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
A1 F1 I1 R1	1357	179.3	9500450	96.1%	9129932	93.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,974,585	A→G	R193R (CGT→CGC)	motA ←	MotA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,974,585	0	A	G	99.2%	405.7 / ‑4.5	129	R193R (CGT→CGC)	motA	MotA
Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (55/73); total (55/74)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.30e-01

Only 100 of 135 total aligned reads displayed.

TAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGACGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACT  >  NC_000913/1974495‑1974674

tAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCg                                                                                         >  1:663589/1‑93 (MQ=255)

tAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCg                                                                                         >  2:3529563/1‑93 (MQ=255)

 aaTGGGGAAATAAATCTGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGa                                                                                        >  2:179927/1‑93 (MQ=255)

 aaTGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGa                                                                                        >  1:4743730/1‑93 (MQ=255)

 aaTGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGa                                                                                        >  2:179926/1‑93 (MQ=255)

 aaTGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGa                                                                                        >  2:3313079/1‑93 (MQ=255)

  aTGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGAt                                                                                       <  1:3097754/93‑1 (MQ=255)

  aTGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGAt                                                                                       <  1:2184637/93‑1 (MQ=255)

  aTGGGGAAATAAAGCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGAt                                                                                       <  1:1092643/93‑1 (MQ=255)

   tGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATc                                                                                      <  2:516507/93‑1 (MQ=255)

   tGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATc                                                                                      <  2:2021472/93‑1 (MQ=255)

   aggggAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATc                                                                                      <  1:131110/92‑1 (MQ=255)

    ggggAAAGAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCTATAAGCGCACCCAGCTCGGCGGCAGGGCGATCg                                                                                     <  1:2484595/93‑1 (MQ=255)

     gggAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCgg                                                                                    <  1:4466673/93‑1 (MQ=255)

      ggAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGc                                                                                   <  2:2632925/93‑1 (MQ=255)

      ggAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGc                                                                                   <  1:4597809/93‑1 (MQ=255)

      ggAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGc                                                                                   <  2:1038090/93‑1 (MQ=255)

      ggAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGc                                                                                   <  2:4646839/93‑1 (MQ=255)

      ggAAATAAATCCGCAATCCAATAAAATGCCGAGGAAAGTCCCCTCCATCGCATGTGCGATAAGCGCACCCAGCCCGGCGGCAGGGCGATCGGc                                                                                   <  2:752058/93‑1 (MQ=255)

       gAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCt                                                                                  <  2:4237288/93‑1 (MQ=255)

         aataaatCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGa                                                                                <  2:1633720/93‑1 (MQ=255)

         aataaatCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATACGCTGa                                                                                >  2:3533103/1‑93 (MQ=255)

          ataaatCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGaa                                                                               >  2:3576983/1‑93 (MQ=255)

             aatCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCTATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCt                                                                            >  2:1994588/1‑93 (MQ=255)

               tCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTaa                                                                          >  1:2677931/1‑93 (MQ=255)

               tCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGACGATCGGCTGAACCTaa                                                                          <  1:1589694/93‑1 (MQ=255)

               accGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTaa                                                                          <  2:1393275/92‑1 (MQ=255)

                ccGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAAc                                                                         >  1:1453753/1‑93 (MQ=255)

                ccGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAAc                                                                         >  2:1153832/1‑93 (MQ=255)

                  gTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAAcgc                                                                       <  2:3068515/93‑1 (MQ=255)

                  gTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAAcgc                                                                       <  1:1450326/93‑1 (MQ=255)

                  gTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAAcgc                                                                       <  1:140233/93‑1 (MQ=255)

                  gTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAAcgc                                                                       <  1:2206677/93‑1 (MQ=255)

                    acgCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCCCGGCGGCAGGGCGATCGGCTGAACCTAACGCGt                                                                     <  1:3544852/91‑1 (MQ=255)

                     aGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTg                                                                    <  1:2745430/93‑1 (MQ=255)

                        cAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAAc                                                                 <  2:4656441/93‑1 (MQ=255)

                        cAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAAc                                                                 <  1:786393/93‑1 (MQ=255)

                          aTAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGTGATAAGCGCACCGAGCTCGGCGGCAGGGCGATCGGCTGAACATAACGCGTGAACGa                                                               <  2:1963838/93‑1 (MQ=255)

                          aTAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGa                                                               >  2:3847043/1‑93 (MQ=255)

                           tAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGAc                                                              <  1:1159375/93‑1 (MQ=255)

                           tAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGAc                                                              <  1:152476/93‑1 (MQ=255)

                            aaaaTGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGAcc                                                             >  1:4274166/1‑93 (MQ=255)

                             aaaTGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGAccc                                                            <  2:3586153/93‑1 (MQ=255)

                             aaaTGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGAccc                                                            >  1:3822080/1‑93 (MQ=255)

                              aaTGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGAcccc                                                           <  1:1897621/93‑1 (MQ=255)

                              aaTGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGAcccc                                                           >  2:2477609/1‑93 (MQ=255)

                              aaTGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGAcccc                                                           <  1:3736002/93‑1 (MQ=255)

                                tGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCa                                                         >  2:3678404/1‑93 (MQ=255)

                                   cGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTa                                                      <  1:3802531/93‑1 (MQ=255)

                                     aGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTAAACCTAACGCGTGAACGACCCCCATTACa                                                    <  2:2907113/93‑1 (MQ=255)

                                      ggAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAg                                                   >  2:1230152/1‑93 (MQ=255)

                                      ggAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAg                                                   >  1:338157/1‑93 (MQ=255)

                                       gAAAGTCCCCACCATCGCATGTGAGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGc                                                  <  2:396862/93‑1 (MQ=255)

                                        aaaGTCCCCACCATCGCATGTGCGATAAGCGCGCCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGcc                                                 <  1:4727357/93‑1 (MQ=255)

                                        aaaGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGcc                                                 <  2:1685504/93‑1 (MQ=255)

                                          aGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGc                                               <  2:2668462/93‑1 (MQ=255)

                                             ccccACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGcaac                                            <  2:40035/93‑1 (MQ=255)

                                              cccACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGcaaca                                           >  1:1973789/1‑93 (MQ=255)

                                              cccACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGcaaca                                           >  2:4508524/1‑93 (MQ=255)

                                               ccaccaTCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCTTTACAGCCGcaacaa                                          >  2:4366907/1‑93 (MQ=255)

                                               ccaccaTCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGcaacaa                                          >  2:3407167/1‑93 (MQ=255)

                                               ccaccaTCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGcaacaa                                          <  2:2132869/93‑1 (MQ=255)

                                                 accaTCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATa                                        >  1:2350491/1‑93 (MQ=255)

                                                 accaTCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATa                                        >  1:2527981/1‑93 (MQ=255)

                                                 accaTCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATa                                        <  2:3179316/93‑1 (MQ=255)

                                                  ccaTCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATAc                                       >  1:4053271/1‑93 (MQ=255)

                                                    aTCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCa                                     >  1:2787492/1‑93 (MQ=255)

                                                     acGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCaa                                    <  1:3871501/92‑1 (MQ=255)

                                                      cGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCaaa                                   <  1:3914410/93‑1 (MQ=255)

                                                      cGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCaaa                                   <  1:774644/93‑1 (MQ=255)

                                                      cGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCaaa                                   <  1:159334/93‑1 (MQ=255)

                                                      cGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCaaa                                   >  1:4216910/1‑93 (MQ=255)

                                                       gCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAAc                                  <  2:170113/93‑1 (MQ=255)

                                                       gCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAACACCacac                                  >  2:4705858/1‑93 (MQ=255)

                                                        cATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACg                                 >  2:4671139/1‑93 (MQ=255)

                                                         aTGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGc                                >  1:3803461/1‑93 (MQ=255)

                                                          tgtgCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGcc                               >  2:4589609/1‑93 (MQ=255)

                                                           gtgCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCg                              >  1:3244051/1‑93 (MQ=255)

                                                             gCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGa                            <  2:1484621/93‑1 (MQ=255)

                                                              cGATAAGCGCACCCAGTTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGaa                           >  2:4661305/1‑93 (MQ=255)

                                                              cGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGaa                           <  2:4441070/93‑1 (MQ=255)

                                                               gATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAg                          >  1:678473/1‑93 (MQ=255)

                                                                aTAAGCGCCCCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGt                         <  2:1475511/93‑1 (MQ=255)

                                                                aTAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGt                         <  1:679340/93‑1 (MQ=255)

                                                                  aaGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGa                       <  1:1806806/93‑1 (MQ=255)

                                                                  aaGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGa                       <  2:2876326/93‑1 (MQ=255)

                                                                  aaGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGa                       <  1:747253/93‑1 (MQ=255)

                                                                   aGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAg                      <  2:2174119/93‑1 (MQ=255)

                                                                     cgcACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTc                    <  2:3699249/93‑1 (MQ=255)

                                                                      gcACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTcc                   >  1:3063710/1‑93 (MQ=255)

                                                                      gcACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTcc                   >  1:4283476/1‑93 (MQ=255)

                                                                          ccAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCgc               >  2:1473355/1‑92 (MQ=255)

                                                                          ccAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGa               >  2:3785335/1‑93 (MQ=255)

                                                                           cAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCTAACGCCGGAAGTGAGTCCCCGAc              >  2:3239705/1‑93 (MQ=255)

                                                                                 ggcggcAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAgcgc        >  2:3866015/1‑93 (MQ=255)

                                                                                  gcggcAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCACACGCCGGAAGTGAGTCCCCGACCAGCGcc       >  2:2090060/1‑93 (MQ=255)

                                                                                  gcggcAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGcc       >  2:3652383/1‑93 (MQ=255)

                                                                                   gggcAGCGCGATCGGCTGAACCTAACGCGTGAACGCCCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCa      <  1:3147663/92‑1 (MQ=255)

                                                                                    ggcAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAg     >  1:3712881/1‑93 (MQ=255)

                                                                                       aGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACt  <  1:2466432/93‑1 (MQ=255)

TAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGACGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACT  >  NC_000913/1974495‑1974674

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 18 ≤` `ATCG/ATCG` `< 26 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

CGCTAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGACGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTC  >  NC_000913/1974492‑1974678

CGCTAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGG                                                                                               <  SRR4302544.3873560/94‑1 (MQ=60)

CGCTAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGG                                                                                               <  SRR4302544.1049017/94‑1 (MQ=60)

 GCTAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGC                                                                                              <  SRR4302544.1591901/94‑1 (MQ=60)

  CTAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCG                                                                                             >  SRR4302544.670141/1‑94 (MQ=60)

   TAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGA                                                                                            >  SRR4302544.4790478/1‑94 (MQ=60)

     ATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATC                                                                                          <  SRR4302544.3127253/94‑1 (MQ=60)

     ATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATC                                                                                          <  SRR4302544.2205303/94‑1 (MQ=60)

     ATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATC                                                                                          <  SRR4302544.213483/94‑1 (MQ=60)

     ATGGGGAAATAAAGCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATC                                                                                          <  SRR4302544.1103515/94‑1 (MQ=60)

     ATGGGGAAATAAACCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATC                                                                                          <  SRR4302544.1750379/94‑1 (MQ=60)

      AGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCG                                                                                         <  SRR4302544.132316/94‑1 (MQ=60)

       GGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGG                                                                                        >  SRR4302544.2488444/1‑94 (MQ=60)

       GGGGAAAGAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCTATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGG                                                                                        <  SRR4302544.2508390/94‑1 (MQ=60)

        GGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGC                                                                                       <  SRR4302544.4511607/94‑1 (MQ=60)

        GGAAAATAAACCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGC                                                                                       <  SRR4302544.1490544/94‑1 (MQ=60)

         GGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCT                                                                                      <  SRR4302544.4643525/94‑1 (MQ=60)

         GGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCT                                                                                      <  SRR4302544.4643524/94‑1 (MQ=60)

                AATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTA                                                                               >  SRR4302544.672412/1‑94 (MQ=60)

                AATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTA                                                                               >  SRR4302544.4102062/1‑94 (MQ=60)

                 ATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAA                                                                              >  SRR4302544.2703594/1‑94 (MQ=60)

                  TCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAAC                                                                             >  SRR4302544.1468199/1‑94 (MQ=60)

                  TCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGACGATCGGCTGAACCTAAC                                                                             <  SRR4302544.1605375/94‑1 (MQ=60)

                     GTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCG                                                                          <  SRR4302544.2227455/94‑1 (MQ=60)

                     GTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCG                                                                          <  SRR4302544.141563/94‑1 (MQ=60)

                     GTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCG                                                                          <  SRR4302544.1464738/94‑1 (MQ=60)

                      TAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGT                                                                         >  SRR4302544.768021/1‑94 (MQ=60)

                       ACGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCCCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTG                                                                        <  SRR4302544.3578792/94‑1 (MQ=60)

                        AGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGA                                                                       <  SRR4302544.2771881/94‑1 (MQ=60)

                           CAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACG                                                                    <  SRR4302544.794000/94‑1 (MQ=60)

                              TAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACC                                                                 <  SRR4302544.1170916/94‑1 (MQ=60)

                              TAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACC                                                                 <  SRR4302544.153955/94‑1 (MQ=60)

                              TAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACC                                                                 >  SRR4302544.4317804/1‑94 (MQ=60)

                               AAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCC                                                                >  SRR4302544.3859967/1‑94 (MQ=60)

                                 AATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCC                                                              <  SRR4302544.1915962/94‑1 (MQ=60)

                                 AATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCC                                                              <  SRR4302544.3773141/94‑1 (MQ=60)

                                      CGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTAC                                                         <  SRR4302544.3840206/94‑1 (MQ=60)

                                        AGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAG                                                       >  SRR4302544.341663/1‑94 (MQ=60)

                                           AAAGTCCCCACCATCGCATGTGCGATAAGCGCGCCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCG                                                    <  SRR4302544.4774012/94‑1 (MQ=60)

                                                CCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACA                                               >  SRR4302544.1992971/1‑94 (MQ=60)

                                                   CACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATA                                            >  SRR4302544.2372758/1‑94 (MQ=60)

                                                   CACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATA                                            >  SRR4302544.2552276/1‑94 (MQ=60)

                                                    CCCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATAC                                           <  SRR4302544.2798876/94‑1 (MQ=60)

                                                    ACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATAC                                           >  SRR4302544.4093638/1‑94 (MQ=60)

                                                      CATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCA                                         >  SRR4302544.2814320/1‑94 (MQ=60)

                                                        TCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAA                                       >  SRR4302544.4259530/1‑94 (MQ=60)

                                                        ACGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAA                                       <  SRR4302544.3909947/94‑1 (MQ=60)

                                                         CGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAAC                                      <  SRR4302544.3953297/94‑1 (MQ=60)

                                                         CGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAAC                                      <  SRR4302544.160893/94‑1 (MQ=60)

                                                         CGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAAC                                      <  SRR4302544.782167/94‑1 (MQ=60)

                                                           CATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGC                                    >  SRR4302544.3841145/1‑94 (MQ=60)

                                                             TGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCG                                  >  SRR4302544.3275106/1‑94 (MQ=60)

                                                                 CGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAG                              >  SRR4302544.685198/1‑94 (MQ=60)

                                                                 CGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAG                              <  SRR4302544.352825/94‑1 (MQ=60)

                                                                   ATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTG                            <  SRR4302544.686077/94‑1 (MQ=60)

                                                                    TAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGA                           <  SRR4302544.2700531/94‑1 (MQ=60)

                                                                     AAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAG                          <  SRR4302544.754572/94‑1 (MQ=60)

                                                                     AAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAG                          <  SRR4302544.1824463/94‑1 (MQ=60)

                                                                        CGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCC                       >  SRR4302544.3092929/1‑94 (MQ=60)

                                                                        CGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCC                       >  SRR4302544.4327229/1‑94 (MQ=60)

                                                                        CGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCC                       >  SRR4302544.377754/1‑94 (MQ=60)

                                                                           CCCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCG                    <  SRR4302544.4477224/94‑1 (MQ=60)

                                                                           ACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGCAGTGAGCCCCCG                    >  SRR4302544.1354822/1‑94 (MQ=60)

                                                                               AGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTaagcccccgcccc                >  SRR4302544.3902076/1‑81 (MQ=60)

                                                                                      CGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAG         <  SRR4302544.3177446/94‑1 (MQ=60)

                                                                                      CGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAG         >  SRR4302544.3749813/1‑94 (MQ=60)

                                                                                          AGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTG     >  SRR4302544.3153666/1‑94 (MQ=60)

                                                                                          AGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTG     <  SRR4302544.2489994/94‑1 (MQ=60)

                                                                                             GCGATCGGCTGAACCTAACGTGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTC  <  SRR4302544.3353988/94‑1 (MQ=60)

                                                                                             GCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTC  <  SRR4302544.3195416/94‑1 (MQ=60)

CGCTAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGACGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTC  >  NC_000913/1974492‑1974678

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 2 ≤` `ATCG/ATCG` `< 23 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`