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
A16 F125 I0 R1	327	181.4	8809959	94.1%	8290171	99.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	3,658,002	C→T	20.4%	intergenic (+435/‑364)	hdeD → / → gadE	acid‑resistance membrane protein/gad regulon transcriptional activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,658,002	0	C	T	20.4%	461.6 / 101.6	218	intergenic (+435/‑364)	hdeD/gadE	acid‑resistance membrane protein/gad regulon transcriptional activator
Reads supporting (aligned to +/- strand): ref base C (98/75); new base T (19/26); total (117/101)
Fisher's exact test for biased strand distribution p-value = 9.49e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.42e-01

Only 100 of 231 total aligned reads displayed.

GCATAAATATCCGTGTCTCCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACTGGTTATTGA  >  NC_000913/3657903‑3658101

gCATAAATATCCGTGTCTCCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATc                                                                                                     <  2:748063/100‑1 (MQ=255)

gCATAAATATCCGTGTCTCCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATc                                                                                                     >  2:583852/1‑100 (MQ=255)

gCATAAATATCCGTGTCTCCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATc                                                                                                     >  2:1735207/1‑100 (MQ=255)

gCATAAATATCCGTGTCTCCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATc                                                                                                     >  2:628770/1‑100 (MQ=255)

 cATAAATATCCGTGTCTCCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATcc                                                                                                    >  2:3111868/1‑100 (MQ=255)

  aTAAATATCCGTGTCTCCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTTAGGTAATTTCAATGCGTTAAAAGACAGCTGGCAATCCa                                                                                                   <  1:2709234/100‑1 (MQ=255)

    aaaTATCCGTGTCTCCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAAt                                                                                                 <  2:3751812/100‑1 (MQ=255)

     aaTATCCGTGTCTCCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAAtt                                                                                                >  2:662086/1‑100 (MQ=255)

         tCCGTGTCTCCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCa                                                                                            >  2:3024693/1‑100 (MQ=255)

         tCCATGTCTCCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCa                                                                                            >  1:3961176/1‑100 (MQ=255)

           cGTGTCTCCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATTGGATTGCCAGc                                                                                          <  1:1134512/100‑1 (MQ=255)

           cGTGTCTCCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATTGGATTGCCAGc                                                                                          <  1:180732/100‑1 (MQ=255)

           cGTGTCTCCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGc                                                                                          <  2:1771760/100‑1 (MQ=255)

            gtgtCTCCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCGATGCGTTAAAAGAAAGCTGGCAATTGGATTGCCAGCt                                                                                         <  1:2352226/100‑1 (MQ=255)

            gtgtCTCCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATTGGATTGCCAGCt                                                                                         <  2:1934978/100‑1 (MQ=255)

            gtgtCTCCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATTGGATTGCCAGCt                                                                                         <  2:4280881/100‑1 (MQ=255)

            gtgtCTACAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCt                                                                                         <  2:819356/100‑1 (MQ=255)

             tgtCTCCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCtt                                                                                        <  1:2147086/100‑1 (MQ=255)

               tctcCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATTGGATTGCCAGCtttc                                                                                      <  1:2195090/100‑3 (MQ=38)

                ctcCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAg                                                                                     >  1:657421/1‑100 (MQ=255)

                ctcCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATACGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAg                                                                                     >  1:3385267/1‑100 (MQ=255)

                  ccAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATTGGATTGCCAGCtttcttt                                                                                   <  1:320797/100‑6 (MQ=38)

                  ccAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTc                                                                                   <  1:208153/100‑1 (MQ=255)

                  ccAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTc                                                                                   >  1:4133778/1‑100 (MQ=255)

                  ccAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTc                                                                                   >  1:1396324/1‑100 (MQ=255)

                   cAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCg                                                                                  >  1:2387766/1‑100 (MQ=255)

                   cAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCg                                                                                  <  1:1106938/100‑1 (MQ=255)

                     gACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATTGGATTGCCAGCtttcttttaa                                                                                <  2:1691399/100‑9 (MQ=37)

                       cGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAAc                                                                              >  1:1257994/1‑100 (MQ=255)

                        gCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACa                                                                             >  1:1471804/1‑100 (MQ=255)

                         cTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACaa                                                                            >  1:1056461/1‑100 (MQ=255)

                          tatataAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAg                                                                           >  1:2889966/1‑100 (MQ=255)

                           atataAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAgg                                                                          >  2:1449355/1‑100 (MQ=255)

                           atataAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAgg                                                                          <  2:3363932/100‑1 (MQ=255)

                            tataAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACagatc                                                                         >  1:3537082/1‑96 (MQ=255)

                            tataAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGga                                                                         >  1:4347148/1‑100 (MQ=255)

                            tataAAAACCTGAAGACATGAATGCGTTATTTACTCAGATAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTAACAGCTTAAATCGAAACAAGga                                                                         >  1:3681116/1‑100 (MQ=255)

                                 aaaCCTGAAGACATGAATGCGTTATATACTCAGATAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGgaga                                                                       <  1:4270655/97‑1 (MQ=255)

                                     cTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGata                                                                <  2:1257999/100‑1 (MQ=255)

                                      tGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGatat                                                               >  1:780510/1‑100 (MQ=255)

                                         aGACATGAATGCGTTATTTACTCAGGTAGTTTCTATGCGTTACAAGAAAGCTGGCAATCTAATTGCGAGCTTGAGTCGAAACAAGGAGACTCGatatgt                                                             >  2:4156377/1‑97 (MQ=255)

                                         aGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTa                                                            <  2:3937203/100‑1 (MQ=255)

                                            cATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAAt                                                         >  1:3502026/1‑100 (MQ=255)

                                            cATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAAt                                                         >  1:3752619/1‑100 (MQ=255)

                                            cATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAAt                                                         >  2:3441729/1‑100 (MQ=255)

                                              tGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATc                                                        >  1:4185243/1‑99 (MQ=255)

                                                aaTGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGa                                                     >  2:3848237/1‑100 (MQ=255)

                                                         tttACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACAtttt                                            >  1:366922/1‑100 (MQ=255)

                                                           tACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTaa                                          >  1:1012909/1‑100 (MQ=255)

                                                               cAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACttt                                      >  2:2611916/1‑100 (MQ=255)

                                                                aGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTa                                     >  2:220834/1‑100 (MQ=255)

                                                                aGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTa                                     <  2:2057258/100‑1 (MQ=255)

                                                                   tAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGt                                   <  1:1726368/99‑1 (MQ=255)

                                                                   tAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTa                                  <  2:250366/100‑1 (MQ=255)

                                                                      tttCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAata                               <  2:110850/100‑1 (MQ=255)

                                                                        tCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATAtt                             >  2:2148067/1‑100 (MQ=255)

                                                                          aaTGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTCACTTTAGTAATAttc                            >  1:2732208/1‑99 (MQ=255)

                                                                          aaTGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATAttct                           <  1:774107/100‑1 (MQ=255)

                                                                            tGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAATGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATAttcttc                         <  1:546944/100‑1 (MQ=255)

                                                                            tGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATAttcttc                         <  1:3253087/100‑1 (MQ=255)

                                                                             gCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATAttcttc                         <  1:1869330/99‑1 (MQ=255)

                                                                              cGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCag                       <  2:4133807/100‑1 (MQ=255)

                                                                              cGTTAAAAGAAAGCTGGCAATCCAATCGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCag                       <  2:4219678/100‑1 (MQ=255)

                                                                                ttAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCagag                     >  1:2942811/1‑100 (MQ=255)

                                                                                ttAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCagag                     <  2:2509213/100‑1 (MQ=255)

                                                                                 tAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAgaga                    <  2:2379391/100‑1 (MQ=255)

                                                                                  aaaaGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGAt                   <  2:3547776/100‑1 (MQ=255)

                                                                                  aaaaGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGAt                   >  1:4304096/1‑100 (MQ=255)

                                                                                   gacttaagCTGGGAATTGGATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATCACATTTTACCTTTAGTAATATTCTTCagag                     >  1:2014705/6‑97 (MQ=37)

                                                                                   aaagaaagCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGAt                   <  1:836277/99‑1 (MQ=255)

                                                                                   aaagaaagCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATc                  >  2:2868919/1‑100 (MQ=255)

                                                                                   aaagaaagCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATc                  >  2:2532996/1‑100 (MQ=255)

                                                                                   aaagaaagCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATc                  >  1:156022/1‑100 (MQ=255)

                                                                                   aaagaaagCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATc                  >  2:1554766/1‑100 (MQ=255)

                                                                                     agaaagCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATcac                <  2:2243928/100‑1 (MQ=255)

                                                                                       taagCTGGCAATTGGATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACaa              >  2:2269102/2‑100 (MQ=39)

                                                                                         agCTGGCAATTGGATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAAc            >  1:2656868/1‑100 (MQ=255)

                                                                                         agCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAAc            <  2:3223951/100‑1 (MQ=255)

                                                                                          ncTGGCAATTGGATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACt           >  2:2151061/2‑100 (MQ=255)

                                                                                          gCTGGCAATTGGATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACt           >  2:1596655/1‑100 (MQ=255)

                                                                                          gCTGGCAATTGGATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACt           >  1:1267634/1‑100 (MQ=255)

                                                                                          gCTGGCAATTGGATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACt           >  2:4114087/1‑100 (MQ=255)

                                                                                          gCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACt           <  1:3160089/100‑1 (MQ=255)

                                                                                          gCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACt           <  1:456719/100‑1 (MQ=255)

                                                                                          gCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACt           >  2:1047222/1‑100 (MQ=255)

                                                                                           cTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACTg          >  2:1425659/1‑100 (MQ=255)

                                                                                            tGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACTgg         >  2:2950684/1‑100 (MQ=255)

                                                                                            tGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACTgg         <  2:183870/100‑1 (MQ=255)

                                                                                             ggCAATTCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACTGGt        <  1:3092141/100‑1 (MQ=255)

                                                                                              gCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACTGGtt       <  2:868118/100‑1 (MQ=255)

                                                                                               cAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACTGGTTa      <  1:4059786/100‑1 (MQ=255)

                                                                                                 aaccAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACTGGTTAtt    <  1:2491952/98‑1 (MQ=255)

                                                                                                 aTCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACTGGTTAtt    <  2:3818110/100‑1 (MQ=255)

                                                                                                 aTCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACTGGTTAtt    <  1:2532984/100‑1 (MQ=255)

                                                                                                  tCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACTGGTTATTg   >  2:4074713/1‑100 (MQ=255)

                                                                                                  tCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACTGGTTATTg   <  1:3349717/100‑1 (MQ=255)

                                                                                                   ccAATTGCCAGCTTAAGTCGAAACAAGGATACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACTGGTTATTGa  <  1:1020628/100‑1 (MQ=255)

                                                                                                   ccAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACTGGTTATTg   <  1:2290504/99‑1 (MQ=255)

                                                                                                   ccAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACTGGTTATTGa  <  2:2911611/100‑1 (MQ=255)

                                                                                                   ccAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACTGGTTATTGa  >  1:1941045/1‑100 (MQ=255)

GCATAAATATCCGTGTCTCCAGACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGAGACTCGATATTTAAATCGGATTACATTTTAACTTTAGTAATATTCTTCAGAGATCACAAACTGGTTATTGA  >  NC_000913/3657903‑3658101

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A