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
A5 F109 I1 R1	31	90.0	1985866	95.2%	1890544	140.9

Breseq alignment

BRESEQ :: Evidence

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

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,455,698	0	C	A	88.0%	314.0 / 39.2	110	coding (1216/1260 nt)	lyrA	Lysostaphin resistance protein A
Reads supporting (aligned to +/- strand): ref base C (1/0); major base A (45/50); minor base . (10/3); total (57/53)
Fisher's exact test for biased strand distribution p-value = 7.36e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
*	USA300TCH1516_ALE	2,455,699	0	A	T	97.4%	338.7 / NA	113	H406L (CAT→CTT)	lyrA	Lysostaphin resistance protein A
Reads supporting (aligned to +/- strand): ref base A (2/1); new base T (56/54); total (58/55)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 113 total aligned reads displayed.

ATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACC  >  USA300TCH1516_ALE/2455565‑2455831

||

aagattgaaaCAAGCATCAACAAGGCACGATTTAACAAACGATTCAAATGAAGATGAAATAGATCAGTCATTAAAAGAACCTGCCA‑CTTATAAAGAAGACCGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGaa                                                                                                                               <  2:60996/134‑1 (MQ=255)

 tCAATTAAACAAGCATCACAAAGTGACGACTTAACAAACGATTCAAATGAAAATGGAACAGAGCAATCATTAAAAGAACCTGCCATGTTAT‑TAGATGACAGATTTTCATTAGTTGTAATTGATGCA‑AAAAAATTATCGaaa                                                                                                                              <  2:162505/141‑1 (MQ=255)

   aGTTGAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGaaaaa                                                                                                                            >  2:685656/1‑141 (MQ=255)

   aGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGaaaaa                                                                                                                            <  1:890914/141‑1 (MQ=255)

    gTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGaaaaaa                                                                                                                           >  1:989154/1‑141 (MQ=255)

    gTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGCTGTAATTGAGACA‑AAAAAATTATCGaaaaaa                                                                                                                           >  2:245225/1‑141 (MQ=255)

       aaaCAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTg                                                                                                                        <  1:57295/141‑1 (MQ=255)

       aaaCAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAAGAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTCGTAATTGATGCA‑AAAAAATTATCGAAAAACCTg                                                                                                                        <  2:365554/141‑1 (MQ=255)

        aaCAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTga                                                                                                                       >  1:801376/1‑141 (MQ=255)

           aaGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTgaaga                                                                                                                    <  2:404982/141‑1 (MQ=255)

           aaGCACCACAAAGTGACGATTTAACAAACGAATCAAATGCAGTTGAAATAGAACAATCATTAAAATAACCTCCGG‑CTTATAAGGAAGGCAGACGGTCAACAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTgaaga                                                                                                                    <  2:977482/141‑1 (MQ=255)

             gCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAGAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAAc                                                                                                                  >  1:429628/1‑141 (MQ=255)

             gCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTgaagaaa                                                                                                                  >  1:958761/1‑140 (MQ=255)

             gCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAAc                                                                                                                  >  1:896097/1‑141 (MQ=255)

              aaccacAAAGTTACGAATTAACAAACGACCAAAACGAAGATCGAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTACAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACa                                                                                                                 <  1:512088/140‑1 (MQ=255)

               cccacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACaa                                                                                                                <  1:314202/140‑1 (MQ=255)

               accacAAAGTAACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACaa                                                                                                                <  1:88133/141‑1 (MQ=255)

                ccacAAAGTGACGATTTAACAAACAAATCAAATGAAGATGAAATAGAGGAATAATTAAACGAACCTGCGT‑CTTATAAAGAGGACAGACGTTCATCAGTAGTAATAGATGCA‑AAACAAAAATCGAAAAAACTGAAGAATaaa                                                                                                               >  2:661700/1‑140 (MQ=255)

                 cacaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATc                                                                                                              >  2:777413/1‑141 (MQ=255)

                 cacaAAGTGACGAGTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATc                                                                                                              >  2:513165/1‑141 (MQ=255)

                  acaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAGTAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCt                                                                                                             >  2:903368/1‑141 (MQ=255)

                  acaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCt                                                                                                             >  2:987170/1‑141 (MQ=255)

                    aaaGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTc                                                                                                           >  1:440877/1‑141 (MQ=255)

                      aGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAg                                                                                                         >  1:367635/1‑141 (MQ=255)

                       gTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTGTCGAAAAAACTGAAGAACAATCTTCAGa                                                                                                        >  2:412123/1‑141 (MQ=255)

                          aCGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaa                                                                                                     >  1:782854/1‑141 (MQ=255)

                            gATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaaaa                                                                                                   <  1:11581/141‑1 (MQ=255)

                                aaaCAAACGATGCAAATGAAGATGAAATAGTGCAATCATGAAAAGAACCCGCGA‑CTTATAAAGAAGACAGACGTTCAACAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACaa                                                                                               <  2:290145/140‑1 (MQ=255)

                                 aaCAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAAAAATCTTCAGATaaaaaacaa                                                                                              >  2:881796/1‑137 (MQ=255)

                                  aCAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAaat                                                                                             <  1:142799/141‑1 (MQ=255)

                                           tCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTACTTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACaaa                                                                                    >  1:663633/1‑141 (MQ=255)

                                           tCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATA‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACaaa                                                                                    >  2:499982/1‑141 (MQ=255)

                                           tCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATACTAACaaa                                                                                    >  1:663821/1‑141 (MQ=255)

                                                tGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCt                                                                               <  1:367344/141‑1 (MQ=255)

                                                    gATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCt                                                                           <  1:915490/141‑1 (MQ=255)

                                                    gATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCt                                                                           <  1:741046/141‑1 (MQ=255)

                                                           tAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAATGCGCTTGCTAGTACct                                                                    <  2:387351/141‑1 (MQ=255)

                                                           tAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACct                                                                    <  1:214358/141‑1 (MQ=255)

                                                           tAGAGCAATCAGTAAAAGAACCCGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACct                                                                    <  2:105190/141‑1 (MQ=255)

                                                           aagagCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACct                                                                    <  1:262224/140‑1 (MQ=255)

                                                              agCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCtt                                                                 <  2:440877/141‑1 (MQ=255)

                                                              agCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCtt                                                                 >  2:10389/1‑141 (MQ=255)

                                                              agCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCtt                                                                 >  1:576323/1‑141 (MQ=255)

                                                                cAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTACTTGAAGCA‑AAAAAATTATCGAAAAAACTGAAGAACACTCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaa                                                               >  1:276768/1‑141 (MQ=255)

                                                                cAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaa                                                               >  2:595765/1‑141 (MQ=255)

                                                                 aactaatAAAACAACCTTCTA‑CTGAGAAACAAGACAGACGTTCATCAGTTGGAATTGATGCA‑AAAAAAAAAACAAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaa                                                              <  2:443134/135‑1 (MQ=255)

                                                                  aTCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaa                                                             <  1:305091/141‑1 (MQ=255)

                                                                      ttAAAAGCACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgat                                                         <  1:158367/141‑1 (MQ=255)

                                                                      ttAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgat                                                         <  1:96301/141‑1 (MQ=255)

                                                                      ttAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgat                                                         <  1:987170/141‑1 (MQ=255)

                                                                       tAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatg                                                        <  1:317032/141‑1 (MQ=255)

                                                                         aaaGGACCTGCGA‑CGTCAAAAGACGACAGACTTTCACCAGTTGTAATTGATGCA‑AAGCAATTACCAAAAACCCTGAAGAACAATCTTCATATAAAAACCAATAATAACAAAGCGCTTGCTAGTACCACTTAAAAAgatcat                                                      >  2:322428/1‑141 (MQ=255)

                                                                         aaaGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatgat                                                      <  2:312485/141‑1 (MQ=255)

                                                                          aaGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGatgatg                                                     >  1:854226/1‑141 (MQ=255)

                                                                               ccTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGc                                                >  1:701874/1‑141 (MQ=255)

                                                                               ccTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGc                                                >  1:18589/1‑141 (MQ=255)

                                                                               ccTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGc                                                >  1:18508/1‑141 (MQ=255)

                                                                                cTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCa                                               <  1:114791/141‑1 (MQ=255)

                                                                                  gCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAACTTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGCTGCTAGCaaa                                             >  2:673765/1‑140 (MQ=255)

                                                                                     a‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgc                                          <  1:614593/141‑1 (MQ=255)

                                                                                     a‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCACTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgc                                          <  2:383190/141‑1 (MQ=255)

                                                                                       cTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCt                                         <  1:307182/141‑1 (MQ=255)

                                                                                         tataACGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCttt                                       <  2:445082/141‑1 (MQ=255)

                                                                                          ataAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAACAGATGATGCTAGCAAGCGCtttt                                      >  1:610639/1‑141 (MQ=255)

                                                                                          ataAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCATGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCtttt                                      >  1:828945/1‑141 (MQ=255)

                                                                                           aaaaGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTc                                     <  2:172638/140‑1 (MQ=255)

                                                                                            aaaGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGACAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTct                                    <  2:922902/141‑1 (MQ=255)

                                                                                               gaagaCAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctata                                 >  2:540498/1‑141 (MQ=255)

                                                                                                aagaCAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatac                                <  1:132792/141‑1 (MQ=255)

                                                                                                aagaCAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatac                                <  1:725227/141‑1 (MQ=255)

                                                                                                   acagacGTACAACAGATGTAATAGATGCA‑AAAAAATTAACGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCCTTCctataccag                             <  2:606830/141‑4 (MQ=255)

                                                                                                     atactttCATAAGTTGAAATTGATGCA‑AAAAAATTATCGCAAACACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatat                           <  1:76545/136‑1 (MQ=255)

                                                                                                     agacGTTCATCAGTTGTCGTTTCGGTA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatat                           >  1:728498/1‑141 (MQ=255)

                                                                                                     agacGTTCATCAGTTGTAATTGCTGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTGGCTAGTACCTCTTAAAAAGATGATCCTAGCATGCGCTGTTctatactaaaa                           >  2:570450/1‑138 (MQ=255)

                                                                                                      gacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatata                          >  1:610731/1‑141 (MQ=255)

                                                                                                      gacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGAAGATGCTAGCAAGAGCTTTTCTATACaatata                          >  2:326906/1‑141 (MQ=255)

                                                                                                        cGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCTCTTTTCTATACTATAtatt                        <  2:865229/141‑1 (MQ=255)

                                                                                                             atcaGTTTCAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAtttt                   <  2:528993/141‑1 (MQ=255)

                                                                                                             atcaGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAtttt                   <  2:370602/141‑1 (MQ=255)

                                                                                                              tcaGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTAAATATTAttttt                  >  2:130473/1‑141 (MQ=255)

                                                                                                              tcaGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCACGCGCTTTTCTATACTATATATTAttttt                  >  2:445535/1‑141 (MQ=255)

                                                                                                              tcaGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAttttt                  >  1:82648/1‑141 (MQ=255)

                                                                                                              tcaGTTGTAATTGACGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAttttt                  >  1:545937/1‑141 (MQ=255)

                                                                                                              tcaGTTGCAATGGACGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCCAGCGCTTTTCTATACTATATATTAttttt                  <  1:245225/141‑1 (MQ=255)

                                                                                                               caGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGCAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTc                 >  1:634381/1‑141 (MQ=255)

                                                                                                               caGTTGTAACTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTc                 <  1:75405/141‑1 (MQ=255)

                                                                                                               caGATGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTc                 <  1:701729/141‑1 (MQ=255)

                                                                                                                aGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCt                >  2:908291/1‑141 (MQ=255)

                                                                                                                aGTTGTAATTGATGCA‑AAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTa               >  1:261230/1‑141 (MQ=255)

                                                                                                                   tGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGAAGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTaaa             >  2:447198/1‑141 (MQ=255)

                                                                                                                    gTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTaaaa            <  2:536359/141‑1 (MQ=255)

                                                                                                                    gTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTaaaa            <  1:595765/141‑1 (MQ=255)

                                                                                                                      aaTTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAAtt          >  2:541461/1‑141 (MQ=255)

                                                                                                                      aaTTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAAtt          >  2:985902/1‑141 (MQ=255)

                                                                                                                       aTTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAAttt         <  2:782854/141‑1 (MQ=255)

                                                                                                                       aTTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCGTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAAttt         >  2:979964/1‑141 (MQ=255)

                                                                                                                         tGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCGTTTCTATACTATAAATTATTTTTCTAAAATTTTa       >  2:815949/1‑141 (MQ=255)

                                                                                                                          tgaggcaaaaaaaTTATCGAAAAAACTGAAGAACAATCTTCAGATAAACACAAATAATAACAACGCGCCTGCTAGTACCTCTTAAAAAGATGATGCTAGAAAGCGCTTTTCTATACTATATCTTATTTTTCTAAAATTTTa       >  2:391242/8‑141 (MQ=255)

                                                                                                                             tgcaaaaaaaTTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAaca    <  2:162273/137‑1 (MQ=255)

                                                                                                                               caaaaaaaTTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACAcc  <  2:367635/139‑1 (MQ=255)

||

ATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGA‑CTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACC  >  USA300TCH1516_ALE/2455565‑2455831

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: `‑`

GATK/CNVnator alignment

N/A