Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	195,286	T→A	intergenic (‑97/‑82)	USA300HOU_RS00900 ← / → USA300HOU_RS00905	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	195,286	0	T	A	100.0%	79.6 / NA	24	intergenic (‑97/‑82)	USA300HOU_RS00900/USA300HOU_RS00905	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (11/13);  total (11/13)

CTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑TAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACG  >  USA300TCH1516_ALE/195159‑195415                                                                                                                                 |                                                                                                                                  cTAACCCTGCTACCACAGATTACTTATCTATAATGATATCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCtt                                                                                                                      <  1:112435/141‑1 (MQ=255)   aaaCTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTCTATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTaa                                                                                                                    >  1:344098/1‑141 (MQ=255)   aaaCTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATTTAATTATT‑ATAAAAATTATCTTat                                                                                                                    >  1:295387/1‑140 (MQ=255)         gCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCt                                                                                                              >  1:427886/1‑141 (MQ=255)                               tAATGATAGCACCCTATATATATGTTTATTTACTTATACCCTAACAGGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGCAATCCGATAAGAATTATAg                                                                                        <  1:266381/141‑1 (MQ=255)                                         ccccTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATAttttt                                                                              <  1:457122/141‑1 (MQ=255)                                           ccTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTc                                                                            <  1:44005/141‑1 (MQ=255)                                           ccTATATATATGGTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTCTAGTAATATTTTTTc                                                                            <  1:371615/141‑1 (MQ=255)                                            cTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTCTAGTAATATTTTTTCa                                                                           >  1:413512/1‑141 (MQ=255)                                                 tatatGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCAt                                                                      <  1:141997/141‑1 (MQ=255)                                                             taCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATaggagg                                                          >  1:174103/1‑141 (MQ=255)                                                              aCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGt                                                         >  1:500462/1‑141 (MQ=255)                                                                 tataCCCTAACATTATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCtt                                                      <  1:234372/141‑1 (MQ=255)                                                                 tataCCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCtt                                                      <  1:373009/141‑1 (MQ=255)                                                                 tataCCCTAACATGATTTTTATACCCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATACTAATGAGTTTTCAACCATTGTTATAGGAGGTCtt                                                      <  1:496742/141‑1 (MQ=255)                                                                         aaCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGa                                              <  1:379590/141‑1 (MQ=255)                                                                           cATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACa                                            >  1:175289/1‑141 (MQ=255)                                                                              gATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACatta                                         >  1:220884/1‑141 (MQ=255)                                                                                   ttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTAttttt                                    >  1:107260/1‑141 (MQ=255)                                                                                     ataCTCTTTGAAAATAGATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTttat                                  <  1:4524/141‑1 (MQ=255)                                                                                           tttGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAg                            <  1:38717/141‑1 (MQ=255)                                                                                                    atatTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGACGCTAGCAAtg                   >  1:167404/1‑140 (MQ=255)                                                                                                       ttttACAGAATTTTATCTAAATATC‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTg                <  1:339725/141‑1 (MQ=255)                                                                                                                      tCTAAATATTAAAAAAAAATATCTTAATATCCTTATAATCCGATAAGAATGATAGTACTATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTTGAAGCTAAAAATCTTAATTTTGCATCaaag  >  1:344052/1‑139 (MQ=255)                                                                                                                                 |                                                                                                                                  CTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑TAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACG  >  USA300TCH1516_ALE/195159‑195415

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: ‑