Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,513,930	A→T	100%	L413F (TTA→TTT)	USA300HOU_1379 →	hypothetical membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,513,930	0	A	T	100.0%	119.1 / NA	41	L413F (TTA→TTT)	USA300HOU_1379	hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (24/17);  total (24/17)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAC  >  CP000730/1513796‑1514064                                                                                                                                       |                                                                                                                                       ttatttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTa                                                                                                                                  >  1:742356/1‑141 (MQ=255)  tatttGTTAGTATCGCTCTATTAGTAGCCATTGGCATAGGGTTTGTTTCTTTGATAATGAGTACAGAAAATAGTGCAACAAAAGTACCTCATCGCGTGAAAGAACCAGCATCTGTTACACTCCTCATAAGATTTATCGTaa                                                                                                                                 >  2:198868/1‑140 (MQ=255)  tatttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAt                                                                                                                                 >  2:801251/1‑141 (MQ=255)    tttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATAACTCATAATATATTTTATAGTATTa                                                                                                                               >  2:704770/1‑141 (MQ=255)         atgtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGatt                                                                                                                          >  2:542763/1‑141 (MQ=255)         atgtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGatt                                                                                                                          >  2:601416/1‑141 (MQ=255)              tCGCTTTATTAGTACCCATTGGCATGGGGTTTTTCTCTTGCAGAAAGCGAACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAATCCAGCATCTCTATCTCTCATAATCTGTTTTATTGTATTAGGATTCTTaa                                                                                                                     <  2:772670/141‑1 (MQ=255)                  tttATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGcc                                                                                                                 >  2:64683/1‑141 (MQ=255)                  tttATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGcc                                                                                                                 >  1:276369/1‑141 (MQ=255)                   ttattaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCa                                                                                                                <  2:707676/141‑1 (MQ=255)                                  ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                                                 >  2:431970/1‑141 (MQ=255)                                      tGGGGTTGGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGCTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTa                                                                                             <  2:306595/141‑1 (MQ=255)                                      agtgatttGCCCCTTAGAAAAAGCCAACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGCTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTa                                                                                             <  2:334201/136‑1 (MQ=255)                                        gggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATc                                                                                           <  1:542763/141‑1 (MQ=255)                                        gggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTCGGATTATCACTTATc                                                                                           <  1:601416/141‑1 (MQ=255)                                                      gATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAATAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAAt                                                                             <  1:222333/141‑1 (MQ=255)                                                      gATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAAt                                                                             <  1:524778/141‑1 (MQ=255)                                                           aGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAt                                                                        >  1:635312/1‑141 (MQ=255)                                                           aGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAt                                                                        >  1:169977/1‑141 (MQ=255)                                                           aGCGGACAAAATATACTGCGATAAAAGTACCACATCGCGGAAAAAAACCAGCATCTATATCCCTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAt                                                                        <  2:256452/141‑1 (MQ=255)                                                               tACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTGTTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTACAATTGAATTAat                                                                    >  1:686645/1‑141 (MQ=255)                                                                    aaaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtattat                                                               <  2:301360/141‑1 (MQ=255)                                                                      aaTACTGCTATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtatat                                                             <  2:342301/141‑1 (MQ=255)                                                                          cTGAAATAAAAGTACAACAACGAATAAAAAAACCAGCATCTATATCACTCATAATATTTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTa                                                         <  2:556860/141‑1 (MQ=255)                                                                           tGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATTCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTTGATTACTTATATATATTaa                                                        >  2:409849/1‑141 (MQ=255)                                                                           tGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATCTATAATTGAATTAATATTATATATTaa                                                        >  1:748947/1‑141 (MQ=255)                                                                                    aGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgtct                                               >  2:98943/1‑140 (MQ=255)                                                                                    aGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATAAATTAAAGAtcgtcg                                               >  2:308652/1‑141 (MQ=255)                                                                                    aGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAAGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgtcg                                               >  2:711533/1‑141 (MQ=255)                                                                                                  tAAAAAAACCAGCATCTATATCACTCATAATATGTTGTATTGTATTCGGTCTAGTAATTCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaataat                                 >  1:314906/1‑141 (MQ=255)                                                                                                     aaaaaCCAGCATCTATATCGCTCATAATATGGTTTCTTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTGGTGCTAAACAATAATCCa                              >  2:724872/1‑141 (MQ=255)                                                                                                     aaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTAAAAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTTAAGATCGTCGTGCTAAACAATAATTCa                              >  1:762001/1‑141 (MQ=255)                                                                                                       aaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACt                            <  1:140937/141‑1 (MQ=255)                                                                                                       aaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACt                            <  2:623093/141‑1 (MQ=255)                                                                                                         aCCAGCATCTATAGCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTa                          <  2:726178/141‑1 (MQ=255)                                                                                                          ccAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGTTTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTTAACAATAATGCCCTTaa                         >  1:434900/1‑141 (MQ=255)                                                                                                            aGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAg                       <  1:569116/141‑1 (MQ=255)                                                                                                            aGCAACTAAATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAg                       <  2:87446/141‑1 (MQ=255)                                                                                                                                tatGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTa   >  2:713959/1‑141 (MQ=255)                                                                                                                                tatGTTTTATTGTATTAGGATTATTAATCCCATTATTTGGAGTATCCACTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCCCTTAAAGTTTTGAACTGACGAAATTTa   >  1:314863/1‑141 (MQ=255)                                                                                                                                 atGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAtttcc  >  1:299168/1‑139 (MQ=255)                                                                                                                                       |                                                                                                                                       TTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAC  >  CP000730/1513796‑1514064

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑