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 I0 R1	76	110.5	2404748	96.5%	2320581	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,064,444	Δ1 bp	27.9%	coding (45/1218 nt)	ywtF ←	Putative transcriptional regulator YwtF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,064,444	0	A	.	27.9%	203.8 / 89.4	86	coding (45/1218 nt)	ywtF	Putative transcriptional regulator YwtF
Reads supporting (aligned to +/- strand): ref base A (30/31); new base . (12/12); total (42/44)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01

ATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCATTACTAATA  >  USA300TCH1516_ALE/1064304‑1064582

aTAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATgaga                                                                                                                                            >  2:674618/1‑141 (MQ=255)

aTAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATgaga                                                                                                                                            >  2:750422/1‑141 (MQ=255)

  aGGTTGTTCTTCGGGATTGACTTTATTATATCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAAc                                                                                                                                          >  1:639752/1‑141 (MQ=255)

    gttgttCTTCGGGATTGACTTTAATATCTCTTAAGGTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCa                                                                                                                                        <  2:653245/141‑1 (MQ=255)

     ttgttCTTCGGGATTGACTTTATTACCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCaa                                                                                                                                       <  2:83154/141‑1 (MQ=255)

     ttgttCTACGCGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCaa                                                                                                                                       <  2:835292/141‑1 (MQ=255)

      tgttCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGATGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAAt                                                                                                                                      >  1:524505/1‑141 (MQ=255)

       gttCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATg                                                                                                                                     >  1:994129/1‑141 (MQ=255)

         tcttcGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTa                                                                                                                                  >  2:666703/1‑141 (MQ=255)

           ttcGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAg                                                                                                                                 >  2:385083/1‑141 (MQ=255)

           ttcGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGACTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTATCGAAGACTATTGGAACAACAATGAGAACCAATGCTAg                                                                                                                                 <  2:893064/141‑1 (MQ=255)

             cGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAg                                                                                                                              >  1:825689/1‑141 (MQ=255)

               ggATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAgg                                                                                                                             >  2:260771/1‑141 (MQ=255)

               ggATTGACTTTATTATCTCTTAAGTTGAATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACCTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGa                                                                                                                            <  2:24517/141‑1 (MQ=255)

                 aTTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGAt                                                                                                                           >  2:90786/1‑141 (MQ=255)

                  ttGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATc                                                                                                                          <  1:1122310/141‑1 (MQ=255)

                  ttGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATc                                                                                                                          <  1:497548/141‑1 (MQ=255)

                   tGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTTTTTTTTTTTTTAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACATCAATTAG‑TCCAATGCTGGAAGGATcta                                                                                                                        >  2:136267/1‑139 (MQ=255)

                         tattatCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGt                                                                                                                   >  2:29274/1‑141 (MQ=255)

                         tattatCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGt                                                                                                                   <  1:229129/141‑1 (MQ=255)

                               ctctTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTa                                                                                                             >  1:1055635/1‑141 (MQ=255)

                                tctTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGGCGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTaaa                                                                                                           >  1:324129/1‑141 (MQ=255)

                                tctTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTaa                                                                                                            <  2:239520/141‑1 (MQ=255)

                                 ctTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTaaa                                                                                                           <  1:291078/141‑1 (MQ=255)

                                          gATTGACGATTAGCATTTTTTTTTTTTTGTGTTGTTTCGCATGCAACTTGGGCGGGATTAAAAAGTAACGTAGCGAAGACTATTGGAGCAACAATGAGAACCATTGCTAGAAGGCTCAAAACGTATTTTGAAATTTTAttt                                                                                                  >  2:134046/1‑140 (MQ=255)

                                           aTTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCa                                                                                                 >  1:199189/1‑141 (MQ=255)

                                             tGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCAtga                                                                                              <  1:445618/141‑1 (MQ=255)

                                              gACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCAtga                                                                                              <  1:457069/141‑1 (MQ=255)

                                              gACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCAtga                                                                                              <  1:614394/141‑1 (MQ=255)

                                               aCGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCAtgat                                                                                             <  1:1092251/141‑1 (MQ=255)

                                               aCGATTAGCATTTTTGCTGACTGTAGAAGATTCCAATGCATCTTGGGCCGTTTTAAAAAGTAACGTAGCGAAGACTATTGTAACAACAATGAGACCCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCAtgat                                                                                             <  1:40322/141‑1 (MQ=255)

                                                 gATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCAtgattg                                                                                           <  2:236652/141‑1 (MQ=255)

                                                   ttAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCAtgattgat                                                                                         <  1:795075/141‑1 (MQ=255)

                                                    tAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGc                                                                                       <  1:1136599/141‑1 (MQ=255)

                                                     aGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGc                                                                                       <  1:837598/141‑1 (MQ=255)

                                                     aGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGc                                                                                       <  1:311399/141‑1 (MQ=255)

                                                       cATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTc                                                                                     >  1:390631/1‑141 (MQ=255)

                                                               cTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTa                                                                             >  2:279754/1‑141 (MQ=255)

                                                               cTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTa                                                                             >  2:18638/1‑141 (MQ=255)

                                                                  tCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAAtt                                                                         >  2:741/1‑141 (MQ=255)

                                                                      gagaAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATTATTGATGCTCCTATATTAAAttttt                                                                      <  2:905505/141‑1 (MQ=255)

                                                                        gaagaTTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGt                                                                    <  1:1021028/141‑1 (MQ=255)

                                                                        gaagaTTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGtt                                                                   >  2:175528/1‑141 (MQ=255)

                                                                           gaTTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTaa                                                                 <  1:952980/141‑1 (MQ=255)

                                                                             ttCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAACTTTTTGTTAaat                                                               >  1:446621/1‑141 (MQ=255)

                                                                             ttCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAaat                                                               >  1:50012/1‑141 (MQ=255)

                                                                             ttCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATAAAAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTGATTCTAGATTGATGCTACTATCTTAAATTTTTATTAaat                                                               >  2:272603/1‑141 (MQ=255)

                                                                             ttCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAAGGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAaat                                                               >  1:522232/1‑141 (MQ=255)

                                                                              tCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAaatca                                                             >  2:170852/1‑141 (MQ=255)

                                                                               cGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGGAGGATCAAAAAGTATTTTAAGAATTTATTCATGATTGATGCTCATATATTAAATTTTTGTTAaatcat                                                            >  2:407335/1‑141 (MQ=255)

                                                                                 aaTGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAaatcata                                                           >  2:891697/1‑141 (MQ=255)

                                                                                 aaTGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAaatcata                                                           >  2:919009/1‑141 (MQ=255)

                                                                                    gCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAaatcataatc                                                        >  1:460423/1‑141 (MQ=255)

                                                                                    gCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAaatcataatca                                                       <  2:1041298/141‑1 (MQ=255)

                                                                                     cATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTGGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAaatcataatcat                                                      <  1:136267/141‑1 (MQ=255)

                                                                                         ttGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATcataatcataat                                                   >  1:997454/1‑141 (MQ=255)

                                                                                             gaagTTGTAAAAAGTCACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTCAAAAAACTACTTATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTa                                               <  1:35234/138‑1 (MQ=255)

                                                                                                  tttAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCACCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAata                                          <  2:639752/141‑1 (MQ=255)

                                                                                                  tttAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTGTTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAatat                                         >  2:858589/1‑141 (MQ=255)

                                                                                                   ttAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAAtata                                        <  1:990608/141‑1 (MQ=255)

                                                                                                     aaaaaGTTACGTAGAGAAGACTATTGGAACAACAATGA‑TGCCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAAt                                      <  2:128802/141‑1 (MQ=255)

                                                                                                     aaaaaGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATaa                                       >  1:233824/1‑141 (MQ=255)

                                                                                                     aaaaaGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCTTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAAt                                      <  1:544014/141‑1 (MQ=255)

                                                                                                     aaaaaGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAAt                                      <  1:1027209/141‑1 (MQ=255)

                                                                                                     aaaaaGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAAt                                      <  1:543998/141‑1 (MQ=255)

                                                                                                      aaaaGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAAt                                      <  1:390804/141‑1 (MQ=255)

                                                                                                       aaaGTAACGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTa                                    >  1:128455/1‑141 (MQ=255)

                                                                                                        aaGTAACGTAGCAAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTa                                    <  1:949155/141‑1 (MQ=255)

                                                                                                         aGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAg                                   <  1:385083/141‑1 (MQ=255)

                                                                                                         aGTAACCGAGCGAAGACTATTGGAACAACAATGATAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAg                                   <  2:93913/141‑1 (MQ=255)

                                                                                                             aCGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGa                               <  1:1091113/141‑1 (MQ=255)

                                                                                                              cGTAGCGAAGACTATTGGAACAACAATGAG‑ACCAATGCTAGTAGGATCAAATAGTATTTTATAAATTCATTCATGATTTGTGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAAc                             <  2:129693/141‑1 (MQ=255)

                                                                                                               gTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAAc                             >  2:629205/1‑141 (MQ=255)

                                                                                                                tAGCGAAGACTATTGGAACAGCGGTGAGAACCAATGCTCGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACg                            >  2:1158349/1‑141 (MQ=255)

                                                                                                                    gAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGatat                        <  1:673651/141‑1 (MQ=255)

                                                                                                                    gAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGatat                        <  1:298356/141‑1 (MQ=255)

                                                                                                                            ttGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGCAGGATATTTGTACaa                >  1:17312/1‑141 (MQ=255)

                                                                                                                             tGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTtatcataa               >  1:558002/1‑136 (MQ=255)

                                                                                                                             tGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAAc               >  1:1089151/1‑141 (MQ=255)

                                                                                                                             tGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTGAGATTATAATTAGTTGAACGATATTTATACAAc               >  1:326106/1‑141 (MQ=255)

                                                                                                                               gAACAAGAATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTc            <  1:105638/141‑1 (MQ=255)

                                                                                                                                 acaacaATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCa           <  2:977021/141‑1 (MQ=255)

                                                                                                                                 acaacaATGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCAt          <  2:825689/141‑1 (MQ=255)

                                                                                                                                    acaaTGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCATTAc       >  1:1034694/1‑141 (MQ=255)

                                                                                                                                    acaaTGAG‑ACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTCGAACGATAGTTATACAACTTAATTat       >  2:780757/1‑140 (MQ=255)

                                                                                                                                     caaTGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATTATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCATTAc       <  1:384873/141‑1 (MQ=255)

                                                                                                                                     caaTGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTAATTaa       >  2:94745/1‑140 (MQ=255)

                                                                                                                                        tGAGAACCAATGCTAGAAGGATCAAAAAGTCTTTTAAAAATTTATTCCTGATTTATGCTGCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCATTATTaa    >  2:543844/1‑141 (MQ=255)

                                                                                                                                          ggaACCAATGCTAGAATGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCATTACTAATa  <  1:581383/140‑1 (MQ=255)

                                                                                                                                          cgaAACAATGCTAGAAGCATCAAAAAGTATTTTGAAAATTTATTCATGATTGATTCGCCTATATTAAATTTTTGTTAAATCATAATCCTAATTTTAAAATATAATTAGTTGAACGATATTTATACCACTTCATTACTAATa  <  2:1105556/140‑1 (MQ=255)

                                                                                                                                          agaACCTATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATACTAATCTTAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCATTACTAATa  <  1:1124557/141‑1 (MQ=255)

                                                                                                                                          agaACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAATTATTATTAGTTGAACGATATTTATACAACTTCATTACTAATa  <  1:1129783/141‑1 (MQ=255)

                                                                                                                                          agaACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCATTACTAATa  <  1:629205/141‑1 (MQ=255)

                                                                                                                                          agaACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCATTACTAATa  <  1:711597/141‑1 (MQ=255)

ATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGCATCTTGGGACGTTTTAAAAAGTAACGTAGCGAAGACTATTGGAACAACAATGAGAACCAATGCTAGAAGGATCAAAAAGTATTTTAAAAATTTATTCATGATTGATGCTCCTATATTAAATTTTTGTTAAATCATAATCATAATTTTAAAATATAATTAGTTGAACGATATTTATACAACTTCATTACTAATA  >  USA300TCH1516_ALE/1064304‑1064582

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A