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
A8 F50 I2 R1	150	68.2	2132745	98.7%	2105019	150.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	250,026	A→G	pseudogene (45/1713 nt)	lfhA ←	pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	250,026	0	A	G	100.0%	176.9 / NA	47	pseudogene (45/1713 nt)	lfhA	pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (22/25); total (22/25)

GCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTC  >  NC_000913/249879‑250171

gcCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATgcgc                                                                                                                                                <  2:601893/151‑1 (MQ=255)

  cGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTc                                                                                                                                              >  2:923348/1‑151 (MQ=255)

      gAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGcc                                                                                                                                          <  1:790092/151‑1 (MQ=255)

         aTCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCt                                                                                                                                       >  2:993951/1‑151 (MQ=255)

          tCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCtt                                                                                                                                      >  1:1057810/1‑151 (MQ=255)

           cGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCtt                                                                                                                                      <  1:641308/150‑1 (MQ=255)

                    tGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTgacgac                                                                                                                            >  2:568333/1‑151 (MQ=255)

                    tGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTgacgac                                                                                                                            >  1:910419/1‑151 (MQ=255)

                     ggCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACa                                                                                                                           <  1:917106/151‑1 (MQ=255)

                       cAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAAt                                                                                                                         <  2:725825/151‑1 (MQ=255)

                       cAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAAt                                                                                                                         <  1:669175/151‑1 (MQ=255)

                         aCATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATaa                                                                                                                       <  1:351019/151‑1 (MQ=255)

                              tttACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTg                                                                                                                  >  2:882770/1‑151 (MQ=255)

                                  cGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTg                                                                                                              <  1:23979/151‑1 (MQ=255)

                                   gCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGt                                                                                                             <  1:134073/151‑1 (MQ=255)

                                     cGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTc                                                                                                            >  2:1050354/1‑150 (MQ=255)

                                       ggTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAAc                                                                                                         >  1:108885/1‑151 (MQ=255)

                                                ctgcgcctgGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGt                                                                                                >  1:679285/1‑151 (MQ=255)

                                                  gcgcctgGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTaa                                                                                              <  1:643586/151‑1 (MQ=255)

                                                  gcgcctgGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTaa                                                                                              <  1:349502/151‑1 (MQ=255)

                                                  gcgcctgGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTa                                                                                               <  1:279653/150‑1 (MQ=255)

                                                   cgcctgGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTaaa                                                                                             <  2:218733/151‑1 (MQ=255)

                                                   cgcctgGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTaa                                                                                              >  2:193870/1‑150 (MQ=255)

                                                      ctgGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATcc                                                                                          >  1:867676/1‑151 (MQ=255)

                                                        ggTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATcc                                                                                          <  2:827532/149‑1 (MQ=255)

                                                        ggTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGa                                                                                        <  1:491150/151‑1 (MQ=255)

                                                             aTCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTg                                                                                   >  1:701078/1‑151 (MQ=255)

                                                                aaTCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGaa                                                                                 >  2:94394/1‑150 (MQ=255)

                                                                     ggCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCAtt                                                                           <  1:718050/151‑1 (MQ=255)

                                                                       cGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTAt                                                                         >  1:587419/1‑151 (MQ=255)

                                                                              aTCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCcgcg                                                                  >  1:780207/1‑151 (MQ=255)

                                                                                 ggCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTg                                                               <  2:870877/151‑1 (MQ=255)

                                                                                             cATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCg                                                   >  2:233373/1‑151 (MQ=255)

                                                                                                cTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGAtt                                                >  1:842151/1‑151 (MQ=255)

                                                                                                  gTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGa                                                  <  2:1830/147‑1 (MQ=255)

                                                                                                    ttGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGAttttt                                             <  1:28481/150‑1 (MQ=255)

                                                                                                        cGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACgg                                        <  1:397178/151‑1 (MQ=255)

                                                                                                         gggCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACgg                                        >  2:980074/1‑150 (MQ=255)

                                                                                                          ggCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACggtg                                      <  1:200936/151‑1 (MQ=255)

                                                                                                             aTCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGgtggtg                                   <  2:922603/151‑1 (MQ=255)

                                                                                                                       aGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGcc                         >  1:82935/1‑151 (MQ=255)

                                                                                                                           aaaGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGtt                      <  1:301322/150‑1 (MQ=255)

                                                                                                                               cGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTtaaat                  >  2:1024920/1‑150 (MQ=255)

                                                                                                                                gggCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTtaaataa                <  1:859291/151‑1 (MQ=255)

                                                                                                                                gggCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTtaaataa                <  1:188550/151‑1 (MQ=255)

                                                                                                                                    aGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATc            >  1:277104/1‑151 (MQ=255)

                                                                                                                                             ggAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGtc    <  2:557166/150‑1 (MQ=255)

                                                                                                                                               aaaTGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGtctc  >  2:170579/1‑150 (MQ=255)

GCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTC  >  NC_000913/249879‑250171

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A