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
A2 F50 I1 R1	170	39.5	1266514	99.2%	1256381	150.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,994,896	G→C	pseudogene (197/633 nt)	ygeK ←	pseudogene, response regulator family, part of T3SS PAI ETT2 remnant; putative 2‑component transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,994,896	0	G	C	100.0%	155.0 / NA	44	pseudogene (197/633 nt)	ygeK	pseudogene, response regulator family, part of T3SS PAI ETT2 remnant; putative 2‑component transcriptional regulator
Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (15/29); total (15/29)

TTCGCCGGGTGACTGGTTTTCCATACGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGGCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATAATGTCCGAGAAATCCAATTATCC  >  NC_000913/2994755‑2995040

ttCGCCGGGTGACTGGTTTTCCATACGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCcatc                                                                                                                                          <  2:246768/150‑1 (MQ=255)

   gCCGGGTGACTGGTTTTCCATACGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTc                                                                                                                                      <  1:506282/151‑1 (MQ=255)

       ggTGACTGGTTTTCCATACGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCAcc                                                                                                                                  <  1:258817/151‑1 (MQ=255)

              ggTTTTCCATACGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCACTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAAt                                                                                                                           <  1:264156/151‑1 (MQ=255)

                 tttCCATACGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCaa                                                                                                                             <  1:181410/146‑1 (MQ=255)

                 tttCCATACGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCaa                                                                                                                             >  2:181405/1‑146 (MQ=255)

                         cGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAaaat                                                                                                                <  1:159174/151‑1 (MQ=255)

                         cGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAaaat                                                                                                                <  1:458063/151‑1 (MQ=255)

                           cATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAaaataa                                                                                                              <  1:373337/151‑1 (MQ=255)

                                 ttCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATAtt                                                                                                         <  1:333254/150‑1 (MQ=255)

                                     cACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGc                                                                                                    >  2:209711/1‑151 (MQ=255)

                                     cACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGc                                                                                                    <  2:172053/151‑1 (MQ=255)

                                      aCCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCt                                                                                                   >  1:270395/1‑151 (MQ=255)

                                         tGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGt                                                                                                 >  2:137578/1‑150 (MQ=255)

                                              cAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGAttt                                                                                           <  2:86716/151‑1 (MQ=255)

                                               aaGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTg                                                                                          <  2:74085/151‑1 (MQ=255)

                                                  cAATTTTATTGAATCAATATACGGCCTCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGtt                                                                                        >  1:8404/1‑150 (MQ=255)

                                                   aaTTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTac                                                                                      <  2:42221/151‑1 (MQ=255)

                                                        tATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTcc                                                                                 >  2:249079/1‑151 (MQ=255)

                                                        tATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTc                                                                                  <  2:544223/150‑1 (MQ=255)

                                                            gAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCt                                                                              >  2:138182/1‑150 (MQ=255)

                                                                cAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAg                                                                          <  1:414712/150‑1 (MQ=255)

                                                                  atatACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCtt                                                                       >  2:390922/1‑151 (MQ=255)

                                                                        ggCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTttcttc                                                                  >  1:573687/1‑150 (MQ=255)

                                                                           aTCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTttcttc                                                                  >  1:481339/1‑147 (MQ=255)

                                                                            tCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTttcttc                                                                  >  2:62189/1‑146 (MQ=255)

                                                                               ttGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCtt                                                           <  2:284483/150‑1 (MQ=255)

                                                                                          gTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCcaa                                               <  1:242770/151‑1 (MQ=255)

                                                                                           taataaTATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCcaac                                              >  1:319224/1‑151 (MQ=255)

                                                                                            aataatATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCcaaca                                             <  2:513724/151‑1 (MQ=255)

                                                                                                    gAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCata                                     <  2:181045/151‑1 (MQ=255)

                                                                                                            atctTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAAt                                <  2:567718/148‑1 (MQ=255)

                                                                                                            atctTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAG‑CCCCAACAACCTCATATAAATCAg                             <  1:330035/150‑1 (MQ=255)

                                                                                                                tATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAgg                            <  2:440715/148‑1 (MQ=255)

                                                                                                                tATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAg                             <  1:252701/147‑1 (MQ=255)

                                                                                                                tATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGa                           <  1:62189/149‑1 (MQ=255)

                                                                                                                 aTGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATaa                        <  1:510802/151‑1 (MQ=255)

                                                                                                                 aTGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATa                         >  2:28736/1‑150 (MQ=255)

                                                                                                                   gCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATAAt                       <  2:345144/150‑1 (MQ=255)

                                                                                                                        ttAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATAATGTCCg                  >  2:107110/1‑150 (MQ=255)

                                                                                                                         tAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAGTAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATAATGTCCga                 <  1:33821/150‑1 (MQ=255)

                                                                                                                              cATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATAATGTCCGAGAAATc           >  2:163285/1‑151 (MQ=255)

                                                                                                                                      gAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATAATGTCCGAGAAATCCAATTATc   <  1:125772/151‑1 (MQ=255)

                                                                                                                                       aGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATAATGTCCGAGAAATCCAATTATcc  <  2:521021/151‑1 (MQ=255)

TTCGCCGGGTGACTGGTTTTCCATACGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGGCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATAATGTCCGAGAAATCCAATTATCC  >  NC_000913/2994755‑2995040

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A