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: ‑