Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	623,777	G→A	7.0%	A253T (GCC→ACC)	USA300HOU_0558 →	glycosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	623,777	0	G	A	7.0%	167.0 / 3.2	57	A253T (GCC→ACC)	USA300HOU_0558	glycosyltransferase
Reads supporting (aligned to +/- strand):  ref base G (25/28);  new base A (2/2);  total (27/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.84e-01

TCAATATTTTCTCCATCAATTATGTAAAAATAATGATCAAATCATATTAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGATATTTCACAATATATTGAAAATAAAATACCAGTTATCAAT  >  CP000730/623638‑623911                                                                                                                                            |                                                                                                                                        tCAATATTTTCTCCATCAATTATGTAAAAATAATGATCAAATCATATTAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGc                                                                                                                                        <  2:398289/141‑1 (MQ=255)             ccATCAATTATGTAAAAATAATGATCAAATCATATTAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTCTTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGtat                                                                                                                            <  1:585603/141‑1 (MQ=255)             ccATCAATTATGTAAAAATAATGATCAAATCATATTAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGtat                                                                                                                            >  1:312716/1‑141 (MQ=255)             ccATCAATTATGTAAAAATAATGATCAAATCATATTAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGtat                                                                                                                            <  2:552060/141‑1 (MQ=255)               aTCAATTATGTAAAAATAATGATCAAATCATATTAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATaa                                                                                                                          <  1:647888/141‑1 (MQ=255)                     tATGTAAAAATAATGATCAAATCATATTAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑tt                                                                                                                   <  2:306951/141‑1 (MQ=255)                         tAAAAATAATGATCAAATCATATTAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTta                                                                                                               >  2:143314/1‑141 (MQ=255)                         tAAAAATAATGATCAAATCATATTAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTta                                                                                                               <  1:666582/141‑1 (MQ=255)                         tAAAAATAATGATCAAATCATATTAGATCGTCCTCATGAATTAGGAAATGTTATACCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTta                                                                                                               >  2:143497/1‑141 (MQ=255)                                  tGATCAAATCATATTAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAgt                                                                                                      >  2:433017/1‑141 (MQ=255)                                   gATCAAATCATATTAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAgtg                                                                                                     >  1:649463/1‑141 (MQ=255)                                   gATCAAATCATATTAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAgtg                                                                                                     <  1:7771/141‑1 (MQ=255)                                    aTCAAATCATATTAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAgtgt                                                                                                    <  2:376738/141‑1 (MQ=255)                                     tCAAATCATATTAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGtt                                                                                                   >  1:393736/1‑141 (MQ=255)                                          tCATATTAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTtaata                                                                                              <  1:563704/141‑1 (MQ=255)                                           cATATTAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTGATGGTATAAAAAG‑TTTTTATAAAACAGTGTTtaataa                                                                                             <  2:502066/141‑1 (MQ=255)                                            atatTAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACGTTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTaataat                                                                                            >  1:398296/1‑141 (MQ=255)                                             tatTAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAAtt                                                                                           >  2:179767/1‑141 (MQ=255)                                                tAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTaa                                                                                        <  1:349567/141‑1 (MQ=255)                                                tAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTaa                                                                                        <  1:141737/141‑1 (MQ=255)                                                           cATGAATTAGGAAATGTTATAGCGGGATTAAATCAACGTATTCCAGTTACTGTTGCACCCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATaaa                                                                             <  1:709380/141‑1 (MQ=255)                                                           cATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑tttt                                                                                                                 <  1:583513/105‑1 (MQ=255)                                                           cATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑tttt                                                                                                                 >  2:583513/1‑105 (MQ=255)                                                           cATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATaaa                                                                             <  2:531403/141‑1 (MQ=255)                                                                aTTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGAt                                                                        >  2:577780/1‑141 (MQ=255)                                                                   aGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGAttgt                                                                     >  2:213425/1‑141 (MQ=255)                                                                    ggAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGAttgtt                                                                    <  1:389773/141‑1 (MQ=255)                                                                        aTGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTAt                                                                >  2:409119/1‑141 (MQ=255)                                                                          gTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAATAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCa                                                              >  2:660026/1‑141 (MQ=255)                                                                              taGCGGGATTAAATCAAAGTATTCCAGTTGTTGTTGTGCTCCATAGTACACATTTATCCGGTACCGGTaa                                                                                                                                  <  2:241532/70‑1 (MQ=255)                                                                              taGCGGGATTAAATCAAAGTATTCCAGTTGTTGTTGTGCTCCATAGTACACATTTATCCGGTACCGGTaa                                                                                                                                  >  1:241400/1‑70 (MQ=255)                                                                              taGCGGGATTAAATCAAAGTATTCCAGTTGTTGTTGTGCTCCATAGTACACATTTATCCGGTACCGGTaa                                                                                                                                  >  1:241532/1‑70 (MQ=255)                                                                              taGCGGGATTAAATCAAAGTATTCCAGTTGTTGTTGTGCTCCATAGTACACATTTATCCGGTACCGGTaa                                                                                                                                  <  2:241400/70‑1 (MQ=255)                                                                                    gATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGc                                                    >  2:149170/1‑141 (MQ=255)                                                                                    gATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGc                                                    <  1:442843/141‑1 (MQ=255)                                                                                          aTCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGcc                                              <  2:623585/141‑1 (MQ=255)                                                                                           tCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAGTTTTTTTTTTTTTTTTTTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAGCAGAAAAGCAATGcc                                              >  2:488802/1‑141 (MQ=255)                                                                                                 tATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGatat                                       >  1:338377/1‑141 (MQ=255)                                                                                                   ttCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGATAttt                                     >  1:525399/1‑141 (MQ=255)                                                                                                     ccAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGATATTTca                                   >  1:15897/1‑141 (MQ=255)                                                                                                        gTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGATAttgtgaaa                                <  2:51104/141‑7 (MQ=255)                                                                                                            ttgttgTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGATATTTCACAatata                            >  1:346885/1‑141 (MQ=255)                                                                                                            ttgttgTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGATATTTCACAatata                            >  2:120792/1‑141 (MQ=255)                                                                                                            ttgttgTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGATATTTCACAatata                            >  2:65067/1‑141 (MQ=255)                                                                                                             tgttgtACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGATATTTCACAatatat                           <  2:705939/141‑1 (MQ=255)                                                                                                               ttgtACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGATATTTCACAATATATTg                         <  2:390584/141‑1 (MQ=255)                                                                                                               ttgtACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGATATTTCACAATATATTg                         <  2:390583/141‑1 (MQ=255)                                                                                                                    cTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGATATTTCACAATATATTGaaaat                    <  1:27796/141‑1 (MQ=255)                                                                                                                    cTCCATAGTACACATTTATCCGGTGCAGGTAATAGAATAAAAAG‑AAATTAAAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGATATTTCaaaaaaaaaaaaaaat                    <  2:474969/141‑13 (MQ=255)                                                                                                                    cTCCATAATACACATTTTTCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTATTGTATCAACAGAAAAGCAATGCCAAGATATTTCACAATATATTGaaaat                    <  2:88099/141‑1 (MQ=255)                                                                                                                     tCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGATATTTCACAATATATTGaaaata                   <  1:113308/141‑1 (MQ=255)                                                                                                                                caTTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGATATTTCACAATATATTGAAAATAAAATACCAgag        >  1:474969/1‑139 (MQ=255)                                                                                                                                caTTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGATATTTCACAATATATTGAAAATAAAAGACCAGtt        >  1:348809/1‑141 (MQ=255)                                                                                                                                    tATGCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAGCACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGATATTTCACAATATATTGAAAATAAAATACCAGTTATCa    >  2:696190/1‑141 (MQ=255)                                                                                                                                    tATCCGGTGCCTGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGATATTTCACAATATATTGAAAATAAAATACCAGTTATCa    <  1:179767/141‑1 (MQ=255)                                                                                                                                     aTCCGGTGCGGGTAAAGGTATAAAAAA‑TTTTTATAACACAGAGTTTAATAATTCAACAAATCATAAAGCGATTGTTGTATCAAAAAAAGAGCAATACCAAAATACTTCACAACATATTGAAAAGAAAATACCACCTATCaa   >  2:514177/1‑141 (MQ=255)                                                                                                                                      tCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGATATTTCACAATATATTGAAAATAAAATACCAGTTATCAat  <  2:393736/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                                        TCAATATTTTCTCCATCAATTATGTAAAAATAATGATCAAATCATATTAGATCGTCCTCATGAATTAGGAAATGTTATAGCGGGATTAAATCAAAGTATTCCAGTTATTGTTGTACTCCATAGTACACATTTATCCGGTGCCGGTAATGGTATAAAAAG‑TTTTTATAAAACAGTGTTTAATAATTTAACACGTTATAAAGCGATTGTTGTATCAACAGAAAAGCAATGCCAAGATATTTCACAATATATTGAAAATAAAATACCAGTTATCAAT  >  CP000730/623638‑623911

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