Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,028,542	G→C	32.7%	L35V (CTC→GTC)	USA300HOU_RS10230 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,028,542	0	G	C	32.7%	18.1 / 21.8	26	L35V (CTC→GTC)	USA300HOU_RS10230	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (7/9);  new base C (4/4);  total (12/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.13e-01

TGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACA  >  USA300TCH1516_ALE/2028407‑2028668                                                                                                                                        |                                                                                                                               tgatgatTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGACTaaaa                                                                                                                           <  2:315692/141‑1 (MQ=255)     gatTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGACTAAAAAGcc                                                                                                                       <  1:54023/141‑1 (MQ=255)              cTTATTAGACAATAATGTTAATGCAATTAATAGCGCGCCTCTCCAAACCGCCAAAAGGCCACGTATTTTATGAAAATAAATATATCCTACATAAACTAATACACATCCCAATAATAGAACTAGTAAAAAGCCAATTTTTTc                                                                                                              <  1:270765/141‑1 (MQ=255)                       cAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGACTAAAAAGCCAATTTTTTCAAAAAatat                                                                                                     >  1:273985/1‑141 (MQ=255)                        aataatGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAAAACGATGAAAAAGCCAATTTTTTCAAAAAatatt                                                                                                    >  1:24875/1‑140 (MQ=255)                                   tGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGACTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAAtt                                                                                         >  2:116206/1‑141 (MQ=255)                                     cAATTAATCGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTgg                                                                                       <  2:124427/141‑1 (MQ=255)                                       aTTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCa                                                                                     >  2:306362/1‑141 (MQ=255)                                          aaTAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCaata                                                                                  <  1:201302/141‑1 (MQ=255)                                              gctctccTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAAAAAAAAAAAAAAATATGTAGTAAAAATTGGCAATAATCa                                                                              <  2:346074/136‑1 (MQ=255)                                                             aCGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGTAATAAACCTTAATGCGGTaaaaa                                                               >  1:50250/1‑141 (MQ=255)                                                                ccAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAAAATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAAAGa                                                            >  2:50449/1‑141 (MQ=255)                                                                    aaGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGACTAGAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCaa                                                        <  2:273985/141‑1 (MQ=255)                                                                                  tATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTTAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGata                                          <  1:150636/141‑1 (MQ=255)                                                                                          tAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTtg                                  <  1:193916/141‑1 (MQ=255)                                                                                                aatCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTc                            <  2:33968/140‑1 (MQ=255)                                                                                                   ccTACATAAACTAATACACATGCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCTATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATg                         >  1:176634/1‑141 (MQ=255)                                                                                                       cATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTc                     <  1:112880/141‑1 (MQ=255)                                                                                                        aTAAACTAATACCGTACCCAAAAATAGAACGATTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTcg                    <  1:331055/141‑1 (MQ=255)                                                                                                          aaaCTAATACACATCCCAATAATAGAACGACTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTcgcc                  >  1:223740/1‑141 (MQ=255)                                                                                                                aTACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTCATATATGAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCttt            >  1:250747/1‑141 (MQ=255)                                                                                                                    acaTCCCAATAATAGAACAAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTAt        >  1:22601/1‑141 (MQ=255)                                                                                                                      aacccAATAATAGAACGACTAAAAATCCATTTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATTATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGc      <  1:303505/139‑1 (MQ=255)                                                                                                                       tCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGcc     >  2:50725/1‑141 (MQ=255)                                                                                                                         ccAATAATAGAACGACTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCcac   >  2:216798/1‑141 (MQ=255)                                                                                                                          cAATAATAGAACTAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATTAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCcaca  <  2:295983/141‑1 (MQ=255)                                                                                                                                        |                                                                                                                               TGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACA  >  USA300TCH1516_ALE/2028407‑2028668

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑