Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000731	25,669	(A)7→6	coding (322/333 nt)	USA300HOU_pUSA300HOUMR0031 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000731	25,663	0	A	.	100.0%	247.1 / NA	54	coding (316/333 nt)	USA300HOU_pUSA300HOUMR0031	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (25/29);  total (25/29)

GTATGTTATTTACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGCAATAGAAAAC  >  CP000731/25526‑25796                                                                                                                                          |                                                                                                                                      gtatGTTATTTACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATaaaa                                                                                                                                    >  1:61953/1‑141 (MQ=255) gtatGTTATTTACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTATCAATGTCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATaaaa                                                                                                                                    <  2:206917/141‑1 (MQ=255)        aTTTACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGAACTATATCTTATTCTGTTTAATTACTATACTACAAATaaaaaataaac                                                                                                                             >  2:77188/1‑136 (MQ=255)          ttACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTAAAAGTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACAt                                                                                                                          <  1:91632/141‑1 (MQ=255)                tAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAg                                                                                                                    <  1:52885/141‑1 (MQ=255)                  gTGCTTAAATTTACAGGTGTGTCACCAATTATTGAAGGATCTTGGTTTTCTCAATATCAAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGt                                                                                                                  <  2:227228/141‑1 (MQ=255)                       tAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAACT‑AAAAAATATACATCCAAAAGTTTAAt                                                                                                             >  2:203971/1‑141 (MQ=255)                        aaaTTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAAtt                                                                                                            >  1:103181/1‑141 (MQ=255)                          aTTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGCAATTTTGTTCAGATGGGTGGCCTTCTTACGGATACGGTGTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTaa                                                                                                          >  2:169976/1‑141 (MQ=255)                          aTTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTaa                                                                                                          >  1:227945/1‑141 (MQ=255)                          aTTTACAGGTTTGTCAACAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTaa                                                                                                          <  2:115257/141‑1 (MQ=255)                               cAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGaaa                                                                                                     >  2:161841/1‑141 (MQ=255)                               aaGGTTTGTCACCAAGTACTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGaaa                                                                                                     <  2:224183/140‑1 (MQ=255)                                 agTTTGTCAACAAGTATTGAAGGATATTGGTTTTATAAATATCCAGAAATTTTATTTATAATTGTAGCAATATATCTAAGTCTGTTTAATTACTATACTAAAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGaaaaa                                                                                                   <  2:73272/140‑1 (MQ=255)                                   tttGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATa                                                                                                 >  1:98220/1‑141 (MQ=255)                                   tttGTCACAAATTATTGAAGGATCTTGGTATTATCAATATCCAGAAATTTTCTTTATAATTGTAGCACTAATTCTTATGCTGTTTAATTAATATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATa                                                                                                 <  2:46511/141‑1 (MQ=255)                                      gTCAACAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGaa                                                                                              <  2:185693/141‑1 (MQ=255)                                       acACGAAGTATTGAAGGATCTTGGTTTTCTCAATATACAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGATGTTTAATTACTATAATACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAAt                                                                                             <  2:139997/140‑1 (MQ=255)                                         aCCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTa                                                                                           >  1:172781/1‑141 (MQ=255)                                         aCCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTa                                                                                           >  1:158597/1‑141 (MQ=255)                                                  tGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAAtata                                                                                  <  1:106102/141‑1 (MQ=255)                                                    aaGGATCTTGTTTTTCTCAATATCCAGAAAGTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGa                                                                                <  1:60690/141‑1 (MQ=255)                                                             ggTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAACACaaaaa                                                                       >  2:128647/1‑141 (MQ=255)                                                             ggTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACaaaaa                                                                       >  2:89361/1‑141 (MQ=255)                                                               ttttCTCAATATCCATAAATTTGCTTTATAATTGTAGCACGATTTCTTATGCTGTTTAAATACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAgg                                                                     <  1:85881/141‑1 (MQ=255)                                                               ttttCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAgg                                                                     <  1:205968/141‑1 (MQ=255)                                                               ttttCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAAATACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAgg                                                                     <  1:176356/141‑1 (MQ=255)                                                                tttCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGa                                                                    >  1:225153/1‑141 (MQ=255)                                                                  tctcAATATCCAGAAATTTTCTTTATAATTGTCGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AGAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAAt                                                                  >  2:210129/1‑141 (MQ=255)                                                                      aaTATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTtct                                                              >  1:106581/1‑141 (MQ=255)                                                                        tatCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAAAGAATATAGAAAAAAAAAAGGAATTTCTCa                                                            >  2:22494/1‑141 (MQ=255)                                                                        tatCCAGAAAGTTTCTTTATAATTGTAGAAATATTTATTATGCTGTTTAATAACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCa                                                            <  2:51932/141‑1 (MQ=255)                                                                        taaccACAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCa                                                            <  1:171382/138‑1 (MQ=255)                                                                            cAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGaa                                                        <  1:61537/141‑1 (MQ=255)                                                                            aaGAAATTTTCTTTATAATTGTAGCACTATTTATTATGCTATTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGaa                                                        <  2:195891/140‑1 (MQ=255)                                                                             aGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGCATATAGAAAACCAAAAGAAATTTATCCAGaaa                                                       >  2:105561/1‑141 (MQ=255)                                                                               aaaTTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAAGAATTACTCAAGaaaat                                                     >  2:142086/1‑139 (MQ=255)                                                                                aaTTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACtt                                                    >  1:138878/1‑141 (MQ=255)                                                                                 aTTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACAAATAAT‑AAAAAAGAAACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACttt                                                   <  1:236125/141‑1 (MQ=255)                                                                                     tCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAAAGAATATAGAAAACAAAAAGAAATGTCTCAAGAAACTTTAAGt                                               >  2:1064/1‑141 (MQ=255)                                                                                      cTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTa                                              >  1:101283/1‑141 (MQ=255)                                                                                          ataATTTGAGTAATAGTTCATATTATGATTAAGTAGTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGa                                          <  2:202667/141‑1 (MQ=255)                                                                                             aTTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAAtt                                       <  1:92981/141‑1 (MQ=255)                                                                                             aTTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAAtt                                       <  1:103010/141‑1 (MQ=255)                                                                                                  aGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAg                                  <  1:108319/141‑1 (MQ=255)                                                                                                  aGCACTATTTCTTATGCTGTTTAATTAATATACAACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAg                                  <  1:171050/141‑1 (MQ=255)                                                                                                   gCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAgt                                 >  1:190962/1‑141 (MQ=255)                                                                                                      atATTTCTTATTCTGTTTAAGTAATAAAATACAAAT‑AAAAAATATACATATAAAGGTTAAATTAATGAAGAATAGAATTAGATAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTc                              <  2:118690/140‑1 (MQ=255)                                                                                                            cTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGAAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCa                        >  2:62721/1‑141 (MQ=255)                                                                                                              tATGCTGTTTAATTACTATAATACAAAT‑AACAAAGATACATCTTGTAAAATGATGAAAGAAAAAAAGAAATAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCaaa                      <  1:173602/141‑1 (MQ=255)                                                                                                                 gCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGACAAACTa                   <  1:134373/141‑1 (MQ=255)                                                                                                                     tttAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAAAATAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTaa               >  2:220242/1‑141 (MQ=255)                                                                                                                         aatactagaataCAAAT‑AAAAAATATACATATAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGCa           <  2:186442/139‑1 (MQ=255)                                                                                                                          ttACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGCaa          >  1:175947/1‑141 (MQ=255)                                                                                                                          ttACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGCaa          >  1:10207/1‑141 (MQ=255)                                                                                                                           tactatactaCAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAAATTCTCAAGAAACTCTAAGTAAAGAATTAAAAGTGTCTACTCAAACTATTAATGCaaa         >  2:238718/1‑140 (MQ=255)                                                                                                                                  ctacAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGCAATAGAAAAc  <  1:63025/141‑1 (MQ=255)                                                                                                                                          |                                                                                                                                      GTATGTTATTTACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGCAATAGAAAAC  >  CP000731/25526‑25796

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: ‑