Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,343,467	T→A	15.4%	A43A (GCT→GCA)	USA300HOU_RS06640 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,343,467	0	T	A	15.4%	76.2 / 2.6	31	A43A (GCT→GCA)	USA300HOU_RS06640	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (17/9);  new base A (2/3);  total (19/12)
Fisher's exact test for biased strand distribution p-value = 3.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAATGATTGCTAATATTAAAAATAAAAGAAATTAATGATAAAAGTGTTACATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTAGTTTAGAAAAAAATACAAGAGATAATTATTTTATTCATGCCATAGACAGAATATACATAAATACTAGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTT  >  USA300TCH1516_ALE/1343333‑1343596                                                                                                                                       |                                                                                                                                  aaaTGATTGCTAATATTAAAAATAAAAGAAATTAATGATAAAAGTGTTACATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGaaaa                                                                                                                              <  2:383733/140‑1 (MQ=255)      aTTGCTAATATTAAAAATAAAAGAAATTAATGATAAAAGTGTTACATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTa                                                                                                                         >  1:38792/1‑140 (MQ=255)      aTTGCTAATATTAAAAATAAAAGAAATTAATGATAAAAGTGTTACATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTa                                                                                                                         >  1:38787/1‑140 (MQ=255)      aTTGCTAATATTAAAAATAAAAGAAATTAATGATAAAAGTGTTACATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCAGAAAAATCTa                                                                                                                         >  1:38791/1‑140 (MQ=255)      aTTGCTAATATTAAAAATAAAAGAAATTAATGATAAAAGTGTTACATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCAGAAAAATCTa                                                                                                                         >  1:38786/1‑140 (MQ=255)       ttGCTAATATTAAAAATAAAAGAAATTAATGATAAAAGTGTTACATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTAg                                                                                                                        <  1:485568/140‑1 (MQ=255)        tGCTAATATTAAAAATAAAAGAAATTAATGATAAAAGTGTTACATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTAGt                                                                                                                       >  2:501396/1‑140 (MQ=255)          cTAATATTAAAAATAAAAGAAATTAATGATAAAAGTGTTACATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTAGttt                                                                                                                     <  1:437961/140‑1 (MQ=255)                            gAAATTAATGATAAAAGTGTTACATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTAGTTTAGAAAAAAATACAAgaga                                                                                                   >  1:117390/1‑140 (MQ=255)                             aaaTTAATGATAAAAGTGTTACATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTAGTTTAGAAAAAAATACAAGAGAt                                                                                                  >  1:159491/1‑140 (MQ=255)                              aaTTAATGATAAAAGTGTTACATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTAGTTTAGAAAAAAATACAAGAGATa                                                                                                 <  2:38792/140‑1 (MQ=255)                              aaTTAATGATAAAAGTGTTACATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCAGAAAAATCTAGTTTAGAAAAAAATACAAGAGATa                                                                                                 <  2:38791/140‑1 (MQ=255)                              aaTTAATGATAAAAGTGTTACATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCAGAAAAATCTAGTTTAGAAAAAAATACAAGAGATa                                                                                                 <  2:38786/140‑1 (MQ=255)                              aaTTAATGATAAAAGTGTTACATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCAGAAAAATCTAGTTTAGAAAAAAATACAAGAGATa                                                                                                 <  2:38787/140‑1 (MQ=255)                                ttAATGATAAAAGTGTTACATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGCTAGCAATGATGAAAAATCTAGTTTAGAAAAAAATACAAGAGATAat                                                                                               >  2:492502/1‑140 (MQ=255)                                     gagaaaaGTGTTAAATATACATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTAGTTTAGAAAAAAATACAAGAGATAAttattt                                                                                          <  1:451324/137‑1 (MQ=255)                                     gATAAAAGTGTTACATATAAATATTTTACTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTAGTTTAGAAAAAAATACAAGAGATAAttattt                                                                                          <  1:152898/140‑1 (MQ=255)                                     caTAAAAGTGTCACATATAACTATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTAGTTTAGAAAAAAATACAAGAGATAAttattt                                                                                          <  1:195436/139‑1 (MQ=255)                                            gtgtTACATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTAGTTTAGAAAAAAATACAAGAGATAATTATTTTATTCAt                                                                                   >  2:394832/1‑140 (MQ=255)                                               ttACATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTAGCTTAGAAAAAAATACAAGATATAATTACTTTATTAATGcc                                                                                >  2:209700/1‑140 (MQ=255)                                                  cATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTAGTTTAGAACAAAATACAAGAGATAATTATTTTATTCACGCCATa                                                                             >  2:233194/1‑140 (MQ=255)                                                                      aatGCTGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTAGTTTAGAAAAAAATACAAGAGATAATTATTTTATTCATGCCATAGACAGAATATACATAAATAc                                                         <  1:56156/140‑1 (MQ=255)                                                                      aatGATGAAAATATGAAGCCTGGTATAATTCAAATGGAAATAGATAGTCTTGAAGTTAGCAATGCTGAAAAATCTAGTTTAGAAAAAAATACAAGAGATAATTATTTTATTCATGCCATAGACAGAATATACATAAATAc                                                         <  1:118717/140‑1 (MQ=255)                                                                           tgaAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAGGTTATCAATGCTGAAAAATCTAGTTTAGAAAAAAATACAAGAGATAATTATTTTATTCATGCCATAGACAGCATATACGTAAATCCTAGTa                                                    >  2:311444/1‑140 (MQ=255)                                                                              aaaTATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTAGTTTAGAAAAAAATACAAGAGATAATTATTTTATTCATGCCATAGACAGAATATACATAAATACTAGTAAAg                                                 >  2:508393/1‑140 (MQ=255)                                                                                               ttattCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTAGTTTAGAAAAAAATACAAGAGATAATTATTTTATTCATGCCATAGACAGAATATACATAAATACTAGTAAAGGGCTATTTCCTGAATCt                                >  1:254607/1‑140 (MQ=255)                                                                                                 attCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTAGTTTAGAAAAAAATACAAGAGATAATTATTTTATTCATGCCATAGACAGAATATACATAAATACTAGTAAAGGGCTATTTCCTGAATCTGa                              >  1:218065/1‑140 (MQ=255)                                                                                                 attCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTAGTTTAGAAAAAAATACAAGAGATAATTATTTTATTCATGCCATAGACAGAATATACATAAATACTAGTAAAGGGCTATTTCCTGAATCTGa                              >  1:200359/1‑140 (MQ=255)                                                                                                          gATATAGATAGTCTTGAAGTTATCAATGGTGAAGAATCTAGGTTAGAAAAAAATACAAGAGATAATTATTTTATTCATGCCATAGACAGAATATACATAAATACTAGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGc                     >  1:572820/1‑140 (MQ=255)                                                                                                             atagatagTCTTGAAGTTATCAATGCTGAAAAATCTAGTTTAGAAAAAAATACAAGAGATAATTATTTTATTCATGCCATAGACAGAATATACATAAATACTAGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATg                  >  2:542745/1‑140 (MQ=255)                                                                                                                             ttATCAATGCTGAAAAATCTAGTTTAGAAAAAAATACAAGAGATAATTATTTTATTCATGCCATAGACAGAATATACATAAATACTAGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATAGGAATAAAGAAAGtat  >  2:540455/1‑138 (MQ=255)                                                                                                                                       |                                                                                                                                  AAATGATTGCTAATATTAAAAATAAAAGAAATTAATGATAAAAGTGTTACATATAAATATTTTCCTAATAATGATGAAAATATTAAGCCTGGTATTATTCAAATGGATATAGATAGTCTTGAAGTTATCAATGCTGAAAAATCTAGTTTAGAAAAAAATACAAGAGATAATTATTTTATTCATGCCATAGACAGAATATACATAAATACTAGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTT  >  USA300TCH1516_ALE/1343333‑1343596

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: ‑