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 I2 R1	1873	183.1	9376148	98.2%	9207377	93.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,968,327	T→C	I228V (ATT→GTT)	tap ←	methyl‑accepting chemotaxis protein IV

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,968,327	0	T	C	99.1%	336.9 / ‑4.4	109	I228V (ATT→GTT)	tap	methyl‑accepting chemotaxis protein IV
Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (46/62); total (47/62)
Fisher's exact test for biased strand distribution p-value = 4.31e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.60e-01

Only 100 of 110 total aligned reads displayed.

CCTGCTGCATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAATGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAGATCGCCGCAA  >  NC_000913/1968237‑1968416

ccTGCTGCATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGc                                                                                         <  1:2380038/93‑1 (MQ=255)

ccTGCTGCATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGc                                                                                         <  1:1142229/93‑1 (MQ=255)

 ctgctgCATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCt                                                                                        <  1:1784232/93‑1 (MQ=255)

 ctgctgCATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCt                                                                                        <  2:2318950/93‑1 (MQ=255)

  tgctgcATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTg                                                                                       <  1:1545169/93‑1 (MQ=255)

  tgctgcATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTg                                                                                       <  2:2682352/93‑1 (MQ=255)

  tgctgcATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTg                                                                                       >  2:387131/1‑93 (MQ=255)

   gctgcATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGt                                                                                      >  1:1606135/1‑93 (MQ=255)

   gctgcATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGt                                                                                      <  1:3007813/93‑1 (MQ=255)

   gctgcATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGt                                                                                      <  2:802938/93‑1 (MQ=255)

    ctgcATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTc                                                                                     >  1:166358/1‑93 (MQ=255)

    ctgcATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTc                                                                                     <  2:3022371/93‑1 (MQ=255)

      gcATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCaa                                                                                   <  2:3617663/93‑1 (MQ=255)

        aTGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCaaaa                                                                                 <  1:1016550/93‑1 (MQ=255)

        aTGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCaaaa                                                                                 <  1:3213375/93‑1 (MQ=255)

        aTGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCaaaa                                                                                 <  2:2344240/93‑1 (MQ=255)

        aTGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCaaaa                                                                                 <  1:3119490/93‑1 (MQ=255)

        aTGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCaaaa                                                                                 <  1:479169/93‑1 (MQ=255)

         tGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAAt                                                                                <  1:955526/93‑1 (MQ=255)

         tGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAAt                                                                                <  2:2644534/93‑1 (MQ=255)

           gTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATgg                                                                              >  2:2813140/1‑93 (MQ=255)

            tCTTCAGACTGGCAAAAATGGCGGTGATCTGATTACGACCATATACCGCAATCGGACGGGCCAGATTACCCGCAGCAACGCTGTCAAAATggt                                                                             >  2:3546920/1‑92 (MQ=255)

            tCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGc                                                                             <  1:2739736/93‑1 (MQ=255)

            tCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGc                                                                             <  1:4478507/93‑1 (MQ=255)

                  gACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGa                                                                       >  2:2082960/1‑93 (MQ=255)

                   aCTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGAt                                                                      >  1:3769050/1‑93 (MQ=255)

                      ggCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAAt                                                                   <  2:3299880/93‑1 (MQ=255)

                      ggCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAAt                                                                   >  2:2140471/1‑93 (MQ=255)

                       gCAAAAATGGCGGTTATCTCATTACGACCATATACCGCAAGCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATg                                                                  <  1:473490/93‑1 (MQ=255)

                       gCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATg                                                                  <  1:819678/93‑1 (MQ=255)

                        cAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATgg                                                                 >  2:4043557/1‑93 (MQ=255)

                           aaaTGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCa                                                              <  1:1957639/93‑1 (MQ=255)

                             aTGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGt                                                            <  1:1892424/93‑1 (MQ=255)

                             aTGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGt                                                            <  1:1666482/93‑1 (MQ=255)

                             aTGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGt                                                            >  2:3979558/1‑93 (MQ=255)

                               ggCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTgg                                                          <  1:1030866/93‑1 (MQ=255)

                                gCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGt                                                         <  1:3948773/93‑1 (MQ=255)

                                gCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGt                                                         <  2:1800079/93‑1 (MQ=255)

                                gCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGt                                                         >  1:4466017/1‑93 (MQ=255)

                                   gTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGa                                                      <  2:4654368/93‑1 (MQ=255)

                                     gATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAAc                                                    <  2:748460/93‑1 (MQ=255)

                                      aTCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATTGCCAGTGGTTGAACa                                                   >  1:850006/1‑93 (MQ=255)

                                       tctcATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACaa                                                  >  1:1508266/1‑93 (MQ=255)

                                        ctcATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAat                                                 <  2:4444128/93‑1 (MQ=255)

                                        ctcATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAat                                                 >  1:272366/1‑93 (MQ=255)

                                        ctcATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAat                                                 <  1:4604002/93‑1 (MQ=255)

                                         tcATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAatc                                                <  1:3774837/93‑1 (MQ=255)

                                         tcATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAata                                                >  2:1103138/1‑92 (MQ=255)

                                          cATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAatca                                               <  1:1158681/93‑1 (MQ=255)

                                           aTTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAGCGCTGTCAAAATGGCTACCGATAATGTCCAGTGGTTGTACAatcat                                              <  2:4562251/93‑1 (MQ=255)

                                           aTTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAatcat                                              >  2:3181968/1‑93 (MQ=255)

                                            ttACGACCATATACCGCAATCGGACGCGCCAGATTGCCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAatcatc                                             <  1:4355019/93‑1 (MQ=255)

                                            ttACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAatcatc                                             <  1:2148098/93‑1 (MQ=255)

                                               cGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTg                                          <  2:2318363/93‑1 (MQ=255)

                                                gACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTgc                                         >  2:655891/1‑93 (MQ=255)

                                                gACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTgc                                         <  2:1824763/93‑1 (MQ=255)

                                                  ccATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTgcgc                                       >  2:4114289/1‑93 (MQ=255)

                                                   cATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGcgcg                                      >  1:3216054/1‑93 (MQ=255)

                                                      ataCCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTcc                                   >  1:3178310/1‑93 (MQ=255)

                                                       taCCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTcca                                  >  2:374582/1‑93 (MQ=255)

                                                         ccGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTccacc                                >  1:3992439/1‑93 (MQ=255)

                                                         ccGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTccacc                                <  1:2844171/93‑1 (MQ=255)

                                                          cGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTccacca                               >  1:1990511/1‑93 (MQ=255)

                                                           gCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCcaccac                              <  2:623564/93‑1 (MQ=255)

                                                           gCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCcaccac                              >  2:1461978/1‑93 (MQ=255)

                                                             aaTCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAg                            >  1:1867182/1‑93 (MQ=255)

                                                             aaTCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAg                            <  1:3023058/93‑1 (MQ=255)

                                                              aTCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCCCCACAgc                           >  1:2154165/1‑93 (MQ=255)

                                                              aTCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAgc                           <  2:2800307/93‑1 (MQ=255)

                                                              aTCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAgc                           >  1:1910590/1‑93 (MQ=255)

                                                              aTCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAgc                           <  2:3061912/93‑1 (MQ=255)

                                                              aTCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAgc                           >  2:582757/1‑93 (MQ=255)

                                                              aTCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAgc                           <  1:2855076/93‑1 (MQ=255)

                                                                 ggACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCa                        <  1:2411563/93‑1 (MQ=255)

                                                                 ggACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCa                        <  2:1974635/93‑1 (MQ=255)

                                                                    cgcgCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCActg                     >  2:4470415/1‑93 (MQ=255)

                                                                     gcgcCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCActgc                    <  1:1310431/93‑1 (MQ=255)

                                                                      cgcCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCActgct                   <  2:2128134/93‑1 (MQ=255)

                                                                       gcCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCActgctg                  >  1:1936871/1‑93 (MQ=255)

                                                                        ccAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGa                 >  2:2628904/1‑93 (MQ=255)

                                                                        ccAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGa                 <  2:1772371/93‑1 (MQ=255)

                                                                         cAGATTCCCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGAt                <  2:2608363/93‑1 (MQ=255)

                                                                         cAGATTCCCCGCAGCAACCCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGAt                <  2:4211879/93‑1 (MQ=255)

                                                                         cAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGAt                >  2:324343/1‑93 (MQ=255)

                                                                          aGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATg               >  2:906588/1‑93 (MQ=255)

                                                                          aGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGATGAACAATCATCTTGCGCGTCAACCACAGCGCACTGCTGaag               >  2:1794397/1‑91 (MQ=255)

                                                                           gATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGt              <  1:4678098/93‑1 (MQ=255)

                                                                           gATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGt              >  1:4458552/1‑93 (MQ=255)

                                                                            aTTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTa             <  2:4425282/93‑1 (MQ=255)

                                                                             ttACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAg            >  1:1807970/1‑93 (MQ=255)

                                                                              tACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAGa           <  1:675990/93‑1 (MQ=255)

                                                                                 ccGCAGCAATGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAGAtag        >  2:1942102/1‑91 (MQ=255)

                                                                                 ccGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAGATcg        >  2:89378/1‑93 (MQ=255)

                                                                                   gcagcaACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAGATcgcc      <  2:2283166/93‑1 (MQ=255)

                                                                                   gcagcaACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAGATcgcc      >  2:150398/1‑93 (MQ=255)

                                                                                     agcaACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAGATcgccgc    >  1:3002204/1‑93 (MQ=255)

                                                                                     agcaACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAGATcgccgc    <  1:3547280/93‑1 (MQ=255)

                                                                                     agcaACGCTGTCAAAATGGCTACCGACAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAGATcgccgc    >  2:73953/1‑93 (MQ=255)

                                                                                      gcaACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAGATCGCCGca   >  2:3833850/1‑93 (MQ=255)

                                                                                       caACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAGATCGCCGcaa  <  1:2693391/93‑1 (MQ=255)

CCTGCTGCATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAATGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAGATCGCCGCAA  >  NC_000913/1968237‑1968416

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 19 ≤` `ATCG/ATCG` `< 27 ≤` `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

AGCCTGCTGCATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAATGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAGATCGCCGCAACA  >  NC_000913/1968235‑1968418

AGCCTGCTGCATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACG                                                                                            <  SRR4302535.32192/94‑1 (MQ=60)

  CCTGCTGCATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCT                                                                                          <  SRR4302535.2397130/94‑1 (MQ=60)

  CCTGCTGCATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCT                                                                                          <  SRR4302535.1150372/94‑1 (MQ=60)

   CTGCTGCATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTG                                                                                         <  SRR4302535.1797145/94‑1 (MQ=60)

    TGCTGCATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGT                                                                                        <  SRR4302535.1556296/94‑1 (MQ=60)

    TGCTGCATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGT                                                                                        >  SRR4302535.1617724/1‑94 (MQ=60)

     GCTGCATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTC                                                                                       >  SRR4302535.167516/1‑94 (MQ=60)

     GCTGCATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTC                                                                                       <  SRR4302535.3028882/94‑1 (MQ=60)

          ATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAAT                                                                                  <  SRR4302535.482532/94‑1 (MQ=60)

          ATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAAT                                                                                  <  SRR4302535.1023775/94‑1 (MQ=60)

          ATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAAT                                                                                  <  SRR4302535.3141210/94‑1 (MQ=60)

          ATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAAT                                                                                  <  SRR4302535.3235628/94‑1 (MQ=60)

           TGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATG                                                                                 <  SRR4302535.962299/94‑1 (MQ=60)

              TCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCT                                                                              <  SRR4302535.4509255/94‑1 (MQ=60)

              TCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCT                                                                              <  SRR4302535.2759268/94‑1 (MQ=60)

                    GACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGAT                                                                        >  SRR4302535.3795064/1‑94 (MQ=60)

                         GCAAAAATGGCGGTTATCTCATTACGACCATATACCGCAAGCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGG                                                                   <  SRR4302535.476804/94‑1 (MQ=60)

                         GCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGG                                                                   <  SRR4302535.825433/94‑1 (MQ=60)

                             AAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAG                                                               <  SRR4302535.1971731/94‑1 (MQ=60)

                               ATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTG                                                             <  SRR4302535.1906051/94‑1 (MQ=60)

                               ATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTG                                                             <  SRR4302535.1678539/94‑1 (MQ=60)

                                 GGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGT                                                           >  SRR4302535.4496651/1‑94 (MQ=60)

                                 GGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGT                                                           <  SRR4302535.1038187/94‑1 (MQ=60)

                                  GCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTT                                                          <  SRR4302535.3975734/94‑1 (MQ=60)

                                       GATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATTGCCAGTGGTTGAACA                                                     >  SRR4302535.855993/1‑94 (MQ=60)

                                        ATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAA                                                    >  SRR4302535.1519109/1‑94 (MQ=60)

                                         TCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAAT                                                   >  SRR4302535.274262/1‑94 (MQ=60)

                                          CTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATC                                                  <  SRR4302535.4635303/94‑1 (MQ=60)

                                          CTCATTACAACCATAGCCCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTGCCGATAATGGCCAGTGGTTGAACAATC                                                  <  SRR4302535.2319579/94‑1 (MQ=60)

                                           TCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCA                                                 <  SRR4302535.3800867/94‑1 (MQ=60)

                                            CATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCAT                                                <  SRR4302535.1166964/94‑1 (MQ=60)

                                              TTACGACCATATACCGCAATCGGACGCGCCAGATTGCCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCT                                              <  SRR4302535.4384829/94‑1 (MQ=60)

                                              TTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCT                                              <  SRR4302535.2163546/94‑1 (MQ=60)

                                                  GACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCG                                          >  SRR4302535.2194424/1‑94 (MQ=60)

                                                    CCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCG                                        >  SRR4302535.3238330/1‑94 (MQ=60)

                                                       TATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCC                                     >  SRR4302535.915539/1‑94 (MQ=60)

                                                       TATACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCC                                     >  SRR4302535.3200292/1‑94 (MQ=60)

                                                         TACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCAC                                   <  SRR4302535.1682195/94‑1 (MQ=60)

                                                          ACCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACC                                  >  SRR4302535.4019749/1‑94 (MQ=60)

                                                           CCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCA                                 <  SRR4302535.2864336/94‑1 (MQ=60)

                                                           CCGCAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCA                                 >  SRR4302535.2004844/1‑94 (MQ=60)

                                                              CAATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAG                              >  SRR4302535.1880637/1‑94 (MQ=60)

                                                               AATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCCCCACAGC                             >  SRR4302535.2169646/1‑94 (MQ=60)

                                                               AATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGC                             >  SRR4302535.1924358/1‑94 (MQ=60)

                                                               AATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGC                             <  SRR4302535.3044225/94‑1 (MQ=60)

                                                                ATCGGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCG                            <  SRR4302535.2875303/94‑1 (MQ=60)

                                                                   GGACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCAC                         <  SRR4302535.2428922/94‑1 (MQ=60)

                                                                    GACGCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACT                        <  SRR4302535.313041/94‑1 (MQ=60)

                                                                       GCGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCT                     <  SRR4302535.1319797/94‑1 (MQ=60)

                                                                        CGCCAGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTG                    >  SRR4302535.1950817/1‑94 (MQ=60)

                                                                          CCAGATTACCCGCAGCAACGCTGTCAAAGTGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGAT                  <  SRR4302535.4451644/94‑1 (MQ=60)

                                                                            AGATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGT                >  SRR4302535.4489131/1‑94 (MQ=60)

                                                                             GATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTA               <  SRR4302535.4709664/94‑1 (MQ=60)

                                                                              ATTACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAG              >  SRR4302535.1821055/1‑94 (MQ=60)

                                                                                TACCCGCAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAGAT            <  SRR4302535.680713/94‑1 (MQ=60)

                                                                                      CAGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAGATCGCCGC      >  SRR4302535.3023250/1‑94 (MQ=60)

                                                                                       AGCAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAGATCGCCGCA     <  SRR4302535.3571907/94‑1 (MQ=60)

                                                                                         CAACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAGATCGCCGCAAC   <  SRR4302535.2712639/94‑1 (MQ=60)

                                                                                          AACGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAGATCGCCGCAACA  >  SRR4302535.2768942/1‑94 (MQ=60)

AGCCTGCTGCATGGTCTTCAGACTGGCAAAAATGGCGGTGATCTCATTACGACCATATACCGCAATCGGACGCGCCAGATTACCCGCAGCAATGCTGTCAAAATGGCTACCGATAATGGCCAGTGGTTGAACAATCATCTTGCGCGTCCACCACAGCGCACTGCTGATGTAGATCGCCGCAACA  >  NC_000913/1968235‑1968418

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 2 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`