Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	9,085	G→A	48.9%	R685H (CGT→CAT)	gyrA →	DNA gyrase subunit A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	9,085	0	G	A	48.9%	‑1.9 / 65.6	49	R685H (CGT→CAT)	gyrA	DNA gyrase subunit A
Reads supporting (aligned to +/- strand):  ref base G (10/15);  new base A (10/14);  total (20/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.57e-01

GGTAAGATTGCGATTTCGTTCAGAGAAGATGATGAGTTAATTGCAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAA  >  USA300TCH1516_ALE/8946‑9220                                                                                                                                            |                                                                                                                                        ggTAAGATTGCGATTTCGTTCAGAGAAGATGATGAGTTAATTGCAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGt                                                                                                                                        <  1:456866/141‑1 (MQ=255)    aaGATTGCGATTTCGTTCAGAGAAGATGATGAGTTAATTGCAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCATACa                                                                                                                                     <  1:73076/141‑1 (MQ=255)    aaGATTGCGATTTCGTTCAGAGAAGATGATGAGTTAATTGCAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCATACa                                                                                                                                     <  1:349796/141‑1 (MQ=255)           cGATTTCGTTCAGAGAAGATGATGAGTTAATTGCAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCCACgg                                                                                                                              >  1:740974/1‑141 (MQ=255)            gATTTCGTTCAGAGAATATGATGAGTTAATTGCAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCATACAGCAACggg                                                                                                                             >  1:431983/1‑141 (MQ=255)              tttCGTTCAGAGAAGATGATGAGTTAATTGCAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCATACAGCAACGGgtg                                                                                                                           <  1:662754/141‑1 (MQ=255)              tttCGTGCAGAGAAGAGGATGAGTTAATTGCAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCATACAGCAACGGgtg                                                                                                                           <  1:290603/141‑1 (MQ=255)                tCGTTCAGAGAAGATGATGAGTTAATTGCAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATCCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGtgtg                                                                                                                         <  1:28725/141‑1 (MQ=255)                 cGTTCAGAGAAGAGGATGAGTTAATTGCAGTTCGCTTAACAAGTGGTCAAGAAGATATCCTGATTGGTACAGCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGa                                                                                                                        <  1:871481/141‑1 (MQ=255)                    tCAGAGAAGATGATGAGTTAATTGCAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCATACAGCAACGGATGTGAAAg                                                                                                                     >  1:439815/1‑141 (MQ=255)                       gagaAGATGATGAGTTAATTGCAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCATTTAGGCCGTAAAGCAACGGGTGGGGAAGGTa                                                                                                                  >  1:93733/1‑141 (MQ=255)                        agaagaTGATGAGTTAATTGCAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTGAGGCCGTACAGCAACGGGTGTGAAAGGTAt                                                                                                                 <  1:88475/141‑1 (MQ=255)                               gatgaGTTAATTGCAGATCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACtt                                                                                                          >  1:485523/1‑141 (MQ=255)                                atgaGTTAATTGCAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCATACAGCAACGGGTGTGAAAGGTATTACACTTc                                                                                                         >  1:656997/1‑141 (MQ=255)                                 tgaGTTAATTGCAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCATACAGCAACGGGTGTGAAAGGTATTACACTTCg                                                                                                        >  1:375918/1‑141 (MQ=255)                                         ttGCAGTTCGCTTAAAAACTGCTCAAGAAGATATCTTGATTGTTACATCACATGCATCATTAATTCGATTCCCTGAATAAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTg                                                                                                <  1:332151/141‑1 (MQ=255)                                            cAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACg                                                                                             <  1:222250/141‑1 (MQ=255)                                            cAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACg                                                                                             >  1:718890/1‑141 (MQ=255)                                                 cGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCATACAGCAACGGGTGTGGAAGGTAGTACACTTCGTGAAGGTGACGAAGtt                                                                                        >  1:722754/1‑141 (MQ=255)                                                        cAAGTGGTCAAGAAGATATCTTGATTGGTACACCCCATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGc                                                                                 <  1:725039/141‑1 (MQ=255)                                                           gTGGTCAAGAAGATCTCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTg                                                                              <  1:542565/141‑1 (MQ=255)                                                           gTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCATACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGCGACGAAGTTGTAGGGCTTg                                                                              <  1:462680/141‑1 (MQ=255)                                                               tCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGt                                                                          >  1:835979/1‑141 (MQ=255)                                                                cAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGGTGTAGGGCTTGATGTa                                                                         >  1:749103/1‑141 (MQ=255)                                                                cAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCATACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTa                                                                         <  1:474589/141‑1 (MQ=255)                                                                cAAGAAGATATCTTGATTGGTACATCACATGCATCATTAAATCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTATAGGGCTTGATGTa                                                                         >  1:622993/1‑141 (MQ=255)                                                                cAAGAAGATATCTTGATTGGGACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCATACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTa                                                                         >  1:527365/1‑141 (MQ=255)                                                                           cTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCaaa                                                              <  1:839926/141‑1 (MQ=255)                                                                            ttGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCATACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAAc                                                             <  1:773537/141‑1 (MQ=255)                                                                                ttGGTACATCCCATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCATACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAgtg                                                         <  1:770495/141‑1 (MQ=255)                                                                                ttGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAgtg                                                         <  1:239467/141‑1 (MQ=255)                                                                                    tACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCATACAGCAACGGGAGTGAAAGGTATTACATTTAGCAAATTGAATGGCGTTGTAGGGGCGGAGTTAGCTCATGCAAACAGTGTtga                                                     >  1:852840/1‑141 (MQ=255)                                                                                        tCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCATACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAGTGTTGATGaa                                                 <  1:371882/141‑1 (MQ=255)                                                                                               catcatTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCATACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATtag                                          <  1:482805/141‑1 (MQ=255)                                                                                                 tcatTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCCTGCAAACAGTGTTGATGAAGTATtagta                                        <  1:552197/141‑1 (MQ=255)                                                                                                   atTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGAATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTagtagt                                      >  1:80485/1‑141 (MQ=255)                                                                                                     tAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCATACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTa                                    <  1:355834/141‑1 (MQ=255)                                                                                                     tAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCAAACAGCAACGAGTGTGAAAGATCATACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTa                                    <  1:684950/141‑1 (MQ=255)                                                                                                        ttCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACTg                                 <  1:711650/141‑1 (MQ=255)                                                                                                            aTTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACTGaaaa                             <  1:469757/141‑1 (MQ=255)                                                                                                                 cTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCGTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGtt                        >  1:247276/1‑141 (MQ=255)                                                                                                                   gAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTAt                      <  1:170613/141‑1 (MQ=255)                                                                                                                      tCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGt                   >  1:327410/1‑141 (MQ=255)                                                                                                                       cAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTa                  <  1:851073/141‑1 (MQ=255)                                                                                                                         aCATTACGTCCTTTAGGCCATACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGATCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACGGAAAATGGTTATGGTaaa                >  1:580168/1‑141 (MQ=255)                                                                                                                          cATTACGTCCTTTAGGCCATACAGCAACGGGTGTGAAAGGTATTAAAATTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTAAAc               >  1:167464/1‑141 (MQ=255)                                                                                                                           aTTACGTCCGTTAGGCCATACAGCAACGGGTGGGAAAGGTATTACACTTCGTGAAGGGGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTAAACg              <  1:494840/141‑1 (MQ=255)                                                                                                                            ttACGTCCTTTAGGCCATACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTAAACGt             <  1:169751/141‑1 (MQ=255)                                                                                                                                       aGGCCATACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTaa  >  1:347788/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                                        GGTAAGATTGCGATTTCGTTCAGAGAAGATGATGAGTTAATTGCAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAA  >  USA300TCH1516_ALE/8946‑9220

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: ‑