Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	37,579	A→C	intergenic (+603/‑234)	USA300HOU_RS14915 → / → ugpQ_1	hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	37,579	0	A	C	100.0%	86.8 / NA	36	intergenic (+603/‑234)	USA300HOU_RS14915/ugpQ_1	hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (16/20);  total (16/20)

GATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGA  >  USA300TCH1516_ALE/37512‑37706                                                                    |                                                                                                                                gATAAGAGGTACGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGAttt                                                        <  2:218573/141‑1 (MQ=11)   caaGTGGTACGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTGGATTACAAAATGGAGCTTGGGACATAAATGAttttt                                                      <  1:296984/140‑1 (MQ=14)     agagGTACGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTa                                                    <  2:822566/141‑1 (MQ=14)     agagGTAAGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTa                                                    <  2:822641/141‑1 (MQ=11)       agGTACGTTAAAAGCAGTTCAAGGCAAAGTTGCAGATAAGAGGTGCGTTAAAAGGAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTaaa                                                  >  1:640516/1‑141 (MQ=14)        gcaacgctAACAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTaaaa                                                 <  1:963906/134‑1 (MQ=14)           acGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAatg                                              >  1:621201/2‑141 (MQ=17)            cGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAatga                                             >  1:907092/1‑141 (MQ=14)              ttAAAAGCAGTTCTAGGCAACGTTGGCGCTAAGAGGTGCGTTAAAAGCAGCTCGCAGCAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAACTTGGGACATAAATGATTTTTTAAAAatgaga                                           >  1:391889/1‑141 (MQ=12)              ttAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAACATGGAGCTTGGGACATAAATGATTTTTTAAAAatgaga                                           <  2:308637/141‑1 (MQ=17)                 aaaGCAGTTCTAGGCAAAATTGCAGATAAGAGCTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTATGCTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAatgagatga                                        <  1:660832/141‑1 (MQ=14)                  aaGTAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAatgagatgag                                       <  1:198634/141‑1 (MQ=17)                  aaGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAatgagatgag                                       <  1:388163/141‑1 (MQ=18)                         tctaggcaaaaTTGCAGATAAGAGGTGCGTTAAAAGTAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGa                                <  1:252364/134‑1 (MQ=18)                          ctaggcaaaaTTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGAt                               >  2:756856/7‑141 (MQ=18)                           taggcaaaaTTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGAtt                              <  1:851400/136‑1 (MQ=18)                            aggcaaaaTTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTa                             <  1:879526/137‑1 (MQ=21)                            aggcaaaaTTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTa                             >  2:293827/5‑141 (MQ=18)                            aggcaaaaTTGCAGATAAGAGGTGCGATAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTGTGGACATAAATGATTTGTTAAAAATGAGATAAGACGAAGATTa                             >  2:263529/5‑141 (MQ=17)                              gcaaaaTTGCAGATAAGAGGAGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAAc                           <  1:991022/139‑1 (MQ=21)                              gacaaaCTGCAGATAAGAGGGGAGGTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAAc                           <  2:153299/138‑1 (MQ=25)                                 aaaTTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTcc                        >  1:646615/1‑141 (MQ=21)                                 aaaTTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTcc                        >  1:251116/1‑141 (MQ=21)                                   aTTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCAt                      <  2:707206/141‑1 (MQ=25)                                   aTTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCAt                      >  1:379725/1‑141 (MQ=21)                                     tgcagATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCCTaa                    >  2:83769/5‑141 (MQ=21)                                     tgcagATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATaa                    <  1:97304/137‑1 (MQ=25)                                                ggtgcgTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAAt         >  1:837221/6‑141 (MQ=38)                                                 gtgcgTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATc        <  2:595386/137‑1 (MQ=38)                                                 gtgcgTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATc        <  2:618913/137‑1 (MQ=38)                                                 gtgcgTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATc        <  2:117320/137‑1 (MQ=38)                                                   gcgTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTa      >  2:125978/3‑141 (MQ=38)                                                   gcgTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTa      >  1:681040/3‑141 (MQ=38)                                                     gTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGACAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATc    <  2:391889/141‑1 (MQ=39)                                                     gTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTTTTTTTTATATGAAAAGTAGATTAACTCCATAATCAATCCGAATCTacg    >  2:238041/1‑139 (MQ=25)                                                       tAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGa  >  1:350516/1‑141 (MQ=39)                                                                    |                                                                                                                                GATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGA  >  USA300TCH1516_ALE/37512‑37706

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: ‑