Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A23 F171 I0 R1	77	151.8	3400288	94.4%	3209871	139.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,361,590	C→T	50.0%	R239H (CGT→CAT)	secY ←	Protein translocase subunit SecY

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,361,590	0	C	T	50.0%	‑3.2 / 197.7	132	R239H (CGT→CAT)	secY	Protein translocase subunit SecY
Reads supporting (aligned to +/- strand): ref base C (39/27); new base T (36/30); total (75/57)
Fisher's exact test for biased strand distribution p-value = 7.25e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.73e-01

Only 100 of 134 total aligned reads displayed.

TGTTCTAGGCAGTAAGAAGAACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGC  >  USA300TCH1516_ALE/2361451‑2361730

tGTTCTAGGCAGTAAGAAGAACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACg                                                                                                                                             >  1:171805/1‑141 (MQ=255)

 gTTCTAGGCAGTAAGAAGAACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGa                                                                                                                                            >  2:1156021/1‑141 (MQ=255)

 gTTCTAGGCAGTAAGAAGAACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGa                                                                                                                                            <  1:1098941/141‑1 (MQ=255)

 gTTCTAGGCAGTAAGAAGAACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGa                                                                                                                                            >  3:244434/1‑141 (MQ=255)

   tCTAGGCAGTAAGAAGAACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAAc                                                                                                                                          <  1:291140/141‑1 (MQ=255)

     tAGGCAGTAAGAAGAACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACgg                                                                                                                                        <  1:1093310/141‑1 (MQ=255)

      aGGCAGTAAGAAGAACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGc                                                                                                                                       <  1:305064/141‑1 (MQ=255)

      aGGCAGTAAGAAGAACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGc                                                                                                                                       <  3:45079/141‑1 (MQ=255)

       ggCAGTAAGAAGAACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCt                                                                                                                                      >  3:385688/1‑141 (MQ=255)

         cAGTAAGAAGAACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTc                                                                                                                                    <  1:448640/141‑1 (MQ=255)

             aagaagAACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGt                                                                                                                                <  3:55331/141‑1 (MQ=255)

              agaagaACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGACTTTTACGAACGGCTTCAAGTa                                                                                                                               >  2:1007998/1‑141 (MQ=255)

               gaagagCGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTGATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTAc                                                                                                                              <  2:129306/141‑1 (MQ=255)

               gaagaaCGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTAc                                                                                                                              <  2:385502/141‑1 (MQ=255)

                aagaaCGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACa                                                                                                                             <  2:1167554/141‑1 (MQ=255)

                 agaaCGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACAt                                                                                                                            <  1:66136/141‑1 (MQ=255)

                  gaaCGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCACTTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACAt                                                                                                                            <  1:874639/141‑1 (MQ=255)

                    aCGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATaaa                                                                                                                         >  2:678781/1‑141 (MQ=255)

                      gCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATa                                                                                                                       <  2:76716/141‑1 (MQ=255)

                        cATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGc                                                                                                                     >  2:422614/1‑141 (MQ=255)

                         aTTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCa                                                                                                                    >  2:291823/1‑141 (MQ=255)

                           tGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCAcc                                                                                                                  <  1:1149515/141‑1 (MQ=255)

                            gCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCt                                                                                                                 >  4:22400/1‑141 (MQ=255)

                             cAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTa                                                                                                                <  4:388947/141‑1 (MQ=255)

                             cAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTa                                                                                                                <  4:59451/141‑1 (MQ=255)

                               aaGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTCGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACa                                                                                                              <  4:432945/141‑1 (MQ=255)

                                agagTACAGGAATAACACCGGCTGAGTCCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAACCTTTGAGCAGTTTGTTTCTTAGCATAATGAATCGGCATTCTATGCACGGCTTCAAGTACATAAATAGCACCCACAg                                                                                                             >  1:893335/1‑141 (MQ=255)

                                 gATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGt                                                                                                            >  4:384555/1‑141 (MQ=255)

                                   ttACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTa                                                                                                          <  2:948181/141‑1 (MQ=255)

                                    tACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTaa                                                                                                         <  2:471251/141‑1 (MQ=255)

                                     aCAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAAt                                                                                                        <  3:307475/141‑1 (MQ=255)

                                     aCAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAAt                                                                                                        <  4:264317/141‑1 (MQ=255)

                                     aCAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAAt                                                                                                        >  1:1036162/1‑141 (MQ=255)

                                       aGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAg                                                                                                      >  1:1084501/1‑141 (MQ=255)

                                       aGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAg                                                                                                      >  1:127958/1‑141 (MQ=255)

                                       aGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAg                                                                                                      >  1:462595/1‑141 (MQ=255)

                                       aGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAg                                                                                                      >  2:1105507/1‑141 (MQ=255)

                                       aGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAg                                                                                                      <  1:1003928/141‑1 (MQ=255)

                                               cacCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAgag                                                                                              <  4:12042/141‑3 (MQ=255)

                                               cacCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTg                                                                                              <  1:513587/141‑1 (MQ=255)

                                               cacCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTg                                                                                              <  2:567048/141‑1 (MQ=255)

                                                acCGGCTGAGTTCGC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGa                                                                                             >  1:736475/1‑141 (MQ=255)

                                                acCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGa                                                                                             >  1:504887/1‑141 (MQ=255)

                                                acCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCGGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGa                                                                                             >  2:727676/1‑141 (MQ=255)

                                                  cGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGaca                                                                                           <  2:757467/141‑1 (MQ=255)

                                                  cGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGaca                                                                                           >  2:77114/1‑141 (MQ=255)

                                                        aGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTaaaa                                                                                     <  3:180922/141‑1 (MQ=255)

                                                        aGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTaaaa                                                                                     >  1:726743/1‑141 (MQ=255)

                                                         gTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAg                                                                                    >  2:89255/1‑141 (MQ=255)

                                                          ttCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGt                                                                                   <  4:224197/141‑1 (MQ=255)

                                                           tCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTc                                                                                  <  2:390294/141‑1 (MQ=255)

                                                           tCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTc                                                                                  >  1:160748/1‑141 (MQ=255)

                                                            cAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTcc                                                                                 >  1:561006/1‑141 (MQ=255)

                                                              c‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTa                                                                               >  2:326139/1‑141 (MQ=255)

                                                                ttttAAAGGTAAATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGAATATTGAAACGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTaa                                                                              <  1:707638/141‑1 (MQ=255)

                                                                 tttAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAAt                                                                             <  2:306341/141‑1 (MQ=255)

                                                                   tAAAGGTTGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATAc                                                                           >  1:945935/1‑141 (MQ=255)

                                                                    aaaGGTAGATAAGTTGCCTGTGAACCTAGCGAATTATCATTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACt                                                                          >  2:950527/1‑141 (MQ=255)

                                                                    aaaGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACt                                                                          >  3:319231/1‑141 (MQ=255)

                                                                      aGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACttt                                                                        >  2:348074/1‑141 (MQ=255)

                                                                      aGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCCAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACttt                                                                        >  1:78557/1‑141 (MQ=255)

                                                                      aGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACttt                                                                        >  4:377950/1‑141 (MQ=255)

                                                                                 ttGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTa                                                             >  2:1135485/1‑141 (MQ=255)

                                                                                 ttGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTa                                                             >  1:221039/1‑141 (MQ=255)

                                                                                    ccTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAatg                                                          >  1:797041/1‑141 (MQ=255)

                                                                                     cTGTGAACCTAATCTTTTAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTGCGAACGGGGTCAAGTGCATGAATAGTACCTACAGTTAATAGTAGCAGGGGCACTAAAAGTCCTAATACTTTCAACCATGCTatttt                                                         >  1:894215/1‑137 (MQ=255)

                                                                                     cTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAatga                                                         <  3:76792/141‑1 (MQ=255)

                                                                                       gtgAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAatgatg                                                       >  2:63164/1‑141 (MQ=255)

                                                                                         gAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTa                                                     >  2:466880/1‑141 (MQ=255)

                                                                                          acccTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCCATAGGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTAt                                                    <  1:21515/139‑1 (MQ=255)

                                                                                          aaCCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTAt                                                    <  2:678026/141‑1 (MQ=255)

                                                                                                aTCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTa                                                                                                    >  1:275684/1‑87 (MQ=255)

                                                                                                aTCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTa                                                                                                    <  2:275684/87‑1 (MQ=255)

                                                                                                  cTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGc                                            <  1:1124382/141‑1 (MQ=255)

                                                                                                  cTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGc                                            <  3:304777/141‑1 (MQ=255)

                                                                                                   tttGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGcc                                           <  1:545237/141‑1 (MQ=255)

                                                                                                     tGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTCCAGAAACAGCACCTGCAGTTAATAGTATCAGTGACACCAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCa                                         <  3:478399/141‑1 (MQ=255)

                                                                                                     tGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCa                                                                  >  3:239031/1‑116 (MQ=255)

                                                                                                       aGCAGTTTGTTTCTTAGCATATTGAATTGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGGGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTGTCTTCTTGCCCaac                                       >  1:509841/1‑141 (MQ=255)

                                                                                                       aGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCaac                                       >  3:396491/1‑141 (MQ=255)

                                                                                                           gtttgtttCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCaacgaac                                   <  3:492462/141‑1 (MQ=255)

                                                                                                              tgtttCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCa                                <  3:184930/141‑1 (MQ=255)

                                                                                                              tgtttCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCa                                >  1:670694/1‑141 (MQ=255)

                                                                                                                tttCTTAGCATATTGGATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGt                              <  1:990560/141‑1 (MQ=255)

                                                                                                                tttCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGt                              <  1:1054364/141‑1 (MQ=255)

                                                                                                                  tCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGttt                            >  1:313514/1‑141 (MQ=255)

                                                                                                                    ttAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCAAACCCGCCAACGAACGCAGTTTGt                          >  1:611595/1‑141 (MQ=255)

                                                                                                                    ttAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGt                          >  1:530753/1‑141 (MQ=255)

                                                                                                                    ttAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGt                          >  1:433199/1‑141 (MQ=255)

                                                                                                                     tAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTc                         >  2:65505/1‑141 (MQ=255)

                                                                                                                     tAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTc                         <  4:307383/141‑1 (MQ=255)

                                                                                                                            ttGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTg                  >  1:915157/1‑141 (MQ=255)

                                                                                                                            ttGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTg                  >  1:1139049/1‑141 (MQ=255)

                                                                                                                                aTCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAAtt              >  3:243511/1‑141 (MQ=255)

                                                                                                                                  cGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAg            >  1:764382/1‑141 (MQ=255)

                                                                                                                                   ggAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTGTCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGa           <  4:181135/141‑1 (MQ=255)

                                                                                                                                        tttATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGActggc      >  4:203542/1‑141 (MQ=255)

                                                                                                                                        tttATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGActggc      <  3:217171/141‑1 (MQ=255)

                                                                                                                                        tttATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGActggc      >  2:483853/1‑141 (MQ=255)

                                                                                                                                            cGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACtggctggc  <  4:244434/141‑1 (MQ=255)

TGTTCTAGGCAGTAAGAAGAACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCAC‑TTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGC  >  USA300TCH1516_ALE/2361451‑2361730

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: `‑`

GATK/CNVnator alignment

N/A