Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	178,705	C→A	23.4%	P227Q (CCA→CAA)	capD →	UDP‑glucose 4‑epimerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	178,705	0	C	A	23.4%	55.0 / 8.1	33	P227Q (CCA→CAA)	capD	UDP‑glucose 4‑epimerase
Reads supporting (aligned to +/- strand):  ref base C (10/15);  new base A (4/4);  total (14/19)
Fisher's exact test for biased strand distribution p-value = 6.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.25e-01

CCTTTAACGATTACAGATCCTGATATGACAAGATTTTTAATGAGCTTAGAAGATGCGGTAGAACTAGTTGTTCATGCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGAATTGTTTGAAGCTGATAATGCAATTGAAATCATTGGTACGCGACATGGAGAGAAAAAAGCAGAAACATTGTTGACGAGAGAAGAATACGCACAAT  >  USA300TCH1516_ALE/178584‑178839                                                                                                                          |                                                                                                                                       ccTTTAACGATTACAGATCCTGATATGACAAGATTTTTTTTTTTTTTTTTATATGCGGAAGGACTAGTTGTTCATGCATTTAAGCTTGCAGAGATACGAGATATTATTGTTCATCAAGCACCAAGCTTCACGGTAGGGGAt                                                                                                                     >  2:164458/1‑141 (MQ=255)       aCGATTACAGATCCTGATATGACAAGATTTTTAATGAGCTTAGAAGATGCGGTAGAACTAGTTGTTCATGCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCg                                                                                                               <  1:187793/141‑1 (MQ=255)               aGATCCTGATATGACAAGATTTTTAATGAGCTTAGAAGATGCGGTAGGACTAGTTGTTCATGCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACAAAGCTCAACGGTAGGGGATCTTGCGACCGCagt                                                                                                       >  1:104448/1‑139 (MQ=255)               aGATCCTGATATGACAAGATTTTTAATGAGCTTAGAAGATGCGGTAGAACTAGTTGTTCATGCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACAAAGCTCAACGGTAGGGGATCTTGCGACCGCatt                                                                                                       >  1:104449/1‑141 (MQ=255)               aGATCCTGATATGACAAGATTTTTAATGAGCTTAGAAGATGCGGTAGAACTAGTTGTTCATGCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACAAAGCTCAACGGTAGGGGATCTTGCGACCGCatt                                                                                                       >  1:104444/1‑141 (MQ=255)               aGATCCTGATATGACAAGATTGTTAATGAGCTTAGAAGATGCGGTAGAACTAGTTGTTCATGCATTTAAGCATGCAGAGACGGGAGATAATATGGTTCAAAAAGCACAAAGCTCAACGGTAGGGGATCTTGCGACCGCatt                                                                                                       >  1:104451/1‑141 (MQ=255)                  tCCTGATATGACAAGATTTTTAATGAGCTTAGAAGATGCGGTAGAACTAGTTGTTCATGCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCattatt                                                                                                    <  1:297974/141‑1 (MQ=255)                     tGATATGACAAGATTTTTAATGAGCTTAGAAGATGCGGTAGAAGTAGTTGTTCATGCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGa                                                                                                 <  2:30833/141‑1 (MQ=255)                      gATATGACAAGATTTTTAATGAGCTTAGAAGATGCGGTAGAACTAGTTGTTCATGCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATCAGaa                                                                                                <  2:340720/141‑1 (MQ=255)                        tatGACAAGATTTTTAATGAGCTTAGAAGATGCGGTAGAACTAGTTGTTCATGCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGAAtt                                                                                              >  2:82872/1‑141 (MQ=255)                           gACAAGATTTTTAATGAGCTTAGAAGATGCGGTAGAACTAGTTGTTCATGCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACCAAGATCAACGGTAGGGGATCTTGCGACCGCCTTATTAGaactact                                                                                           >  2:130794/1‑136 (MQ=255)                            aCAAGATTTTTAATGAGCTTAGAAGATGCGGTAGAACTAGTTGTTCATGCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGAATTGttt                                                                                          <  1:313842/141‑1 (MQ=255)                             aaaGATTTTTAATGAGCTTAGAAGATGCGGTAGAACTAGTTGTTCATGCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGAATTGTTTg                                                                                         <  2:132891/140‑1 (MQ=255)                                 aTTTTTAATGAGCTTAGAAGATGCGGTAGAACTAGTTGTTCATGCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGAATTGTTTGAAGc                                                                                     >  1:96154/1‑141 (MQ=255)                                       aaTGAGCTTAGAAGATGCGGTAGAACTAGTTGTTCATGCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACAGCATTATTAGAATTGTTTGAGGATGATaa                                                                               >  2:307096/1‑141 (MQ=255)                                                      tGCGGTAGAACTAGTTGTTCATGCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGAATTGTTTGAAGCTGATAATGCAATTGAAATCAt                                                                >  1:53532/1‑141 (MQ=255)                                                             gaatgaGTTGTTCATGCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGAATTATTTGAAGCTGATAATGCAATTGAAATCATTGGTAcg                                                         <  2:288843/136‑1 (MQ=255)                                                             caaCTAGGTGTTCATGCATTTAAGCATGCAGAGACAGGAGATATTATGTTTAAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGCATTGTTTGACGCTGATCATGCAATTGAAATCATTGGTCcg                                                         <  2:237020/140‑1 (MQ=255)                                                              aattAGTTGTTACAGCATGTTAGTATGCAGATACAGGAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGAATTGTTTGAAGCTGATAATGCAATTGAAATCATTGGTAcgc                                                        <  2:135900/138‑1 (MQ=255)                                                                  aGTTGTTCATGCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGAATTGTTTGAAGCTGATAATGCAATTGAAATCATTGGTACGCGACa                                                    >  1:313481/1‑141 (MQ=255)                                                                   gttgttCATGCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGAATTGTTTGAAGCTGATAATGCAATTGAAATCATTGGTACGCGACAt                                                   >  2:61586/1‑141 (MQ=255)                                                                            gCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGAATTGTTTGAAGCTGATAATACAAACCTAATCATTGTTACGCGACATGGAGAGaaa                                          >  2:55155/1‑141 (MQ=255)                                                                                       gtgaaagaCAGGATAGAGTATGGTTCAAAAAGCACCAAGCGAAACGGTAGGGGATCTTGCGACCGCATTATTAGAATTGTTTGAAGCTGATATTGTAATTAAAATAATTAGTACGCGACATGGAGAGAAAAAAGCAGAAAc                               <  2:156857/136‑1 (MQ=255)                                                                                         cAGAGACAGGAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGAATTGTTTGAAGCTGATAATGCAATTGAAATCATTGGTACGCGACATGGAGAGAAAAAAGCAGAAACAt                             <  1:55504/141‑1 (MQ=255)                                                                                          agagACAGGAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGAATTGTTTGAAGCTGATAATGCAATTGAAATCATTGGTACGCGACATGGAGAGAAAAAAGCAGAAACAtt                            <  1:335363/141‑1 (MQ=255)                                                                                              acgggggaTATTAGGGTTTAAAAAGCACAGAGCTCAACGGTATGGGATCTTGCGACCGCATTATTAGAGTTGTTTGAAGGTGATAATGCAATTGAAATCATTGGTACGAGACATGGAGTGAAAAAAGCAGCGACAttgttg                        <  2:104448/135‑1 (MQ=255)                                                                                              aCAGGAGATATTATGGTTCAAAAAGCACAAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGAATTGTTTGAAGCTGATAATGCAATTGAAATCATTGGTACGCGACATGGAGAGAAAAAAGCAGAAACAttgttg                        <  2:104449/141‑1 (MQ=255)                                                                                              aCAGGAGATATTATGGTGAAAAGAGGACAAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGAATTGTTTGAAGCTGATAATGCAATTGAAATCATTGGTACGCGACATGGAGAGAAAAAAGCAGAAACAttgttg                        <  2:104444/141‑1 (MQ=255)                                                                                              aCAGGAGATAATATGGTTCAAAAAGCTCAAAGCTAAACGGTAGTGGAACTTGCGACCGCATTATTAGAATTGTTTGAAACTGATAATGTAATTGAAATCATTGGTACGCGACAAGGAGAGAAAAAAGCACAAACTttcttt                        <  2:104451/141‑2 (MQ=255)                                                                                                 ggAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATGATTAGAATTGTTTGAAGCTGATAATGCAATTGAAATCATTGGTACGCGACATGGAGAGAAAAAAGCAGAAACATTGTTGACg                     <  1:3191/141‑1 (MQ=255)                                                                                                  gagaTAGTATGGTTCAAAAAGAACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGAATTGTTTGAAGCTGATAATGCAATTGAAATCATTGGTACGCGACATGGAGAGAAAAAAGCAGAAACATTGTTGACga                    <  2:208783/141‑1 (MQ=255)                                                                                                    gaTATAATGGTTCAAATACCACCAAGCTCAACGGTAGGGGATCTGGCGACCGCATTATTAGAATTGTTTGAAGCTGATAATGCAATTGAAATCATTGGTACGCGACATGGAGAGAAAAAAGCAGAAACATTGTTGACgaga                  <  1:281384/141‑1 (MQ=255)                                                                                                                    aaGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGAATTGTTTGAAGCTGATAATGCAATTGAAATCATTGGTACGCGACATGGAGAGAAAAAAGCAGAAACATTGTTGACGAGAGAAGAATACGCACAAt  >  1:228677/1‑141 (MQ=255)                                                                                                                          |                                                                                                                                       CCTTTAACGATTACAGATCCTGATATGACAAGATTTTTAATGAGCTTAGAAGATGCGGTAGAACTAGTTGTTCATGCATTTAAGCATGCAGAGACAGGAGATATTATGGTTCAAAAAGCACCAAGCTCAACGGTAGGGGATCTTGCGACCGCATTATTAGAATTGTTTGAAGCTGATAATGCAATTGAAATCATTGGTACGCGACATGGAGAGAAAAAAGCAGAAACATTGTTGACGAGAGAAGAATACGCACAAT  >  USA300TCH1516_ALE/178584‑178839

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: ‑