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%	100.9 / NA	31	L413F (TTA→TTT)	USA300HOU_1379	hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (15/16);  total (15/16)

TTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAC  >  CP000730/1513800‑1514064                                                                                                                                   |                                                                                                                                       ttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAg                                                                                                                              >  2:218144/1‑141 (MQ=255) ttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAg                                                                                                                              >  2:32479/1‑141 (MQ=255)                tattaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATATTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCat                                                                                                               <  1:210839/141‑1 (MQ=255)                           aTTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTa                                                                                                    >  2:332615/1‑141 (MQ=255)                                cATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACt                                                                                               <  2:111117/141‑1 (MQ=255)                                 gtGGGGTTTGTCTGTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAGACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACtt                                                                                              <  2:140850/140‑1 (MQ=255)                                          gTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTa                                                                                     <  2:148602/141‑1 (MQ=255)                                          gTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTa                                                                                     <  1:384450/141‑1 (MQ=255)                                                      aaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGaa                                                                         <  1:68681/141‑1 (MQ=255)                                                           tACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAat                                                                    >  1:103232/1‑141 (MQ=255)                                                             aaaaaaaTACTGCAATAAAAGTACCACATAGAGTAAAAAAACCAGGATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAatat                                                                  <  2:256030/140‑1 (MQ=255)                                                                      cTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTa                                                         >  1:340836/1‑141 (MQ=255)                                                                       tGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTaa                                                        >  2:321582/1‑141 (MQ=255)                                                                                  tagcaaacaggttAAAAAAACCATCACCTATATCAGTCGTAATATGTTATAGTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATCATTTAATTAATATTATATATTAAAGATCTTCGTg                                             >  2:205209/13‑141 (MQ=255)                                                                                   aCCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGc                                            >  2:291265/1‑141 (MQ=255)                                                                                       aatagcgGAAAAAAACCAGGATCTATATCACTCATAATATGTTTTATTGTATTAGTATTATTAATTCCATTATTTGGATTATCACTTATCCTTGTATTTAGAAGTGAATGAATATTATATATTAAAGATCGTCGTGCTaaa                                        <  2:247560/137‑1 (MQ=255)                                                                                        aTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAAc                                       <  1:19424/141‑1 (MQ=255)                                                                                                aaaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAtt                                                                                   <  1:270198/89‑1 (MQ=255)                                                                                                aaaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAtt                                                                                   >  2:270198/1‑89 (MQ=255)                                                                                                   aaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACt                            >  2:90124/1‑141 (MQ=255)                                                                                                    aaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACtt                           <  2:81933/141‑1 (MQ=255)                                                                                                    aaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACtt                           <  1:154686/141‑1 (MQ=255)                                                                                                           aTCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGttt                    >  2:69875/1‑141 (MQ=255)                                                                                                                tatCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAAc               >  1:387381/1‑141 (MQ=255)                                                                                                                 atCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACt              <  2:73454/141‑1 (MQ=255)                                                                                                                      tCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGa         >  2:272398/1‑141 (MQ=255)                                                                                                                        ataataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGaaa       >  2:146457/1‑141 (MQ=255)                                                                                                                        ataataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGATAAACAATAATGCACTTAAAGTTTTGAACTGACGaaa       <  2:118749/141‑1 (MQ=255)                                                                                                                             atGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAc  <  2:136089/141‑1 (MQ=255)                                                                                                                               gTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTta                                                                                 <  1:293970/60‑1 (MQ=255)                                                                                                                               gTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTta                                                                                 >  2:293970/1‑60 (MQ=255)                                                                                                                                   |                                                                                                                                       TTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAC  >  CP000730/1513800‑1514064

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑