Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,041,405	T→C	7.0%	V39V (GTT→GTC)	USA300HOU_0984 →	glycosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,041,405	0	T	C	7.0%	163.2 / 3.6	57	V39V (GTT→GTC)	USA300HOU_0984	glycosyltransferase
Reads supporting (aligned to +/- strand):  ref base T (27/26);  new base C (2/2);  total (29/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.08e-01

CTGAGGTAAAGGAATAATTATAATGAAAAAAATATTTATGATGGTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAGTATTTTAAACAAATTTCAAATAATAAACATTTTAAGTCTAAT  >  CP000730/1041267‑1041543                                                                                                                                           |                                                                                                                                            cTGAGGTAAAGGAATAATTATAATGAAAAAAATATTTATGATGGTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTAc                                                                                                                                           >  2:88342/1‑141 (MQ=255)   gAGGTAAAGGAATAATTATAATGAAAAAAATATTTATGATGGTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACtt                                                                                                                                         >  1:758019/1‑141 (MQ=255)     ggTAAAGGAATAATTATAATGAAAAAAATATTTATGATGGTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTc                                                                                                                                       >  2:282012/1‑141 (MQ=255)     ggTAAAGGAATAATTATAATGAAAAAAATATTTATGATGGTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTc                                                                                                                                       >  2:373207/1‑141 (MQ=255)           ggAATAATTATAATGAAAAAAATATTTATGATGGTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTAc                                                                                                                                 >  1:742327/1‑141 (MQ=255)               taatTATAATGAAAAAAATATTTATGATGGTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAg                                                                                                                             >  2:738602/1‑141 (MQ=255)               taatTATAATGAAAAAAATATTTATGATGGTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAg                                                                                                                             <  2:564404/141‑1 (MQ=255)                 atTATAATGAAAAAAATATTTATGATGGTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGa                                                                                                                           <  2:77988/141‑1 (MQ=255)                 atTATAATGAAAAAAATATTTATGATGGTACATGAGTTACATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGa                                                                                                                           <  1:580663/141‑1 (MQ=255)                       aTGAAAAAAATATTTATGATGGTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTat                                                                                                                     <  1:337840/141‑1 (MQ=255)                         gAAAAAAATATTTATGATGGTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTatga                                                                                                                   >  2:442753/1‑141 (MQ=255)                            aaaaaTATTTATGATGGTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTAtgatga                                                                                                                <  1:413063/141‑1 (MQ=255)                            aaaaaTATTTATGATGGTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTAtgatga                                                                                                                <  2:176543/141‑1 (MQ=255)                            aaaaaTATTTATGATGGTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTAtgatga                                                                                                                <  2:595662/141‑1 (MQ=255)                                  atTTATGATGGTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAattat                                                                                                          >  2:627628/1‑141 (MQ=255)                                    ttATGATGGTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAAttatta                                                                                                        <  1:614247/141‑1 (MQ=255)                                    ttATGATGGTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAAttatta                                                                                                        <  2:713193/141‑1 (MQ=255)                                         atgGTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCt                                                                                                   <  2:405870/141‑1 (MQ=255)                                           ggTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCttt                                                                                                 >  2:222577/1‑141 (MQ=255)                                           ggTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCttt                                                                                                 <  1:412717/141‑1 (MQ=255)                                            gTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTg                                                                                                <  2:776368/141‑1 (MQ=255)                                            gTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTg                                                                                                <  1:213804/141‑1 (MQ=255)                                            gTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAAAAAAAAGTTTTATGATGAGGACATACCTGCTGATATTGTTACCTTCAATTACAAAGGAAACTATGATTAAATTATaaaaaaaaaa                                                                                                <  2:776350/141‑7 (MQ=255)                                                 tGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑aaaaa                                                                                          >  1:92174/1‑141 (MQ=255)                                                        gATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGt                                                                                   <  1:517962/141‑1 (MQ=255)                                                              aaTAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATg                                                                             >  1:289067/1‑141 (MQ=255)                                                               aTAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATgg                                                                            <  2:413393/141‑1 (MQ=255)                                                                    ggtggtATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTGAAAAAAACAAGGTAAAATGGATCg                                                                        >  1:14503/1‑141 (MQ=255)                                                                    ggtggtATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTCACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCga                                                                       >  2:761262/1‑141 (MQ=255)                                                                    ggtggtATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTCACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCga                                                                       >  2:761285/1‑141 (MQ=255)                                                                      tggtATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCgaag                                                                     >  2:28382/1‑141 (MQ=255)                                                                       ggtATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCgaaga                                                                    >  2:481729/1‑141 (MQ=255)                                                                                      aTGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAaatgtataat                                                     >  2:699310/1‑141 (MQ=255)                                                                                       tGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAaatgtataatg                                                    >  2:364809/1‑141 (MQ=255)                                                                                       tGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGAATCGAAGAACGAAaatgtataaag                                                    >  2:669621/1‑139 (MQ=255)                                                                                           cAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTAtt                                                >  2:174983/1‑141 (MQ=255)                                                                                            aaTAGAAGTAAATAGTTTTATAATGCGGACATACCTGCTAATATTGTTACTTACGATTACAAAGGAAACTATGATGAAATTAAAAAAAAAAAA‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTAttt                                               <  2:780815/141‑1 (MQ=255)                                                                                               aGAAGTAAAGAGTTATATGATGCGGACATACCTGCTGATATTGTTACCTCCGATTACAAAGGAAACTATGATGAAATTAAAAAAAAAAAA‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAg                                            <  2:378583/141‑1 (MQ=255)                                                                                                     aaaGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAGTAtttt                                      >  2:291058/1‑141 (MQ=255)                                                                                                          gTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAGTATTTTAAACa                                 >  2:403038/1‑141 (MQ=255)                                                                                                             ttATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAGTATTTTAAAAAAAt                              >  2:246923/1‑141 (MQ=255)                                                                                                                    gCGGTCATACCTGCTGATATTGTTACTTTCGATTAAAAAGGAAACTATGATGAAATTAATAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAGTATTTTAAACAAATTTCAaat                       <  2:363953/141‑1 (MQ=255)                                                                                                                       gACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAGTATTTTAAACAAATTTCAaataat                    >  1:429515/1‑141 (MQ=255)                                                                                                                       gACATACCTGCTGATATTGTTAATTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAGTATTTTAAACTATTTTCAaatatt                    <  2:675247/141‑3 (MQ=255)                                                                                                                         cATACCTGCTGATATTGTCACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAGTATTTTAAACAAATTTCAAAtaataa                  <  1:761262/141‑1 (MQ=255)                                                                                                                         cATACCTGCTGATATTGTCACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAGTATTTTAAACAAATTTCAAAtaataa                  <  1:761285/141‑1 (MQ=255)                                                                                                                           tACCTGCTGTTATTGTTACTTTCGATTACAAATGTATTTTTGTTTTTGTTTGTATATTTTTT‑ATAAAACTTTGTAAAATTTATCGAAGAACGAAAATGTATAATGTATTTGAGTATTTTAAACAAATTTCAAATAATAAAc                <  1:704131/141‑1 (MQ=255)                                                                                                                            aCCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAGTATTTTAAACAAATTTCAAATAATAAACa               >  1:667431/1‑141 (MQ=255)                                                                                                                            aCCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAGTATTTTAAACAAATTTCAAATAATAAACa               <  1:338186/141‑1 (MQ=255)                                                                                                                               tgctgATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAGTATTTTAAACAAATTTCAAATAATAAACAttt            <  1:640926/141‑1 (MQ=255)                                                                                                                                gctgATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAGTATTTTAAACAAATTTCAAATAATAAACAtttt           >  1:218422/1‑141 (MQ=255)                                                                                                                                       ttGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAGTATTTTAAACAAATTTCAAATAATAAACATTTTAAGTCta    <  1:158276/141‑1 (MQ=255)                                                                                                                                        tGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAGTATTTTAAACAAATTTCAAATAATAAACATTTTAAGTCtaa   <  1:270150/141‑1 (MQ=255)                                                                                                                                        tGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAGTATTTTAAACAAATTTCAAATAATAAACATTTTAAGTCtaa   >  2:491230/1‑141 (MQ=255)                                                                                                                                        tGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAATATTTTACACAAATTTCAAATAATAAACATTCTAAGTCtaa   >  2:491226/1‑141 (MQ=255)                                                                                                                                        tGTTACTATCGATTACAAAGGAAACTATGATGAAATTATTAAAGCATAG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAGTATTTTAAACAAATTTCAAATAATAAACATTTTAAGTCtaa   <  2:553129/141‑1 (MQ=255)                                                                                                                                         gTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAGTATTTTAAACAAATTTCAAATAATAAACATTTTAAGTCtaat  >  2:295678/1‑141 (MQ=255)                                                                                                                                           |                                                                                                                                            CTGAGGTAAAGGAATAATTATAATGAAAAAAATATTTATGATGGTACATGAGTTAGATGTGAATAAAGGTGGTATGACCTCTTCGATGTTCAATAGAAGTAAAGAGTTTTATGATGCGGACATACCTGCTGATATTGTTACTTTCGATTACAAAGGAAACTATGATGAAATTATTAAAGCTTTG‑AAAAAACAAGGTAAAATGGATCGAAGAACGAAAATGTATAATGTATTTGAGTATTTTAAACAAATTTCAAATAATAAACATTTTAAGTCTAAT  >  CP000730/1041267‑1041543

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: ‑