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	4,497,958	C→T	intergenic (+18/‑314)	intB → / → insC1	pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase/IS2 repressor TnpA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,497,958	0	C	T	100.0%	181.4 / NA	46	intergenic (+18/‑314)	intB/insC1	pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase/IS2 repressor TnpA
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (17/29); total (17/29)

CCATAAAGCAGAGCATCTGGAAGAACGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCCCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAGGGGGGATTATCAGAATCCGCGGTTATTCATTATTTATATACATTCAATAAAAAAGTAACC  >  NC_000913/4497811‑4498102

ccATAAAGCAGAGCATCTGGAAGAACGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCg                                                                                                                                                <  2:480331/150‑1 (MQ=255)

    aaaGCAGAGCATCTGGAAGAACGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAat                                                                                                                                           >  1:411444/1‑151 (MQ=255)

      aGCAGAGCATCTGGAAGAACGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAatt                                                                                                                                          >  1:613922/1‑150 (MQ=255)

        cAGAGCATCTGGAAGAACGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAattatt                                                                                                                                       >  1:299349/1‑151 (MQ=255)

             cATCTGGAAGAACGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAgg                                                                                                                                  >  1:185438/1‑151 (MQ=255)

                  ggAAGAACGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGatta                                                                                                                              <  2:299342/150‑1 (MQ=255)

                  ggAAGAACGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGat                                                                                                                                <  1:206421/148‑1 (MQ=255)

                  ggAAGAACGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGa                                                                                                                                 <  1:577673/147‑1 (MQ=255)

                     agaaCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTAtttt                                                                                                                          >  2:49516/1‑151 (MQ=255)

                        aCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCtt                                                                                                                       >  1:450534/1‑151 (MQ=255)

                          ggCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTg                                                                                                                     <  2:411437/151‑1 (MQ=255)

                             gATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTa                                                                                                                  <  2:151100/151‑1 (MQ=255)

                                 gATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTaaaaa                                                                                                              <  2:548880/151‑1 (MQ=255)

                                          gtggtgGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACg                                                                                                     <  1:408205/151‑1 (MQ=255)

                                            ggtggGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATGATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGt                                                                                                   <  1:622713/151‑1 (MQ=255)

                                             gtggGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTa                                                                                                  <  1:271992/151‑1 (MQ=255)

                                               gggCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTAtt                                                                                                <  1:49516/151‑1 (MQ=255)

                                                     aTTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGa                                                                                          <  2:378683/151‑1 (MQ=255)

                                                         tCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGt                                                                                       <  1:534641/150‑1 (MQ=255)

                                                            ggATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGtattt                                                                                   <  1:226526/151‑1 (MQ=255)

                                                            ggATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGtattt                                                                                   >  1:301301/1‑151 (MQ=255)

                                                             gATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGtattta                                                                                  <  1:49798/151‑1 (MQ=255)

                                                             gATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGtattta                                                                                  <  1:235568/151‑1 (MQ=255)

                                                                  aaaCAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGtatttactat                                                                              <  1:299790/150‑1 (MQ=255)

                                                                     cAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGtatttactatttac                                                                          >  2:523445/1‑151 (MQ=255)

                                                                            aGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTccc                                                                   <  1:599061/151‑1 (MQ=255)

                                                                             ggTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACAGCTCCCt                                                                  >  1:291095/1‑151 (MQ=255)

                                                                                     aGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAggggg                                                          >  1:456642/1‑151 (MQ=255)

                                                                                       tCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAgggggg                                                         >  2:395378/1‑150 (MQ=255)

                                                                                           tttGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAGGGGGGATTAt                                                    >  2:512297/1‑151 (MQ=255)

                                                                                               aaTATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAGGGGGGATTATc                                                   >  2:95248/1‑148 (MQ=255)

                                                                                               aaTATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAGGGGGGATTATCAGa                                                <  2:185433/151‑1 (MQ=255)

                                                                                               aaTATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAGGGGGGATTATCAGa                                                <  1:179626/151‑1 (MQ=255)

                                                                                                         gATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAGGGGGGATTATCAGAATCCGCGGtt                                      <  2:52450/151‑1 (MQ=255)

                                                                                                             aataatCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAGGGGGGATTATCAGAATCCGCGGTTAtt                                   <  1:393995/150‑1 (MQ=255)

                                                                                                                aatCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAGGGGGGATTATCAGAATCCGCGGTTATTCatt                               <  1:605479/151‑1 (MQ=255)

                                                                                                                aatCCATTAAAACAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAGGGGGGATTATCAGAATCCGCGGTTATTCatt                               >  1:361921/1‑151 (MQ=255)

                                                                                                                         aaaCAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAGGGGGGATTATCAGAATCCGCGGTTATTCATTATTtatat                       >  2:52465/1‑150 (MQ=255)

                                                                                                                           aCAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAGGGGGGATTATCAGAATCCGCGGTTATTCATTATTTATATACa                    <  1:454645/151‑1 (MQ=255)

                                                                                                                           aCAGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAGGGGGGATTATCAGAATCCGCGGTTATTCATTATTTATATACa                    <  1:181483/151‑1 (MQ=255)

                                                                                                                             aGTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAGGGGGGATTATCAGAATCCGCGGTTATTCATTATTTATATACAtt                  >  1:477483/1‑151 (MQ=255)

                                                                                                                              gTAATCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAGGGGGGATTATCAGAATCCGCGGTTATTCATTATTTATATACATTc                 >  1:539572/1‑151 (MQ=255)

                                                                                                                                aaTCATCCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAGGGGGGATTATCAGAATCCGCGGTTATTCATTATTTATATACATTCa                <  2:529663/150‑1 (MQ=255)

                                                                                                                                 atcatcCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAGGGGGGATTATCAGAATCCGCGGTTATTCATTATTTATATACATTCAAt              <  1:601000/151‑1 (MQ=255)

                                                                                                                                    atcCCGGGCAAATGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAGGGGGGATTATCAGAATCCGCGGTTATTCATTATTTATATACATTCAATaaa           <  2:525043/151‑1 (MQ=255)

                                                                                                                                             aaaTGCTCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAGGGGGGATTATCAGAATCCGCGGTTATTCATTATTTATATACATTCAATAAAAAAGTAAcc  <  2:206399/151‑1 (MQ=255)

CCATAAAGCAGAGCATCTGGAAGAACGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCCCGGGAATTATTCTAGGATTATTTTCTTTGTTAAAAAAGACAAACGGTATTAACTGATGTATTTACTATTTACCGCTCCCTGCAGGGGGGATTATCAGAATCCGCGGTTATTCATTATTTATATACATTCAATAAAAAAGTAACC  >  NC_000913/4497811‑4498102

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A