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
A3 F67 I0 R1	44	83.9	1894234	96.6%	1829830	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,744,443	C→A	16.7%	V77F (GTT→TTT)	apt ←	Adenine phosphoribosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,744,443	0	C	A	16.7%	142.7 / 20.1	70	V77F (GTT→TTT)	apt	Adenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand): ref base C (29/29); new base A (5/7); total (34/36)
Fisher's exact test for biased strand distribution p-value = 7.54e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.54e-01

GTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCA  >  USA300TCH1516_ALE/1744304‑1744582

gTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACa                                                                                                                                            >  2:250602/1‑141 (MQ=255)

  aGCTAATAAATCATCTTTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACggg                                                                                                                                          <  2:184216/141‑1 (MQ=255)

   gCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGt                                                                                                                                         <  2:510392/141‑1 (MQ=255)

       ataaATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCCCGAGGTAATTTCCCTTC‑TTTTCTAACAGGAGcta                                                                                                                                     >  1:290809/1‑139 (MQ=255)

       ataaATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAAAAGGTGCaa                                                                                                                                     <  2:616842/141‑1 (MQ=255)

            atatcTTTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAATCATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTGATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCa                                                                                                                                <  2:491733/139‑1 (MQ=255)

             catcTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCATTC‑TTTTCTCACCGCTGCAAACCCac                                                                                                                               >  2:55582/1‑140 (MQ=255)

             catcTGTAATTAACACACGTTGACCTGGTTTAATTGCATATTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTTCAAACA‑GTGCAAAGACaa                                                                                                                               >  2:863228/1‑141 (MQ=255)

             catcTGTAATTAACACACGATGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATCTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTT‑TTTTCTAACAGGTGCAAAGCCaa                                                                                                                               <  2:675190/141‑1 (MQ=255)

             catcTGTAAGTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCaa                                                                                                                               <  1:459772/141‑1 (MQ=255)

                cTGTAATTAACACACGTTGACCTGGTTTACTTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCGCGAGGTACTTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCACTcc                                                                                                                            >  1:276407/1‑141 (MQ=255)

                cTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATcc                                                                                                                            >  2:917410/1‑141 (MQ=255)

                cTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTATACCATATTCTAGGTCATACTCATAACGAATGACCTCACGCGGTATTTTCCCTTC‑TTTTCTAACCGGTTCAAAGCCAATcc                                                                                                                            >  1:174896/1‑141 (MQ=255)

                  gTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATcccc                                                                                                                          >  2:859948/1‑141 (MQ=255)

                     aTTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACTAATGACTTCACGAGGTAATTTCCCTCC‑TTTTCTAACAGGTGCAAAGCCAATCCCCAtt                                                                                                                       >  2:622279/1‑141 (MQ=255)

                      ttAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAAAAGGTGCAAAGCCAATCCCCATTg                                                                                                                      <  2:246803/141‑1 (MQ=255)

                      ttAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAAAAGGTGCAAAGCCAATCCCCATTg                                                                                                                      <  2:56321/141‑1 (MQ=255)

                      tgaaCACACGTTGACCGGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTg                                                                                                                      <  2:212346/139‑1 (MQ=255)

                              cGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCt                                                                                                              >  1:596864/1‑141 (MQ=255)

                               ggtGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCACATTGAATAAGCTa                                                                                                             <  2:305680/139‑1 (MQ=255)

                                ttGACCTGGTTTAATTGCATCTTTGTTGATGTTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTAc                                                                                                            <  2:423776/141‑1 (MQ=255)

                                 tGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACa                                                                                                           >  1:126828/1‑141 (MQ=255)

                                   aCCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAgg                                                                                                         <  1:320108/141‑1 (MQ=255)

                                                    cTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGc                                                                                        <  2:323912/141‑1 (MQ=255)

                                                       tgtgCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGATGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCAc                                                                                     >  1:868280/1‑141 (MQ=255)

                                                          gCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCAcgcg                                                                                  >  1:449996/1‑141 (MQ=255)

                                                           cATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACgcgc                                                                                 <  2:487634/141‑1 (MQ=255)

                                                             ttGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCtt                                                                               >  1:804548/1‑141 (MQ=255)

                                                             ttGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGATCAAGAACAGCCAATGATAAAGCCACGCGCtt                                                                               >  2:614683/1‑141 (MQ=255)

                                                              tGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTc                                                                              <  1:152523/141‑1 (MQ=255)

                                                                       aTTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTAc                                                                     >  2:91442/1‑141 (MQ=255)

                                                                         ttGTACCATATTCTATGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACaa                                                                   <  2:207643/141‑1 (MQ=255)

                                                                         ttGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACaa                                                                   >  2:408263/1‑141 (MQ=255)

                                                                         ttGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACaa                                                                   >  2:763882/1‑141 (MQ=255)

                                                                          tGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCCGGTCCTACAAc                                                                  >  2:130157/1‑141 (MQ=255)

                                                                               cATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAAAAAGTGCAAAGCCAATCCCAATTGAATAATCTACAGTACAGCCAATGATAAAAACACGCGCTTCAGGTCCTACAACAatat                                                             >  2:614836/1‑141 (MQ=255)

                                                                                   ttCTCGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAAAAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAAc                                                         <  1:56557/141‑1 (MQ=255)

                                                                                   ttCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAAAAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAAc                                                         <  1:671998/141‑1 (MQ=255)

                                                                                   tccTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAAAAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAAc                                                         <  1:521407/139‑1 (MQ=255)

                                                                                    tCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGATGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACa                                                        <  1:392215/141‑1 (MQ=255)

                                                                                    tCTACGTCACACTCATAACGAATGACTTCACGAGCTAATTTCCCTCC‑TTTTCTAACAGGTGCAAAGCCAAACCCCATTGAATAAGCTACACTACAGCCAATGATAAAGCCACGCGCTTCAAGTCCTACAACGATATCAACa                                                        <  2:615265/141‑1 (MQ=255)

                                                                                          tCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAAAAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTg                                                  >  1:650384/1‑141 (MQ=255)

                                                                                          tCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAAAAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACACCCAATGATAAAGCCACGCCCTTCAGGTCCTACAACGATATCAACATCTCTg                                                  >  2:613384/1‑141 (MQ=255)

                                                                                           cagaCTCATAACGAATGCACGCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCACTCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGt                                                 <  2:10821/138‑1 (MQ=255)

                                                                                           cATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCCACATCTCTGt                                                 >  1:837804/1‑141 (MQ=255)

                                                                                             tACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCt                                               >  1:946735/1‑141 (MQ=255)

                                                                                               cTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCttt                                             <  1:742312/141‑1 (MQ=255)

                                                                                               cTCATAACGAATGACTTCACGACGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCttt                                             <  2:384978/141‑1 (MQ=255)

                                                                                                tCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCtttt                                            >  2:258946/1‑141 (MQ=255)

                                                                                                     aCGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCgca                                       >  1:789119/1‑139 (MQ=255)

                                                                                                     aCGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGATGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTa                                       >  1:589597/1‑141 (MQ=255)

                                                                                                     aCGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGATGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACAACTATGTCTTTTGAGTa                                       >  2:492252/1‑141 (MQ=255)

                                                                                                         aTGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGATCCAGGTCCAACAACGATATCAACATCTCTGTATTTTGCTTATTCt                                   >  1:638447/1‑141 (MQ=255)

                                                                                                         aTGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGCCAGCCAATGATAAAGCCACGACCGTCAGGTCCTACAACGATATCAACATCCCTGTCTTTTGCGCATTCt                                   >  2:108612/1‑141 (MQ=255)

                                                                                                           gaatgcACGAGGTAATTCCCCTTC‑TTTTCTAACAGGTGCAAAGGCAATCCCCATGGAATAAGCTACAGGACAGCCAATGATAATGCCACGCGCTTCAGGTCGTACAACGAGATCAACATCTCTGTCTTTTGCGCATTCTAc                                 <  2:99820/136‑1 (MQ=255)

                                                                                                             cTTCACGAGGTAATTTCCCTTC‑TTTTCTAAAAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGCCTTTTACGTATTCTACaa                               >  2:635366/1‑141 (MQ=255)

                                                                                                                cacaaagTAATTTCTCTTC‑TTTTCTAACATGTGCAAAGCCAATCCTCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACTATATCAACATCTCTGTCTTTTGCGCATTCTACAAttt                            <  2:330444/135‑1 (MQ=255)

                                                                                                                cACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAGTAAGCTACAGGACAGCCAATGTTAAAGCCACGCGCTTCAGGTCCTACAACGCTATCAAAATCTCTGTCTTTTGCGCATACAACAAtat                            >  1:77887/1‑139 (MQ=255)

                                                                                                                cACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAAttt                            <  2:805107/141‑1 (MQ=255)

                                                                                                                   gAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTAt                         <  1:763882/141‑1 (MQ=255)

                                                                                                                   gAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTAt                         <  1:408263/141‑1 (MQ=255)

                                                                                                                    aGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATc                        <  1:91442/141‑1 (MQ=255)

                                                                                                                               cttc‑ttTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGCATTCTACAATTTTATCTGTTGCATAGc             <  2:449996/141‑1 (MQ=255)

                                                                                                                               cttc‑ttTTCTAAACGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCAGAGc             >  2:62659/1‑141 (MQ=255)

                                                                                                                                 tc‑ttTTCAAACAGGTGCAAAGCAAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCCTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCa           <  2:290809/141‑1 (MQ=255)

                                                                                                                                  ttttttCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGCATTCTACAATTTTATCTGTTGCATAGCCa           <  1:250602/139‑1 (MQ=255)

                                                                                                                                    ttttCTAAAAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCata         <  2:760116/141‑1 (MQ=255)

                                                                                                                                      ttCTAACACGTGCAAAGCCAACCCCCATCGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCTTACAACGATATCAACATCTCTGTCTTTTGCGCATTCTACAATTTTATCTGTTGCATAGCCATATg       <  1:655005/141‑1 (MQ=255)

                                                                                                                                        cTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGCATTCTACAATTTTATCTGTTGCATATCCATATGCt     >  1:427424/1‑141 (MQ=255)

                                                                                                                                           aCAGATGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGTGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCa  <  1:769344/141‑1 (MQ=255)

GTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTC‑TTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCA  >  USA300TCH1516_ALE/1744304‑1744582

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