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	1,963,691	G→A	A175A (GCC→GCT)	flhB ←	FlhB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,963,691	0	G	A	99.2%	442.3 / ‑5.3	123	A175A (GCC→GCT)	flhB	FlhB
Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (67/55); total (67/56)
Fisher's exact test for biased strand distribution p-value = 4.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.25e-01

Only 100 of 127 total aligned reads displayed.

TCCCACCATTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCGGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGCTTTAAG  >  NC_000913/1963601‑1963780

tCCCACCATTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGc                                                                                         <  2:841858/93‑1 (MQ=255)

accccccATTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGc                                                                                         <  2:3671482/92‑1 (MQ=255)

  ccaccaTTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCa                                                                                       <  1:120250/93‑1 (MQ=255)

  ccaccaTTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCa                                                                                       >  2:1922589/1‑93 (MQ=255)

  ccaccaTTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCa                                                                                       <  1:4465375/93‑1 (MQ=255)

   caccaTTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCAt                                                                                      >  1:2121435/1‑93 (MQ=255)

    accaTTGGAATGACACCAAGCAACACCAGCAGCGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATc                                                                                     >  2:3392106/1‑93 (MQ=255)

     ccaTTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCa                                                                                    >  2:404401/1‑93 (MQ=255)

     ccaTTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCa                                                                                    >  1:867513/1‑93 (MQ=255)

      caTTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCaa                                                                                   >  1:121518/1‑93 (MQ=255)

      caTTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCaa                                                                                   >  1:1316349/1‑93 (MQ=255)

      caTTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCaa                                                                                   <  2:2784093/93‑1 (MQ=255)

       aTTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAg                                                                                  >  1:578729/1‑93 (MQ=255)

        ttGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAgc                                                                                 >  1:2900620/1‑93 (MQ=255)

             aTGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGcatc                                                                            <  1:2923797/93‑1 (MQ=255)

              tGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGcatca                                                                           <  1:3399633/93‑1 (MQ=255)

               gACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGcatcat                                                                          >  2:1743305/1‑93 (MQ=255)

               gACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGcatcat                                                                          <  2:2319676/93‑1 (MQ=255)

               gACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGcatcat                                                                          >  1:3288141/1‑93 (MQ=255)

                acacCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCatcatc                                                                         <  2:1109943/93‑1 (MQ=255)

                 cacCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCt                                                                        >  2:1241861/1‑93 (MQ=255)

                 cacCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCt                                                                        >  1:20478/1‑93 (MQ=255)

                  acCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTg                                                                       >  1:2255565/1‑93 (MQ=255)

                   ccAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGc                                                                      <  1:2466733/93‑1 (MQ=255)

                    cAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCg                                                                     >  1:3558915/1‑93 (MQ=255)

                      aGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGc                                                                   >  2:3051147/1‑93 (MQ=255)

                      aGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGc                                                                   >  1:3382538/1‑93 (MQ=255)

                       gCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGcc                                                                  >  1:633031/1‑93 (MQ=255)

                       gCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGcc                                                                  <  1:2154546/93‑1 (MQ=255)

                          ccaccaGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGt                                                               >  2:2544717/1‑93 (MQ=255)

                          ccaccaGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGt                                                               >  2:4328903/1‑93 (MQ=255)

                           caccaGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTg                                                              <  2:185247/93‑1 (MQ=255)

                            accaGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGa                                                             <  2:1827223/93‑1 (MQ=255)

                            accaGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGa                                                             <  2:4652901/93‑1 (MQ=255)

                               agcagTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGc                                                          <  2:3358599/93‑1 (MQ=255)

                                gcagTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGcc                                                         >  1:894956/1‑93 (MQ=255)

                                   gTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCaga                                                      <  1:3316780/93‑1 (MQ=255)

                                   gTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCaga                                                      >  1:4594324/1‑93 (MQ=255)

                                       gcATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGaaa                                                  >  1:4153070/1‑93 (MQ=255)

                                       gcATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGaaa                                                  <  1:2968213/93‑1 (MQ=255)

                                         aTAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGaaaaa                                                >  2:4081808/1‑93 (MQ=255)

                                         aTAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGaaaaa                                                >  2:260066/1‑93 (MQ=255)

                                         aTAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGaaaaa                                                >  2:2984778/1‑93 (MQ=255)

                                            gCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAAcc                                             >  1:4003147/1‑93 (MQ=255)

                                            gCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAAcc                                             >  1:2984911/1‑93 (MQ=255)

                                             cccTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAAccc                                            <  1:2630275/93‑1 (MQ=255)

                                              ccTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAAcccc                                           <  2:1886709/93‑1 (MQ=255)

                                              ccTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAAcccc                                           >  2:130416/1‑93 (MQ=255)

                                               cTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCg                                          >  2:39266/1‑93 (MQ=255)

                                               cTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCg                                          >  2:199934/1‑93 (MQ=255)

                                                tACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGt                                         <  1:939526/93‑1 (MQ=255)

                                                tACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGt                                         <  1:893131/93‑1 (MQ=255)

                                                tACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGt                                         >  2:4204133/1‑93 (MQ=255)

                                                tACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGt                                         >  1:3743066/1‑93 (MQ=255)

                                                 aCCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTc                                        <  2:3912929/93‑1 (MQ=255)

                                                 aCCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTc                                        <  2:3409078/93‑1 (MQ=255)

                                                  ccAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCa                                       >  1:559466/1‑93 (MQ=255)

                                                  ccAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCa                                       >  1:4487142/1‑93 (MQ=255)

                                                   cAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCAc                                      >  1:1732995/1‑93 (MQ=255)

                                                   cAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGACAGAGAAAAAACCCCGTCAc                                      >  1:1343244/1‑93 (MQ=255)

                                                      aTCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCt                                   >  2:336551/1‑93 (MQ=255)

                                                         cATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGcc                                >  2:228480/1‑93 (MQ=255)

                                                          aTCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCa                               >  2:979734/1‑93 (MQ=255)

                                                           tCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCCAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGccca                              >  1:2035883/1‑91 (MQ=255)

                                                           tCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCaa                              >  2:977864/1‑93 (MQ=255)

                                                            cGCATTACCCATGGCGGTAATCGGAGACTCGGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAAc                             <  2:3097484/93‑1 (MQ=255)

                                                             gCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAAcc                            <  2:1409854/93‑1 (MQ=255)

                                                              cATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCa                           <  2:1484699/93‑1 (MQ=255)

                                                              cATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCa                           >  2:1116592/1‑93 (MQ=255)

                                                               aTTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATTCCAGAGAAAAAACCCCGTCACGCTGCCAACCAg                          <  1:3576581/93‑1 (MQ=255)

                                                               aTTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAg                          <  1:4170228/93‑1 (MQ=255)

                                                               aTTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAg                          >  2:3477854/1‑93 (MQ=255)

                                                                 tACCCATGGCGTTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGa                        <  1:2517921/93‑1 (MQ=255)

                                                                 tACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGa                        <  1:1747339/93‑1 (MQ=255)

                                                                  aCCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGAt                       <  2:2103891/93‑1 (MQ=255)

                                                                  aCCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGAt                       <  2:551147/93‑1 (MQ=255)

                                                                    ccATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATgg                     >  1:1110553/1‑93 (MQ=255)

                                                                      aTGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGtt                   <  2:4344411/93‑1 (MQ=255)

                                                                      aTGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGtt                   >  1:1254213/1‑93 (MQ=255)

                                                                      aTGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGtt                   <  1:3801177/93‑1 (MQ=255)

                                                                       tGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGttt                  <  2:911208/93‑1 (MQ=255)

                                                                         gCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTc                >  1:2780990/1‑93 (MQ=255)

                                                                         gCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTc                <  2:825852/93‑1 (MQ=255)

                                                                           ggTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCCACCAGGATGGTTTTCaa              >  2:2696921/1‑93 (MQ=255)

                                                                            gTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCaaa             >  2:872569/1‑93 (MQ=255)

                                                                             tAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCaaaa            <  2:2152336/93‑1 (MQ=255)

                                                                              aaTCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAAt           >  1:1507843/1‑93 (MQ=255)

                                                                               aTCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAAtt          <  2:3594193/93‑1 (MQ=255)

                                                                               aTCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAAtt          <  1:2655429/93‑1 (MQ=255)

                                                                               aTCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAAtt          <  1:4097765/93‑1 (MQ=255)

                                                                                tCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTg         >  2:2190893/1‑93 (MQ=255)

                                                                                tCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTGTTCAAAATTg         >  1:1334173/1‑93 (MQ=255)

                                                                                 cGGATACTCAGCCATCAAGCTCATCAGCTGCGGCCAGTGATTCGAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGc        <  2:1403623/93‑1 (MQ=255)

                                                                                 cGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGc        <  1:2809343/93‑1 (MQ=255)

                                                                                  ggAGACTCAGCCATCAAGCGCATCATCTGCTGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGCt       <  2:391915/93‑1 (MQ=255)

                                                                                  ggAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGCt       >  1:3057259/1‑93 (MQ=255)

                                                                                   gagaCTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGCtt      <  1:714535/93‑1 (MQ=255)

                                                                                     gaCTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGCTTTa    <  2:671950/93‑1 (MQ=255)

                                                                                      aCTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGCTTTaa   <  2:2903094/93‑1 (MQ=255)

                                                                                       cTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGCTTTAAg  >  2:4188442/1‑93 (MQ=255)

TCCCACCATTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCGGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGCTTTAAG  >  NC_000913/1963601‑1963780

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 23 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

AATCCCACCATTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCGGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGCTTTAAGC  >  NC_000913/1963599‑1963781

AATCCCACCATTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAG                                                                                           >  SRR4302535.2433041/1‑94 (MQ=60)

    CCACCATTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCAT                                                                                       <  SRR4302535.121092/94‑1 (MQ=60)

    CCACCATTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCAT                                                                                       >  SRR4302535.2136732/1‑94 (MQ=60)

    CCACCATTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCAT                                                                                       <  SRR4302535.4496003/94‑1 (MQ=60)

     CACCATTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCCTC                                                                                      >  SRR4302535.3434669/1‑94 (MQ=60)

      ACCATTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCA                                                                                     >  SRR4302535.873654/1‑94 (MQ=60)

       CCATTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAA                                                                                    >  SRR4302535.1325751/1‑94 (MQ=60)

       CCATTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAA                                                                                    >  SRR4302535.122368/1‑94 (MQ=60)

        CATTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAG                                                                                   >  SRR4302535.582796/1‑94 (MQ=60)

         ATTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGC                                                                                  >  SRR4302535.2921123/1‑94 (MQ=60)

               ATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCA                                                                            <  SRR4302535.2944415/94‑1 (MQ=60)

                TGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCAT                                                                           >  SRR4302535.3311003/1‑94 (MQ=60)

                TGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCAT                                                                           <  SRR4302535.3423290/94‑1 (MQ=60)

                  ACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCT                                                                         >  SRR4302535.20630/1‑94 (MQ=60)

                   CACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTG                                                                        >  SRR4302535.2271623/1‑94 (MQ=60)

                     CCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCG                                                                      <  SRR4302535.2484514/94‑1 (MQ=60)

                     CCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCG                                                                      >  SRR4302535.3583597/1‑94 (MQ=60)

                       AAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGC                                                                    >  SRR4302535.3406053/1‑94 (MQ=60)

                        AGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCC                                                                   >  SRR4302535.637444/1‑94 (MQ=60)

                         GCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCA                                                                  <  SRR4302535.2170029/94‑1 (MQ=60)

                                 AGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCC                                                          >  SRR4302535.901303/1‑94 (MQ=60)

                                   CAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAG                                                        >  SRR4302535.2088153/1‑94 (MQ=60)

                                    AGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGA                                                       >  SRR4302535.4625589/1‑94 (MQ=60)

                                     GTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAG                                                      <  SRR4302535.3339858/94‑1 (MQ=60)

                                        CGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAA                                                   >  SRR4302535.4181509/1‑94 (MQ=60)

                                         GCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAA                                                  <  SRR4302535.2989043/94‑1 (MQ=60)

                                          CATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAA                                                 >  SRR4302535.2295750/1‑94 (MQ=60)

                                            TAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAAC                                               >  SRR4302535.4264011/1‑94 (MQ=60)

                                             AGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACC                                              >  SRR4302535.4030529/1‑94 (MQ=60)

                                             AGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACC                                              >  SRR4302535.3005848/1‑94 (MQ=60)

                                               CCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCC                                            <  SRR4302535.2649118/94‑1 (MQ=60)

                                                 CTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGT                                          >  SRR4302535.3768962/1‑94 (MQ=60)

                                                  TACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTC                                         <  SRR4302535.946180/94‑1 (MQ=60)

                                                  TACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTC                                         <  SRR4302535.899460/94‑1 (MQ=60)

                                                   ACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCA                                        >  SRR4302535.563378/1‑94 (MQ=60)

                                                   ACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCA                                        >  SRR4302535.4517945/1‑94 (MQ=60)

                                                    CCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCAC                                       >  SRR4302535.1745520/1‑94 (MQ=60)

                                                    CCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGACAGAGAAAAAACCCCGTCAC                                       >  SRR4302535.1352832/1‑94 (MQ=60)

                                                            ATCGCATTACCCATGGCGGTAATCGGAGACTCAGCCATCCAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCCA                               >  SRR4302535.2050548/1‑94 (MQ=60)

                                                                 ATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATTCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGG                          <  SRR4302535.3601377/94‑1 (MQ=60)

                                                                 ATTACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGG                          <  SRR4302535.4198781/94‑1 (MQ=60)

                                                                   TACCCATGGCGTTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGAT                        <  SRR4302535.2536071/94‑1 (MQ=60)

                                                                   TACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGAT                        <  SRR4302535.1759976/94‑1 (MQ=60)

                                                                   TACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGAT                        <  SRR4302535.1643541/94‑1 (MQ=60)

                                                                   TACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGAT                        <  SRR4302535.3211689/94‑1 (MQ=60)

                                                                    ACCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGCCACGCTGCCAACCAGGATG                       >  SRR4302535.862893/1‑94 (MQ=60)

                                                                     CCCATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGG                      >  SRR4302535.1118481/1‑94 (MQ=60)

                                                                       CATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTT                    >  SRR4302535.1263183/1‑94 (MQ=60)

                                                                        ATGGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTT                   <  SRR4302535.3827378/94‑1 (MQ=60)

                                                                          GGCGGTAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTC                 >  SRR4302535.2800788/1‑94 (MQ=60)

                                                                               TAATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAAT            >  SRR4302535.1518684/1‑94 (MQ=60)

                                                                                 ATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTG          <  SRR4302535.4125813/94‑1 (MQ=60)

                                                                                 ATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTG          <  SRR4302535.2674455/94‑1 (MQ=60)

                                                                                 ATCGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTGTTCAAAATTG          >  SRR4302535.1343688/1‑94 (MQ=60)

                                                                                   CGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGCT        <  SRR4302535.2829314/94‑1 (MQ=60)

                                                                                   CGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGCT        <  SRR4302535.1316460/94‑1 (MQ=60)

                                                                                   CGGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGCT        >  SRR4302535.3078651/1‑94 (MQ=60)

                                                                                    GGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGCTT       <  SRR4302535.2974693/94‑1 (MQ=60)

                                                                                    CGAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCTGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGCTT       <  SRR4302535.2797622/94‑1 (MQ=60)

                                                                                     GAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGGTTT      <  SRR4302535.3963309/94‑1 (MQ=60)

                                                                                     GAGACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGCTTT      <  SRR4302535.719551/94‑1 (MQ=60)

                                                                                        ACTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGCTTTAAG   <  SRR4302535.4655523/94‑1 (MQ=60)

                                                                                         CTCAGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGCTTTAAGC  >  SRR4302535.4433290/1‑94 (MQ=60)

AATCCCACCATTGGAATGACACCAAGCACCACCAGCAGTGCGCATAGCCCTACCAAATCCATCGCATTACCCATGGCGGTAATCGGAGACTCGGCCATCAAGCGCATCATCTGCGGCCAGTGATGCCAGAGAAAAAACCCCGTCACGCTGCCAACCAGGATGGTTTTCAAAATTGCTTTAAGC  >  NC_000913/1963599‑1963781

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 2 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`