                                  <  2:4217853/91‑1 (MQ=11)

                                                            atctgaGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGtctgagtcgctgtctgagtctgagtcgctgtctgag                                >  2:4095899/1‑91 (MQ=39)

                                                             tctgaGTCGCTGTCTGAGTCTGAATCGCTGTCTGAATCTGAGTCGCTATCTGAGTctgagtcgctgtctgagtctgagtcgctgtctgagt                               >  2:1676595/1‑91 (MQ=255)

                                                             tctgaGTCGCTGTCTGAGTCTGAATCGCTATCTGAATctgagtcgctgtctgagtctgagtcgctgtctgagtctgagtcgctgtctgagt                               >  2:5023068/1‑91 (MQ=17)

                                                             tctgaGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTctgagtcgctgtctgagtctgagtcgctgtctgagt                               >  2:893127/1‑91 (MQ=40)

                                                             tctgaGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTctgagtcgctgtctgagtctgagtcgctgtctgagt                               >  2:3098467/1‑91 (MQ=39)

                                                                gaGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGagtcgctgtctgagtctgagtcgctgtctgagtctg                            <  1:3071814/91‑1 (MQ=255)

                                                                gaGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGagtcgctgtctgagtctgagtcgctgtctgagtctg                            <  1:4426653/91‑1 (MQ=255)

                                                                 aGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAgtcgctgtctgagtctgagtcgctgtctgagtctga                           <  1:5446101/91‑1 (MQ=255)

                                                                  gTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGaa                          >  2:2269798/1‑91 (MQ=40)

                                                                  gTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGaa                          >  1:1256395/1‑91 (MQ=255)

                                                                    cGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATc                        <  1:2640335/91‑1 (MQ=255)

                                                                    cGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATc                        >  2:2353129/1‑91 (MQ=255)

                                                                      cTGTCTGAGTCTGTATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGc                      <  2:365970/91‑1 (MQ=255)

                                                                      cTGTCTGAGTCTGAATCGCTATTTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCtgtctgagtctgagtcgctgtctgagtctgagtcgc                      >  2:4311285/1‑91 (MQ=255)

                                                                      cTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGc                      <  1:732113/91‑1 (MQ=255)

                                                                      cTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGc                      <  1:5584379/91‑1 (MQ=255)

                                                                       tGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCt                     <  1:809590/91‑1 (MQ=255)

                                                                        gtctgagtctgaATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCtg                    >  2:1820282/1‑90 (MQ=255)

                                                                        gtctgagtctgaATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTa                    >  1:99238/1‑91 (MQ=255)

                                                                        gtctgagtctgaATCGCTATCTGAATCTGAATCGCTAACTGAGTCTGAGTCACTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTa                    >  2:561268/1‑91 (MQ=255)

                                                                          ctgagtctgaATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTatc                  >  1:4192466/1‑91 (MQ=255)

                                                                          ctgagtctgaATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTatc                  <  2:454422/91‑1 (MQ=255)

                                                                           tgagtctgaATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTatct                 >  1:2786853/1‑91 (MQ=255)

                                                                            gagtctgaATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTatctg                <  1:1178238/91‑1 (MQ=255)

                                                                              gtctgaGTCGCTGTCTGAGTCTGAGTCGCTATCTGAGTCTGAGTCCCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTatctgaa              <  2:5484658/91‑1 (MQ=11)

                                                                                ctgaATCGCTGTCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTatctgaatc            <  2:785718/91‑1 (MQ=255)

                                                                                 tgaATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTgtctgagtct           >  2:2977242/1‑91 (MQ=255)

                                                                                  gaATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTatctgaatctg          <  2:2200386/91‑1 (MQ=255)

                                                                                  gaATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTatctgaatctg          <  2:1875741/91‑1 (MQ=255)

                                                                                  gaATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTatctgaatctg          <  1:2376666/91‑1 (MQ=255)

                                                                                   aaTCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTatctgaatctga         >  2:2889248/1‑91 (MQ=255)

                                                                                   aaTCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTgtctgaatctga         >  2:3083580/1‑91 (MQ=12)

                                                                                    aTCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAg        >  1:1074019/1‑91 (MQ=255)

                                                                                     tCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTgtctgagtctgaat       >  2:3522785/1‑89 (MQ=255)

                                                                                     tCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCGGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGt       <  2:5128992/91‑1 (MQ=255)

                                                                                        cTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTGTCTGAGTCTGAGTCGc    >  2:3463866/1‑91 (MQ=255)

                                                                                          atctgaatctgaGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAGTCTGAGTCGCTg  >  2:1096878/1‑91 (MQ=255)

                                                                                          atctgaatctgaGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTg  <  1:1358281/91‑1 (MQ=255)

                                                                                          atctgaatctgaGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTg  >  1:2968509/1‑91 (MQ=255)

                                                                                          atctgaatctgaGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTg  <  1:549785/91‑1 (MQ=255)

ATCCGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTG  >  USA300TCH1516_ALE/2774885‑2775065

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