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 F178 I1 R1	28	89.4	2015306	95.8%	1930663	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	39,672	C→A	V488F (GTT→TTT)	pbp ←	Beta‑lactam‑inducible penicillin‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	39,672	0	C	A	98.8%	244.2 / NA	81	V488F (GTT→TTT)	pbp	Beta‑lactam‑inducible penicillin‑binding protein
Reads supporting (aligned to +/- strand): ref base C (1/0); new base A (49/30); total (51/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTACCACTTCATATCTTGTAA  >  USA300TCH1516_ALE/39537‑39806

aaaGGATCTGTACGGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCt                                                                                                                                    <  2:597945/140‑1 (MQ=255)

    gATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGtt                                                                                                                                >  1:420934/1‑140 (MQ=255)

    gATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAAtt                                                                                                                                >  1:764826/1‑140 (MQ=255)

    gATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCAACAAAACCTAGtt                                                                                                                                >  1:535582/1‑140 (MQ=255)

     aTCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTAACCAAAACCTAGttt                                                                                                                               <  1:748465/140‑1 (MQ=255)

      tCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGtttt                                                                                                                              >  1:784145/1‑140 (MQ=255)

        tGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATACCTTCACCAACACCTAGtttttt                                                                                                                            >  2:261535/1‑140 (MQ=255)

        tGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATACCTTCACCAAAACCTAGtttttt                                                                                                                            >  2:228571/1‑140 (MQ=255)

          tACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTct                                                                                                                          >  2:746291/1‑139 (MQ=255)

            cTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATg                                                                                                                        >  1:373058/1‑140 (MQ=255)

            cTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATg                                                                                                                        >  2:431334/1‑140 (MQ=255)

            cTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTGGGTATATCTTCACCAAAACCTAGTTTTTTCAta                                                                                                                        >  2:797473/1‑139 (MQ=255)

             tGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGc                                                                                                                       <  1:806288/140‑1 (MQ=255)

                  tAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCtttt                                                                                                                  <  1:778180/140‑1 (MQ=255)

                    aTCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTc                                                                                                                <  1:182186/140‑1 (MQ=255)

                     tCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATTTTTCATTATCTAAATTTTCGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACTAAAACCTAGTTTTTTCATGCCTTTTTCa                                                                                                               <  1:647314/140‑1 (MQ=255)

                     tCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCa                                                                                                               <  2:293688/140‑1 (MQ=255)

                     tCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCa                                                                                                               <  1:737043/140‑1 (MQ=255)

                     tCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCa                                                                                                               >  2:59544/1‑140 (MQ=255)

                     tCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATAACTTCACCAAAACCTAGTCTTTTCATGCCTTTTTCa                                                                                                               >  2:68560/1‑140 (MQ=255)

                         tATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAAtt                                                                                                           >  1:819174/1‑140 (MQ=255)

                         tATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAAtt                                                                                                           >  2:382584/1‑140 (MQ=255)

                           tttCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTc                                                                                                         <  2:182488/140‑1 (MQ=255)

                              cACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCCTCTTAAAATGGATAATAACTTGGTATATCTTCACCAGAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTa                                                                                                      >  1:481064/1‑140 (MQ=255)

                               aCCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTAc                                                                                                     >  2:261264/1‑140 (MQ=255)

                                   tGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGCTTTTTCATGCCTTTTTCAAATTTCTTACTGcc                                                                                                 >  2:558684/1‑140 (MQ=255)

                                   tGTCCGTAACCTGAACCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGcc                                                                                                 <  2:784145/140‑1 (MQ=255)

                                      ccGTAAGCTGAATCAGCGAATAATATATCATTATCTAAATTTTTGTTTGAAATTGGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCGAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTaa                                                                                              <  1:54586/140‑1 (MQ=255)

                                        gTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATGACTTGGTATATCTTCAACAAAACCTAGGTTTTTCATGCATTTTTCAAATTTCTTATTTCCTAAtt                                                                                            >  2:123406/1‑140 (MQ=255)

                                         tAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTc                                                                                           <  1:693592/140‑1 (MQ=255)

                                           aCCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGa                                                                                         <  2:810736/140‑1 (MQ=255)

                                             cTGAATCAGCTAATCATATTTCATTATCTAAATCTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATGTTCACTAAAACCTAGTTTTTTCATGCCTTTTTCAAATGTCTTACTGCCTAATTCGAGt                                                                                       <  1:610586/140‑1 (MQ=255)

                                             cTGAATCAGCTAATAATATTTTATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGt                                                                                       <  1:787542/140‑1 (MQ=255)

                                             cTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGt                                                                                       >  1:564731/1‑140 (MQ=255)

                                              tGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTg                                                                                      >  1:152893/1‑140 (MQ=255)

                                                     gCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTActct                                                                               >  1:534873/1‑140 (MQ=255)

                                                      cTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTa                                                                              >  1:105361/1‑140 (MQ=255)

                                                      cTAATAATATTTCATTATCTAAATTTTTCTTTGAAATTTGAGCATTATAAAATGAATAATCACTTGGTATATCTTCACCGAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTa                                                                              >  1:648677/1‑140 (MQ=255)

                                                         ataataTTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAAACTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCa                                                                           >  2:63419/1‑140 (MQ=255)

                                                         ataataTTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTAACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATCTCTTACTGCCTAATTCGAGTGATACTCTAGCa                                                                           >  2:561741/1‑140 (MQ=255)

                                                           aataTTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGCGTGCTACTCTAGCaaa                                                                         >  2:75544/1‑140 (MQ=255)

                                                              atTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGaa                                                                      >  1:171824/1‑140 (MQ=255)

                                                                ttCATTATCTACATTTTTGTTTGAAATTTGAGCATGATAAAATGGATAATCACTTGGTATATCTTCACCTAAACCTATTTTTTTCATGCCTTTTTCAAATTTCTTACTTCCTAATTCGAGTGCTACTCTAGCAAAGaaaa                                                                    <  2:779124/140‑1 (MQ=255)

                                                                ttCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTTTAGC‑AAGaaaag                                                                   >  2:126624/1‑139 (MQ=255)

                                                                ttCATTATCGAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATTACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGaaaa                                                                    <  2:508502/140‑1 (MQ=255)

                                                                  cgttATCTAAATTTTTGGTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGCGCTACTCTAGCAAAGAAAATg                                                                  <  1:515524/138‑1 (MQ=255)

                                                                  cATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTTCCCAATTCGAGTGCTACTCTCGCACAGAAAATg                                                                  >  2:102815/1‑140 (MQ=255)

                                                                        cTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAAACTAGTTTTTTCATGCCTTTTTCAATTTTCTTACTCCCTTATTCGAGTGCTACTCTATAAAAGCAAATGTTATCt                                                            >  2:584216/1‑140 (MQ=255)

                                                                           aaTTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCCATTGGTATTTCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCCAATTCGAGTGCTACTCTAGCCAACCAAATGTTATCtgat                                                         >  1:441120/1‑140 (MQ=255)

                                                                           aaTTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTTTTTTTTTTTTCTGCCTAATTCGAGTGATATTCTCACAAAGAATATCTTTTCtgtt                                                         >  2:329960/1‑138 (MQ=255)

                                                                           aaTTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCTTAATTCGAATACTACTCTAACAAAAAAAATATTCTCagat                                                         >  1:39695/1‑140 (MQ=255)

                                                                           aaTTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTCTCtggt                                                         >  1:339012/1‑138 (MQ=255)

                                                                           aaTTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCtgat                                                         >  2:642592/1‑140 (MQ=255)

                                                                               tttgtttgAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGAtt                                                     <  2:832545/140‑1 (MQ=255)

                                                                                 tgtttgAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGAGTCt                                                   <  2:588086/140‑1 (MQ=255)

                                                                                  ttttgAAATTTGAGTATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTa                                                  <  1:4594/139‑1 (MQ=255)

                                                                                  gtttgAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTa                                                  <  2:389290/140‑1 (MQ=255)

                                                                                  gtttgAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTa                                                  >  1:450054/1‑140 (MQ=255)

                                                                                   tttgAAATTTGGGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCCACTCTAGCAAAGAAAATGTTATCTGATGATTCTAt                                                 <  1:390194/140‑1 (MQ=255)

                                                                                   tttgAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACGAAAACCTAGGTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTAt                                                 <  1:606039/140‑1 (MQ=255)

                                                                                        aaTTTGAGCATGATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCtt                                            <  2:270758/140‑1 (MQ=255)

                                                                                           ttGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTTATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGtt                                         <  2:152366/140‑1 (MQ=255)

                                                                                            tGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTTAATTTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGTTGATTCTATTGCTTGttt                                        >  2:128292/1‑140 (MQ=255)

                                                                                              aGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTa                                      >  2:920218/1‑140 (MQ=255)

                                                                                               gCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTaa                                     >  2:127829/1‑140 (MQ=255)

                                                                                                  ttATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATTTGATGATTCTATTGATTGTTTTAAGTc                                  >  1:796965/1‑140 (MQ=255)

                                                                                                  ttATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTc                                  >  1:141536/1‑140 (MQ=255)

                                                                                                  ttATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTc                                  <  1:316989/140‑1 (MQ=255)

                                                                                                         aTGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTTTATTTTTTTAATGCCTAATTCGAGTGATACTCTAGCAAAGAAAATTTTCTCTGCTGAATCTTTTCCCTCTTTTAAGTCGATACTa                           >  2:16023/1‑140 (MQ=255)

                                                                                                              tAATCACTTGGTATATCTTCACCACAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTGTGAGGTCGATATTACCAtt                      <  2:714355/140‑1 (MQ=255)

                                                                                                              tAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTATATTGCTTGTTTTAAGTCGATATTACCAtt                      >  2:189482/1‑140 (MQ=255)

                                                                                                              tAATCACTTGGTATAGCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCAtt                      >  1:746788/1‑140 (MQ=255)

                                                                                                               aaTCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTCATCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGCGATTACCAttt                     >  2:852003/1‑140 (MQ=255)

                                                                                                                  cACTTGGTATTTCTTCACCATAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTAcc                  <  2:61433/140‑1 (MQ=255)

                                                                                                                  cACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTTTTTTTTTTTTCTTCCTAATTCGAGGGCTACTCTAGCAAAGAATGTGTTGTTTGATGATTCTTTTGCTTGTTTTCAGTCTATATTACTATTTTcc                  >  2:714784/1‑140 (MQ=255)

                                                                                                                  cACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTAcc                  >  2:642637/1‑140 (MQ=255)

                                                                                                                    cTTGGTATATCTTCACCCGTGTCAAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTAccgc                >  2:216371/1‑138 (MQ=255)

                                                                                                                           tatCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCACAGCGAGACAAAGTGGGTGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTACCACTTCatat         >  1:986614/1‑140 (MQ=255)

                                                                                                                           tatCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATCCTAGTGGTCCTTTTTCTAGGAAAATGTTATCTGGTGATGCGATTGCTTGTGTTAAGTCGATATTACCATTTGCCACTTCatat         >  1:990578/1‑140 (MQ=255)

                                                                                                                             tCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTACCACTTCATATCt       <  1:795352/140‑1 (MQ=255)

                                                                                                                                  aCCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCGTTTACCACTTCATTTCTTGTaa  >  1:263631/1‑140 (MQ=255)

AAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTACCACTTCATATCTTGTAA  >  USA300TCH1516_ALE/39537‑39806

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