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 F54 I1 R1	12	114.1	2913296	89.9%	2619053	134.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,664,005	G→A	P134L (CCT→CTT)	pbpH ←	Penicillin‑binding protein H

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,664,005	0	G	A	92.2%	268.8 / 11.0	104	P134L (CCT→CTT)	pbpH	Penicillin‑binding protein H
Reads supporting (aligned to +/- strand): ref base G (5/3); new base A (46/48); total (53/51)
Fisher's exact test for biased strand distribution p-value = 7.15e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.54e-01

Only 100 of 104 total aligned reads displayed.

TAAATCTTTAGAAGACAATTCATCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAGGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATTGTGTTGTTTTTCGACCCCTAGTATATGTAATA  >  USA300TCH1516_ALE/1663869‑1664142

tAAATCTTTAGAAGACAATTCATCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATg                                                                                                                                       >  2:152075/1‑141 (MQ=255)

 aaaTCTTTAGAAGACAATTCATCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGc                                                                                                                                      <  1:577429/141‑1 (MQ=255)

 aaaTCTTTAGAAGACAATTCATCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGc                                                                                                                                      <  1:991209/141‑1 (MQ=255)

 aaaTCTTTAGAAGACAATTCATCTAATTGTGATTTTACGATTTTCGATAACAGTTGTTTATCATATTGGTCTTGTTTAATACTTCCATATGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATga                                                                                                                                      >  1:332518/1‑140 (MQ=255)

  aaTCTTTAGAAGACAATTCATCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCa                                                                                                                                     <  1:365882/141‑1 (MQ=255)

  aaTCTTTAGAAGACAATTCATCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCa                                                                                                                                     >  2:889087/1‑141 (MQ=255)

   aTCTTTAGAAGACAATTCATCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCaa                                                                                                                                    <  1:701314/141‑1 (MQ=255)

   aTCTTTAGAAGACAATTCATCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCaa                                                                                                                                    <  1:701325/141‑1 (MQ=255)

      tttAGAAGACAATTCATCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTg                                                                                                                                 <  4:403878/141‑1 (MQ=255)

         agaagaCAATTCATCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGTTGCAACTGAAt                                                                                                                              >  1:482134/1‑141 (MQ=255)

         agaagaCAATTCATCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAAt                                                                                                                              >  2:159512/1‑141 (MQ=255)

         agaagaCAATTCATCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAAt                                                                                                                              >  2:113128/1‑141 (MQ=255)

           aagaCAATTCATCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATcc                                                                                                                            <  2:950153/141‑1 (MQ=255)

           aagaCAATTCATCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATcc                                                                                                                            >  3:50191/1‑141 (MQ=255)

           aagaCAATTCATCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATcc                                                                                                                            <  4:334067/141‑1 (MQ=255)

            agaCAATTCATCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCa                                                                                                                           <  2:296450/141‑1 (MQ=255)

             gaCAATTCATCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAg                                                                                                                          >  4:236532/1‑141 (MQ=255)

                   tCATCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAAtct                                                                                                                    >  2:365610/1‑141 (MQ=255)

                      tCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAAtctttc                                                                                                                 >  1:13006/1‑141 (MQ=255)

                        tAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGAGCTTGTTTAAGACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAAtctttctt                                                                                                               <  1:854710/141‑1 (MQ=255)

                          aTTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTAt                                                                                                             <  3:269723/141‑1 (MQ=255)

                             gtgATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCAc                                                                                                          <  3:72389/141‑1 (MQ=255)

                               gATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGt                                                                                                        <  1:778558/141‑1 (MQ=255)

                                 ttttCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTc                                                                                                      <  1:598802/141‑1 (MQ=255)

                                 ttttCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTc                                                                                                      >  2:975738/1‑141 (MQ=255)

                                   ttCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTg                                                                                                    <  2:151257/141‑1 (MQ=255)

                                   ttCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTGTAGGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTg                                                                                                    >  2:969098/1‑141 (MQ=255)

                                     ccGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTa                                                                                                  <  1:247749/141‑1 (MQ=255)

                                      cGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCAGGTTCTGTaa                                                                                                 <  1:891711/141‑1 (MQ=255)

                                             cGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAGGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCtt                                                                                          >  2:710440/1‑141 (MQ=255)

                                             cGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAGGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCtt                                                                                          >  2:76347/1‑141 (MQ=255)

                                             cGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCtt                                                                                          <  2:705863/141‑1 (MQ=255)

                                             cGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCATTTGCTTTTTTAGGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCtt                                                                                          >  2:540811/1‑141 (MQ=255)

                                              gATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTa                                                                                         >  1:294354/1‑141 (MQ=255)

                                                tAACAGTTGTTTATCAGATTGAGCTTGGTTAATATGTCCATCTTCTAACATAGCTTTTCCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCGTATCACGTTCTGTAATTTTCTTAGt                                                                                       >  2:857613/1‑141 (MQ=255)

                                                    aGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATcc                                                                                   <  2:787939/141‑1 (MQ=255)

                                                       tgttTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATc                                                                                >  1:902546/1‑141 (MQ=255)

                                                          ttATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTg                                                                             <  3:237390/141‑1 (MQ=255)

                                                           tATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATGTTCTTAGTATCCATCTTGa                                                                            <  2:3330/141‑1 (MQ=255)

                                                            aTCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAGGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGAt                                                                           <  1:970563/141‑1 (MQ=255)

                                                            aTCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGAt                                                                           >  1:873874/1‑141 (MQ=255)

                                                             tCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGAtt                                                                          <  2:902546/141‑1 (MQ=255)

                                                                tatTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGc                                                                       <  3:295053/141‑1 (MQ=255)

                                                                  ttGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCtt                                                                     <  1:162012/141‑1 (MQ=255)

                                                                  ttGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCtt                                                                     <  1:162026/141‑1 (MQ=255)

                                                                    gATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTg                                                                   <  1:331054/141‑1 (MQ=255)

                                                                    gATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTg                                                                   >  3:20237/1‑141 (MQ=255)

                                                                    gATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTg                                                                   >  1:73149/1‑141 (MQ=255)

                                                                    gATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTg                                                                   <  1:363863/141‑1 (MQ=255)

                                                                    gATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTg                                                                   <  1:364193/141‑1 (MQ=255)

                                                                     aTCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGa                                                                  <  1:181570/141‑1 (MQ=255)

                                                                     aTCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGa                                                                  >  1:174552/1‑141 (MQ=255)

                                                                      tCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCATCTGAATCCAGAAATCTTTCTTATCACGTGCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGAt                                                                 >  1:707945/1‑141 (MQ=255)

                                                                      tCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGAt                                                                 <  3:187821/141‑1 (MQ=255)

                                                                         tGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAAc                                                              >  1:948607/1‑141 (MQ=255)

                                                                         tGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAAc                                                              <  3:44650/141‑1 (MQ=255)

                                                                           tttAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACtt                                                            >  1:848621/1‑141 (MQ=255)

                                                                             tAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACtttt                                                          >  3:285889/1‑141 (MQ=255)

                                                                             tAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACtttt                                                          >  1:1000946/1‑141 (MQ=255)

                                                                              aaTACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTTTTTTTTTTCTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACttttt                                                         >  2:870932/1‑140 (MQ=255)

                                                                              aaTACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTc                                                         <  2:909701/141‑1 (MQ=255)

                                                                               aTACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAGGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCa                                                        >  2:127185/1‑141 (MQ=255)

                                                                                 aCTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGc                                                      <  1:20966/141‑1 (MQ=255)

                                                                                       aTCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCCTTATTAGTTTTGATAACTTTTCATCCGTATc                                                >  4:262315/1‑141 (MQ=255)

                                                                                        tCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTg                                                                                                    <  1:434131/88‑1 (MQ=255)

                                                                                        tCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTg                                                                                                    >  2:434131/1‑88 (MQ=255)

                                                                                          tGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCaa                                             >  2:273383/1‑141 (MQ=255)

                                                                                           gCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAAc                                            >  1:724465/1‑141 (MQ=255)

                                                                                            cTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACa                                           >  2:584543/1‑141 (MQ=255)

                                                                                            cTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACa                                           >  1:452658/1‑141 (MQ=255)

                                                                                            cTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACa                                           >  3:314691/1‑141 (MQ=255)

                                                                                               aCATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACAttt                                        >  4:24064/1‑141 (MQ=255)

                                                                                                   aGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGa                                    >  1:691060/1‑141 (MQ=255)

                                                                                                    gCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGc                                                      >  1:244713/1‑122 (MQ=255)

                                                                                                      ttGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATtg                                 <  1:365610/141‑1 (MQ=255)

                                                                                                       tgtgCTTTTGTCAGCGTTGCTTTTGCTTTTTCAGGAGGCAGCTGAATCCAGGAATCCTATTTTTCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATtgt                                <  1:854393/141‑1 (MQ=255)

                                                                                                       tGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATtgt                                <  2:834944/141‑1 (MQ=255)

                                                                                                       tGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCAACTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATtgt                                >  3:239251/1‑141 (MQ=255)

                                                                                                        gTTCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATtgtg                               <  2:409605/141‑1 (MQ=255)

                                                                                                         ttCTTTTGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATTgtgt                              >  2:497401/1‑141 (MQ=255)

                                                                                                            ttttGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATTGtgttgt                           >  2:867613/1‑141 (MQ=255)

                                                                                                            ttttGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATTGtgttgt                           <  1:375672/141‑1 (MQ=255)

                                                                                                             tttGTCATCATTGCTTTTGCTTTTTTATTTTGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATTGTgttgtt                          >  4:135580/1‑141 (MQ=255)

                                                                                                             tttGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATTCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATTGTgttgtt                          <  4:23160/141‑1 (MQ=255)

                                                                                                               tGTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATTGTGTTGtttt                        >  1:248849/1‑141 (MQ=255)

                                                                                                                gTCATCATTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATTGTGTTGttttt                       <  2:822180/141‑1 (MQ=255)

                                                                                                                 tcatcaTTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATTGTGTTGTTTTTc                      >  2:182830/1‑141 (MQ=255)

                                                                                                                    tcatTGCTTTTGCTTTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATTGTGTTGTTTTTCGAc                   <  2:294354/141‑1 (MQ=255)

                                                                                                                     tatTGCTTTTCCATCTTTAAGATCCATCTAAACTGAGACATCTGTATTCTCTCGTTCTGTAATTTTATATGTAAACAACTATAATAGCTTTGATAACTTTTCAGCCTTATCCAATAGTTCCGATTGGGTTGtttttgtacc                  <  4:191926/140‑6 (MQ=255)

                                                                                                                       ttgcttttgcttTTTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATTGTGTTGTTTTTCGAcccc                <  1:510387/141‑1 (MQ=255)

                                                                                                                            tttgcttttTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATTGTGTTGTTTTTCGACCCCTAGta           >  2:918100/1‑141 (MQ=255)

                                                                                                                             ttgcttttTTAATATGCAACTTAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGTTTGTGTTGTTTTTCGACCCCTAGtat          >  2:511287/1‑141 (MQ=255)

                                                                                                                             ttgcttttTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATTGTGTTGTTTTTCGACCCCTAGtat          <  3:402683/141‑1 (MQ=255)

                                                                                                                              tgcttttTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTa                                                                                                  >  1:932655/1‑52 (MQ=255)

                                                                                                                              tgcttttTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTa                                                                                                  <  2:932655/52‑1 (MQ=255)

                                                                                                                                cttttTTAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATTGTGTTGTTTTTCGACCCCTAGTATATg       >  4:1678/1‑141 (MQ=255)

                                                                                                                                    tttAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATTGTGTTGTTTTTCGACCCCTAGTATATGTAAt   >  1:28248/1‑141 (MQ=255)

                                                                                                                                    tttAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATTGTGTTGTTTTTCGACCCCTAGTATATGTAAt   >  2:167527/1‑141 (MQ=255)

                                                                                                                                    tttAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATTGTGTTGTTTTTCGACCCCTAGTATATGTAAt   >  2:961362/1‑141 (MQ=255)

                                                                                                                                     ttAAGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATTGTGTTGTTTTTCGACCCCTAGTATATGTAATa  <  2:161348/141‑1 (MQ=255)

TAAATCTTTAGAAGACAATTCATCTAATTGTGATTTTCCGATTTTCGATAACAGTTGTTTATCATATTGATCTTGTTTAATACTTCCATCTGCTAACATAGCTTGTTCTTTTGTCATCATTGCTTTTGCTTTTTTAGGATGCAACTGAATCCAGAAATCTTTCTTATCACGTTCTGTAATTTTCTTAGTATCCATCTTGATTAGCTTTGATAACTTTTCAGCCGTATCCAACATTTCCGATTGTGTTGTTTTTCGACCCCTAGTATATGTAATA  >  USA300TCH1516_ALE/1663869‑1664142

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