Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,272,141	T→C	D288G (GAT→GGT)	espX5 ←	T3SS effector pentapeptide repeat protein EspX5

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,272,141	0	T	C	100.0%	176.3 / NA	46	D288G (GAT→GGT)	espX5	T3SS effector pentapeptide repeat protein EspX5
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (24/22);  total (24/22)

TCGGTACATATAACCATTTCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGATCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTAAATAAATTAATATATGGCGCTATTACTTTATAAAGATTTACCTCAGCCATGTATGCCATATAAAAATTTGAATAATC  >  NZ_CP009273/4272027‑4272271                                                                                                                   |                                                                                                                                   tCGGTACATATAACCATTTCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAAt                                                                                                            <  2:471505/139‑1 (MQ=255) tCGGTACATATAACCATTTCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAAt                                                                                                            >  1:471505/1‑139 (MQ=255)   ggTACATATAACCATTTCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATc                                                                                                           >  1:144420/1‑138 (MQ=255)   ggTACATATAACCATTTCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATc                                                                                                           >  2:845076/1‑138 (MQ=255)   ggTACATATAACCATTTCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATc                                                                                                           >  2:656223/1‑138 (MQ=255)     tACATATAACCATTTCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAg                                                                                                        >  1:27948/1‑139 (MQ=255)           taACCATTTCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTaga                                                                                                  <  2:277718/139‑1 (MQ=255)           taACCATTTCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTag                                                                                                   <  2:144420/138‑1 (MQ=255)             aCCATTTCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTagag                                                                                                 <  1:589943/138‑1 (MQ=255)             aCCATTTCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTagag                                                                                                 <  2:788670/138‑1 (MQ=255)             aCCATTTCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTagag                                                                                                 <  2:254921/138‑1 (MQ=255)               cATTTCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAg                                                                                              <  2:736878/139‑1 (MQ=255)                 tttCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGc                                                                                             >  1:686416/1‑138 (MQ=255)                 tttCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGc                                                                                             >  1:673559/1‑138 (MQ=255)                 tttCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCt                                                                                            <  2:27948/139‑1 (MQ=255)                  ttCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTagag                                                                                                 <  1:853643/133‑1 (MQ=255)                  ttCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTagag                                                                                                 >  2:853643/1‑133 (MQ=255)                  ttCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCt                                                                                            >  2:503668/1‑138 (MQ=255)                   tCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCt                                                                                            >  2:128843/1‑137 (MQ=255)                   tCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCt                                                                                            >  1:631975/1‑137 (MQ=255)                                     aaCCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTaaataaat                                                                        >  1:243116/1‑139 (MQ=255)                                      aCCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTaaataaat                                                                        <  1:418795/138‑1 (MQ=255)                                          cgTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTagag                                                                                                 >  1:518586/1‑109 (MQ=255)                                          cgTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTagag                                                                                                 <  2:518586/109‑1 (MQ=255)                                          cgTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGt                                                                                       <  1:270790/119‑1 (MQ=255)                                          cgTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGt                                                                                       >  2:270790/1‑119 (MQ=255)                                              aaaaaGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTAAATAAATTAatatat                                                                <  1:503668/138‑1 (MQ=255)                                                      tttGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTAAATAAATTAATATATGGCGCTAtt                                                       <  1:845076/139‑1 (MQ=255)                                                         gCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTAAATAAATTAATATATGGCGCTATTACt                                                    >  1:585237/1‑139 (MQ=255)                                                                        tataTTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTAAATAAATTAATATATGGCGCTATTACTTTATAAAGATTTAc                                      <  1:466297/138‑1 (MQ=255)                                                                         atatTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTAAATAAATTAATATATGGCGCTATTACTTTATAAAGATTTACCt                                    >  2:778339/1‑139 (MQ=255)                                                                            ttCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTAAATAAATTAATATATGGCGCTATTACTTTATAAAGATTTACCTCa                                  <  2:585237/138‑1 (MQ=255)                                                                            ttCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTAAATAAATTAATATATGGCGCTATTACTTTATAAAGATTTACCTCAg                                 <  2:686416/139‑1 (MQ=255)                                                                              cTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTAAATAAATTAATATATGGCGCTATTACTTTATAAAGATTTACCTCAGc                                <  1:778339/138‑1 (MQ=255)                                                                               tGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGttaatt                                                                                                                <  2:849830/57‑1 (MQ=255)                                                                               tGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGttaatt                                                                                                                >  1:849830/1‑57 (MQ=255)                                                                               tGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTAAATAAATTAATATATGGCGCTATTACTTTATAAAGATTTACCTCAg                                 <  2:166933/136‑1 (MQ=255)                                                                               tGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTAAATAAATTAATATATGGCGCTATTACTTTATAAAGATTTACCTCAg                                 >  2:116747/1‑136 (MQ=255)                                                                               tGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTAAATAAATTAATATATGGCGCTATTACTTTATAAAGATTTACCTCAg                                 <  1:116747/136‑1 (MQ=255)                                                                               tGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTAAATAAATTAATATATGGCGCTATTACTTTATAAAGATTTACCTCAg                                 >  1:166933/1‑136 (MQ=255)                                                                                         cTTTATTCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTAAATAAATTAATATATGGCGCTATTACTTTATAAAGATTTACCTCAGCCATGTATGCCa                     >  1:790644/1‑138 (MQ=255)                                                                                              ttCAGGTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTAAATAAATTAATATATGGCGCTATTACTTTATAAAGATTTACCTCAGCCATGTATGCCATATaa                >  1:140223/1‑138 (MQ=255)                                                                                                   gTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGctct                                                                                >  2:338653/1‑69 (MQ=255)                                                                                                   gTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGctct                                                                                <  1:338653/69‑1 (MQ=255)                                                                                                   gTTGACACGAGACAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTAAATAAATTAATATATGGCGCTATTACTTTATAAAGATTTACCTCAGCCATGTATGCCATATAAAAAttt          >  1:193208/1‑139 (MQ=255)                                                                                                             gaCAGACCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTAAATAAATTAATATATGGCGCTATTACTTTATAAAGATTTACCTCAGCCATGTATGCCATATAAAAATTTGAATAATc  >  1:323512/1‑137 (MQ=255)                                                                                                                   |                                                                                                                                   TCGGTACATATAACCATTTCGAGGAACGTATTTGTTAACCGCGTAAAAAAGAGTTTGCTATCAATTAAGTTTATATTCTGGAGGGTTGCTTTATTCAGGTTGACACGAGACAGATCAGCATGTTCAAAGTTAATTAAATCAAGTTTAGAGAAGCTAAGGTCGGCTCTAAATAAATTAATATATGGCGCTATTACTTTATAAAGATTTACCTCAGCCATGTATGCCATATAAAAATTTGAATAATC  >  NZ_CP009273/4272027‑4272271

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑