Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	1,513,930	A→T	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%	109.0 / NA	33	L413F (TTA→TTT)	USA300HOU_1379	hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (19/14);  total (19/14)

TATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATA‑TATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACA  >  CP000730/1513803‑1514065                                                                                                                                |                                                                                                                                         tatgtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGat                                                                                                                             >  2:196217/1‑141 (MQ=255)     tatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGattatt                                                                                                                         >  1:337107/1‑141 (MQ=255)           tttATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGcc                                                                                                                   <  1:260989/141‑1 (MQ=255)               ttaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCatta                                                                                                               >  2:330665/1‑141 (MQ=255)               ttaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCatta                                                                                                               >  2:330681/1‑141 (MQ=255)                    agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTgg                                                                                                          <  1:238279/141‑1 (MQ=255)                     gCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGa                                                                                                         <  1:259214/141‑1 (MQ=255)                        aTTGGTATGGGGTTTGTCTTTTGGATAAAGCATAAAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGAtat                                                                                                      <  2:51655/141‑3 (MQ=255)                             cATGGGGTTTGTCACTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCAAATAGAGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACt                                                                                                 <  2:310413/141‑1 (MQ=255)                              aTGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACtt                                                                                                <  2:164232/141‑1 (MQ=255)                                               gATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAAt                                                                               >  1:337814/1‑141 (MQ=255)                                                   aaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGaa                                                                           >  2:222390/1‑141 (MQ=255)                                                    aGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCATCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAt                                                                          <  2:239379/141‑1 (MQ=255)                                                     gCGTACAAAAAATCCTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTTAAAATATGCTTTATTGTTTTAGGATTCTTAATGCCCTTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                                         >  1:145851/1‑141 (MQ=255)                                                     gCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                                         >  2:89695/1‑141 (MQ=255)                                                      cGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTa                                                                        <  1:298385/141‑1 (MQ=255)                                                       gTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGat                                                                                                                             >  2:5263/1‑87 (MQ=255)                                                       gTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGat                                                                                                                             <  1:5263/87‑1 (MQ=255)                                                        tACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAat                                                                      >  2:38532/1‑141 (MQ=255)                                                                 tACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCAGTCATGATATGTTTTATTGTATTAGGATTATTAGTGCGATGATTTGTATTATGACTTATCCTTGTCTTTATAATTGACTTAATATTata‑tat                                                            >  2:279157/1‑141 (MQ=255)                                                                  aCTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATA‑TAtt                                                           >  1:284898/1‑141 (MQ=255)                                                                      cAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATA‑TATTAAAg                                                       >  1:151755/1‑141 (MQ=255)                                                                                aCCCCATCGCGTAAATAAACCAGCAGCTACATCACTCATAATATGTTTTATTGAAGTAGGATTATTAATGCCATTACTTGGATTTTCAATTAATCTTTTATATTTAATTTAATTAAGATTATATTATTaatctagtttttc                                              >  2:159690/1‑130 (MQ=255)                                                                                 ccACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATA‑TATTAAAGATCGTCGTGCt                                            >  1:305145/1‑141 (MQ=255)                                                                                                  aCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATA‑TATTAAAGATCGTCGTGCTAAACAATAATGCACTTa                           >  2:54708/1‑141 (MQ=255)                                                                                                      gCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATA‑TATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGt                       <  1:330681/141‑1 (MQ=255)                                                                                                      gCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATA‑TATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGt                       >  2:333060/1‑141 (MQ=255)                                                                                                      gCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATA‑TATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGt                       <  1:330665/141‑1 (MQ=255)                                                                                                      gCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATA‑TATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGt                       >  1:202922/1‑141 (MQ=255)                                                                                                        aTCTATATCACTCACAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGCATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATA‑TATTAAAGCTCGTCGTCCTAAATAATAATGCACTTAAAGttt                     <  2:91913/141‑1 (MQ=255)                                                                                                            agatCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTGATAATTGAATTAATATTATA‑TATTAAAGATCGTCGTGCTAAACAATAATGCATTTAAAGTTTTGaa                 <  2:313164/139‑1 (MQ=255)                                                                                                                     ataataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATA‑TATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGaaa        <  2:2837/141‑1 (MQ=255)                                                                                                                           tGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATA‑TATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACa  >  1:325045/1‑141 (MQ=255)                                                                                                                                |                                                                                                                                         TATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATA‑TATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACA  >  CP000730/1513803‑1514065

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑