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
A15 F70 I0 R1	32	71.1	1611198	94.9%	1529026	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,300,370	C→G	20.1%	A156P (GCT→CCT)	emrY ←	putative multidrug resistance protein EmrY

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,300,370	0	C	G	20.1%	138.0 / 31.5	64	A156P (GCT→CCT)	emrY	putative multidrug resistance protein EmrY
Reads supporting (aligned to +/- strand): ref base C (21/30); new base G (4/9); total (25/39)
Fisher's exact test for biased strand distribution p-value = 5.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.72e-01

CGCTTATCTAATTTCGTATATTTCACTTCATTGTAACTCGAGATTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATAACGTAAATTGCATTAAGGGCATAAGTACGCCTGCACCCATCGCTTGAATT  >  USA300TCH1516_ALE/2300231‑2300509

cGCTTATCTAATTTCGTATATTGCACTTCATTGTAACTCGAGATTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGAGCAATAATTGATCctgtagc                                                                                                                                             >  1:174016/1‑140 (MQ=255)

   ttATCTAATTTCGTATATTTCACTTCATTGTAACTCGAGATTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATCATACACATTCATCCGCGTCAACTCGCTTGATCAATAATTAATCctgtagctgt                                                                                                                                          >  2:777643/1‑140 (MQ=255)

    tATCTAATTTCGTATATTTCACTTCATTGTAACTCGAGATTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCACTAATTAATCctgtaggtgta                                                                                                                                         >  2:638525/1‑140 (MQ=255)

     aTCTAATTTCGTATATTTCACTTCATTGTAACTCGAGATTGACACCAAACCGACAGCAAAGGCAAGTAGAGCAATCCCTAAAATTATACTAACAGGAACTTACCAACTCGATTGATCACTAATGAATCcggtagctgtag                                                                                                                                        >  2:194227/1‑140 (MQ=255)

      tCTAATTTCGTATATTTCACTTCATTGTAACTCGAGATTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAgg                                                                                                                                       <  1:164740/140‑1 (MQ=255)

       cTAATTTCGTATATTTCACTTCATTGTAACTCGAGATTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGt                                                                                                                                      <  1:514705/140‑1 (MQ=255)

            ttggTATATTTCACTTCATTGTAACTCGAGATTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGGTGTAGGTCCTAt                                                                                                                                 <  2:564878/137‑1 (MQ=255)

              cGTATATTTCACTTCATTGTAACTCGAGATTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGGAGCTGTAGGTCCTATTg                                                                                                                               >  1:189351/1‑140 (MQ=255)

                 atatTTCACTTCATTGTAACTCGAGATTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTg                                                                                                                            >  1:615030/1‑140 (MQ=255)

                 atatTTCACTTCATTGTAACTCGAGATTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTg                                                                                                                            >  1:212241/1‑140 (MQ=255)

                   atTTCACTTCATTGTAACTCGAGATTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGGTGTAGGTCCTATTGCTGGt                                                                                                                          <  1:560124/140‑1 (MQ=255)

                   atTTCACTTCATTGTAACTCGAGATTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGt                                                                                                                          <  1:525779/140‑1 (MQ=255)

                    tttCACTTCATTGTAACTCGAGATTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTg                                                                                                                         <  1:559101/140‑1 (MQ=255)

                       cACTTCATTGTAACTCGAGATTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCaa                                                                                                                      <  1:516772/140‑1 (MQ=255)

                             agtGTAACTCGAGATTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGaa                                                                                                                <  1:570816/138‑1 (MQ=255)

                               tGTAACTCGAGATTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAAtt                                                                                                              <  2:672340/140‑1 (MQ=255)

                               tGTAACTCGAGATTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAAATGCCCATCTCACTTGATCAATAATCAACCCGGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAAtt                                                                                                              <  1:590655/140‑1 (MQ=255)

                                  aaCTCGAGATTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACt                                                                                                           >  1:413748/1‑140 (MQ=255)

                                        acaTTGAAACCAAACCGAAAACAATGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGGTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCt                                                                                                     <  2:310823/138‑1 (MQ=255)

                                         gaTTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTg                                                                                                    <  2:212241/140‑1 (MQ=255)

                                         gaTTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTg                                                                                                    <  2:615030/140‑1 (MQ=255)

                                           tggAAACCAAACCGAACACAAAGGCAACGATAGCAATTCCTAAAATTATAATAAATCGAACTCGCCAACTCGCTTGATCAATTATTAATCCTTTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCt                                                                                                  <  2:261234/138‑1 (MQ=255)

                                            tGAAACCAGACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGGACTCGCCAACTCGCTTGATCAGTAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTa                                                                                                 <  2:296229/140‑1 (MQ=255)

                                             gAAACCACACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGAAACCCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTCGTGCAAATTGAATCACTAAACCTGCCAg                                                                                                >  2:141072/1‑140 (MQ=255)

                                                accaaaccGAAAACAAAGGCAAGTATAGCCATGCCTAGAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGGTGCAGGCCCTATCGCGGGTGCAAACGGAATTACTGAAACTGCCAGccc                                                                                             >  2:657319/1‑140 (MQ=255)

                                                     accGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGGTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTg                                                                                        <  1:552793/140‑1 (MQ=255)

                                                      ccGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCCTTTCGCCACATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGc                                                                                       <  1:587047/140‑1 (MQ=255)

                                                      ccGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGc                                                                                       <  2:62763/140‑1 (MQ=255)

                                                      ccGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGc                                                                                       <  1:291537/140‑1 (MQ=255)

                                                            aCAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAAcc                                                                                 >  1:121033/1‑140 (MQ=255)

                                                             cAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGCTCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTCCTAAACCTACTAGTCCCATTGCAAAACCt                                                                                >  2:157024/1‑140 (MQ=255)

                                                             cAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGAAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATGGCAAAACCt                                                                                >  2:477725/1‑140 (MQ=255)

                                                             cAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATACTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCt                                                                                >  2:355045/1‑140 (MQ=255)

                                                              aaaGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTc                                                                               <  2:119152/140‑1 (MQ=255)

                                                                aGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGa                                                                             >  2:632257/1‑140 (MQ=255)

                                                                 ggCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGAt                                                                            <  1:694445/140‑1 (MQ=255)

                                                                    aattataGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGGTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGtt                                                                         <  1:38258/137‑1 (MQ=255)

                                                                    aaGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGtt                                                                         <  2:271238/140‑1 (MQ=255)

                                                                     aGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGGTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTc                                                                        <  2:100140/140‑1 (MQ=255)

                                                                              aTTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGaa                                                               <  1:505772/140‑1 (MQ=255)

                                                                               ttCCTAAAATTATAATAACTGGTTAACGAAAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCATATTGCTGGTGCAAATTGAATTACTAAACCTGATACTCCCCTTGCAAAACCTCGATGTTCTCTACTGAAc                                                              >  2:59760/1‑140 (MQ=255)

                                                                                   tAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATg                                                          >  2:189731/1‑140 (MQ=255)

                                                                                   tAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATg                                                          >  1:437443/1‑140 (MQ=255)

                                                                                   tAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTATAGGTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATg                                                          >  2:115601/1‑140 (MQ=255)

                                                                                        ttATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGGTGTAGGTCCTATTGCTGGTGCAAATTAAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAAt                                                     >  1:717933/1‑140 (MQ=255)

                                                                                        ttATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAACTAATGCGAACAAGGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAACGTAAAt                                                     <  1:586800/140‑1 (MQ=255)

                                                                                               aactGGGACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATAACGTaa                                              <  2:570046/137‑1 (MQ=255)

                                                                                               aaaTGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCCTTGCAAAACCTCGATGTTCTTTACTGAACACTGTAAATAACGTaa                                              >  1:87230/1‑140 (MQ=255)

                                                                                               aaaTGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACACTGTAAATAACGTaa                                              >  2:41562/1‑140 (MQ=255)

                                                                                               aaaTGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATAACGTaa                                              <  2:762684/140‑1 (MQ=255)

                                                                                                aaTGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATAACGTaaa                                             <  1:346197/140‑1 (MQ=255)

                                                                                                 aTGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGGTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATACCGTAAAt                                            >  1:551331/1‑140 (MQ=255)

                                                                                                 aTGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTACGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAATACCTCGATGTTCTTTACTGAACAATGTAAATAACGTAAAt                                            <  2:779698/140‑1 (MQ=255)

                                                                                                   ggAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATAACGTAAATTg                                          <  1:641383/140‑1 (MQ=255)

                                                                                                    gAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATAACGTAAATTGc                                         <  1:331486/140‑1 (MQ=255)

                                                                                                         cGCCATCTCGCTTGATCCATAATTAGTCCTGTAGGTGGAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCGTTGCAAAGCCTCGATGTTCTTTACTGAACAATGTAAATAACGTAAATTGCATTaa                                    <  2:482266/140‑1 (MQ=255)

                                                                                                         cGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATAACGTAAATTGCATTaa                                    <  2:43409/140‑1 (MQ=255)

                                                                                                         cGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATAACGTAAATTGCATTaa                                    <  2:165329/140‑1 (MQ=255)

                                                                                                                    ttGATCAATAATTAATCCTGTAGGTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATAACGTAAATTGCATTAAGGGCATAAGTa                         <  2:333928/140‑1 (MQ=255)

                                                                                                                     tGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATAACGTAAATTGCATTAAGGGCATAAGTAc                        >  2:296855/1‑140 (MQ=255)

                                                                                                                      gATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATAACGTAAATTGCATTAAGGGCATAAGTACg                       >  1:118711/1‑140 (MQ=255)

                                                                                                                            taattaatCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATAACGTAAATTGCATTAAGGGCATAAGTACGCATGCa                 >  2:621141/1‑140 (MQ=255)

                                                                                                                                taatCCTGTAGGTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATAACGTAAATTGCATTAAGGGCATAAGTACGCCTGCACCCa             <  2:71891/140‑1 (MQ=255)

                                                                                                                                taatCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGAAAAACCTCGCTGTTCTTTACTGAACAATGTAAATAACGTAAATTGCATTAAGTGCATAAGTACAACTGCAcccc             >  1:506563/1‑139 (MQ=255)

                                                                                                                                taatCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATGGAATTACTAAACATGCTAGTTCCGTTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATAACGTGACTTGCATTAAGGGCGTAAGGACGCCTGCGCCCa             >  1:305904/1‑140 (MQ=255)

                                                                                                                                 aatCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATAACGTAAATTGCATTAAGGGCATAAGTACGCCTGCACCCAt            >  2:421507/1‑140 (MQ=255)

                                                                                                                                 aatCCTGTAGCTGGAGGTCGTACTGCTGGTGCAAATTGAATCACTAAACCTGCTAGTCCCATTGCAAAACCTCGAGGTTCGTTACTGAACAATGTAACTACCGTAGTTTTCATTAATGGCATAAGTACGCCTGCACCCAt            <  2:174016/140‑1 (MQ=255)

                                                                                                                                  atCCTGTAGCTGTAGGGCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGACGATCTTTACTGAACAATGTAAATAACGTAAATTGCATTAAGGGCATAAGTACGCCTGCACCCATc           <  1:719363/140‑1 (MQ=255)

                                                                                                                                     ctgttggtgtagGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATAACGTAAATTGCATTAAGGGCATAAGTACGCCTGCACCCATCGCt        <  2:554858/140‑1 (MQ=255)

                                                                                                                                     ctgtagctgtagGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATAACGGAAATTGCATTAAGGGCATAAGTACGCCTGCACCCATCGCt        >  2:219476/1‑140 (MQ=255)

                                                                                                                                       gtagctgtagGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCCTTGCAACACCTCGATGTTCTTTACTGCACAATCCGCGGTTCGGTAATTGCATTAAGGGCATAAGTACTCCTGCACCCATCGCTTg      >  1:584186/1‑140 (MQ=255)

                                                                                                                                       gtagctgtagGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATAACGTAAATTGCATTAAGGGCATAAGTACGCCTGCACCCATCGCTTg      >  1:553187/1‑140 (MQ=255)

                                                                                                                                           ctgtagGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACGATGTTAATAACGTAAATTGCATTAAGGGCATAAGTACGCCTGCACCCATCGCTTGAAtt  <  1:114722/140‑1 (MQ=255)

CGCTTATCTAATTTCGTATATTTCACTTCATTGTAACTCGAGATTGAAACCAAACCGAAAACAAAGGCAAGTATAGCAATTCCTAAAATTATAATAAATGGAACTCGCCAACTCGCTTGATCAATAATTAATCCTGTAGCTGTAGGTCCTATTGCTGGTGCAAATTGAATTACTAAACCTGCTAGTCCCATTGCAAAACCTCGATGTTCTTTACTGAACAATGTAAATAACGTAAATTGCATTAAGGGCATAAGTACGCCTGCACCCATCGCTTGAATT  >  USA300TCH1516_ALE/2300231‑2300509

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