Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,679,710	G→T	100%	G65V (GGC→GTC)	USA300HOU_2536 →	possible secretory antigen

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,679,710	0	G	T	100.0%	88.2 / NA	33	G65V (GGC→GTC)	USA300HOU_2536	possible secretory antigen
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (19/14);  total (19/14)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTA  >  CP000730/2679574‑2679837                                                                                                                                         |                                                                                                                                gcagATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCaa                                                                                                                              >  1:255649/1‑140 (MQ=255)   agATTTCACTTATCAATCCTTTGAACTAACGCATCAATCGCATGCCGCTTTTAATTATTATAGTAAAAACCAATGTACATTGTTGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATg                                                                                                                            <  2:265993/140‑1 (MQ=255)    gATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGc                                                                                                                           <  1:281931/140‑1 (MQ=255)     aTTTCACTTATCAAACCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCt                                                                                                                          <  1:55847/140‑1 (MQ=255)     aTTTCAATTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCACGCACAAGTCGGTAAACATGTTCATAATAAGTGGGTCACTGcg                                                                                                                          >  2:156129/1‑139 (MQ=255)                    ccGTCGAACAAACGCATCAATCGCATGCCGCAGTTACTTATTATAGTAAAAACCAATGTACATGATGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTaa                                                                                                           >  1:75749/1‑139 (MQ=255)                           aCAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCAc                                                                                                    >  1:204758/1‑140 (MQ=255)                             aaaCGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGt                                                                                                  <  1:101580/140‑1 (MQ=255)                               aCGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACAAGGTTCGCATATAAACGTCGCGCACAAGTCAGTAAACCTATATCTAATAGGAGGTTCAATGCTAAAAAATGGTATTACAATGCACGTaa                                                                                                >  1:30792/1‑140 (MQ=255)                                                cGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTg                                                                               >  1:341960/1‑140 (MQ=255)                                                 gCAGTTAATTAATATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTgg                                                                              <  1:211552/140‑1 (MQ=255)                                                         ttattaTAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTacac                                                                      >  2:352976/1‑140 (MQ=255)                                                            ttatAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCaa                                                                   <  1:51813/140‑1 (MQ=255)                                                             tataGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCTCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAg                                                                  <  1:120328/140‑1 (MQ=255)                                                                aGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAATTTGGGAAACCTGTTTCTAATAAATGGGTCAATGCTAAAAATTGGTATTACAAAGCACGTAAATCAAAATAAGCGACTAGTCGTACACCAAGaaa                                                               >  2:1661/1‑140 (MQ=255)                                                                    aaaaCCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTGAGTAAAAGTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAAttt                                                           >  2:195846/1‑140 (MQ=255)                                                                     gaatcAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTg                                                          <  2:30792/136‑1 (MQ=255)                                                                     aaaCCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACAAAGAAAATTTg                                                          >  1:133219/1‑140 (MQ=255)                                                                       atctaTGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCt                                                        <  1:91453/136‑1 (MQ=255)                                                                           aTGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCa                                                    >  1:295126/1‑140 (MQ=255)                                                                             gTACATGATGGGCATTTAAACGTCGCGCACAAATCGGTAAACCTGTTTATAATAGATAGGTCAATGCTCAAAATTGGTAATAACATGCACGTAAGTCAACAAAAGCGACAGGTCGTACCCCAACaaacattgatgcgctt                                                  >  2:336455/1‑127 (MQ=255)                                                                                   ggtggGCATTTAAACGTCGCGTAAAAGTCGGTAAACCTGTTTATAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCa                                            <  2:19646/140‑1 (MQ=255)                                                                                        gCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTACTGTCATGCAATCAACTGc                                       >  1:320304/1‑140 (MQ=255)                                                                                           tttAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAgg                                    <  2:204758/140‑1 (MQ=255)                                                                                                  gTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACAGAAGGAtattat                             >  1:123068/1‑140 (MQ=255)                                                                                                       gcACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACa                        >  1:131700/1‑140 (MQ=255)                                                                                                        cacaAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAACTCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTAAAGGATATCATGGAAAt                       >  1:190400/1‑140 (MQ=255)                                                                                                           aaGTCGTTAAACCTGTTTCTAATAGATGGGTCGATGCTAAAAATTGTTCTTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACGTGTc                    <  1:242754/140‑1 (MQ=255)                                                                                                                    aaCCTGTTTCTGATAGATGGGTCAATGCTCACAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACTTGTCGCAgttgtt           <  2:104255/140‑1 (MQ=255)                                                                                                                     aCCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGATATGCCGCAGttgttg          >  1:146022/1‑140 (MQ=255)                                                                                                                       cTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGCTATTATGGACATATCGCAATTGTTGac        >  2:225549/1‑139 (MQ=255)                                                                                                                         gTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGAAATCAACTGCAGGATATTATGGACATGTAGCAGTTGTTGacaa      >  2:352888/1‑137 (MQ=255)                                                                                                                             cTAATAGTGGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAATAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGta  <  2:80118/140‑1 (MQ=255)                                                                                                                                         |                                                                                                                                GCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTA  >  CP000730/2679574‑2679837

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑