Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,874,199	T→C	T100A (ACT→GCT)	USA300HOU_RS09305 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,874,199	0	T	C	100.0%	38.1 / NA	15	T100A (ACT→GCT)	USA300HOU_RS09305	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (6/9);  total (6/9)

CAGATAATGCATTTTTATTCTTTTTTAAATCTTCTTCAGTGACGATACGTAAATTATTATTTGGTGCTGCGCCACCTTCATCATCAAATTTACCTTTTTCAATACTTTCGTCAGTCTTATTGTCATATTCGGTAAATTTTGATTTTTCTTCTTTGAAAAATGCTTTTGGATTATTTTTTAATCTATTAGCATATTCTTTCGGATTTGTTTTTACTTCTTTAATTGTTTCATTAG  >  USA300TCH1516_ALE/1874085‑1874318                                                                                                                   |                                                                                                                        cAGATAATGCATTTTTATTCTTTTTTAAATCTTCTTCAGTGACGATACGTAAATTATTATTTGGTGCTGCGCCACCTTCATCATCAAATTTACCTTTTTCAATACTTTCGTCAGCCTTATTGTCATATTCGGTAAATTTTg                                                                                               >  1:121255/1‑141 (MQ=255) cAGATAATGCATTTTTATTCTTTTTTAAATCTTCTTCAGTGACGATACGTAAATTATTATTTGGTGCTGCGCCACCTTCATCATCAAATTTACCTTTTTCAATACTTTCGTAAGCCTTATTGTCATATTCGGTAAAttttt                                                                                               >  1:119317/1‑140 (MQ=255)          gaTTTTTATTCTTTTTTAAATCTTCTTCAGTGACGATACGTAAATTATTATTTGGTGCTGCGTCACCTTCATCATCAAATTTTCCTTTTTCAATACTTTCGTCAGCCTTATTGTCATATTCGGTAAATTTTGATTTttctt                                                                                      <  2:168833/140‑1 (MQ=255)                 aTTCTTTTTTAAATCTTCTTCAGTGACGATACGTAAATTATTATTTGGTGCTGCGCCACCTTCATCATCAAATTTACCTTTTTCAATACTTTCGTCAGCCTTATTGTCATATTCGGTAAATTTTGATTTTTCTTCTTTGaa                                                                               >  1:21820/1‑141 (MQ=255)                   tCTTTTTTAAATCTTCTTCAGTGACGATACGTAAATTATTATTTGGTGCTGCGCCACCTTCATCATCAAATTTACCTTTTTCAATACTTTCGTGAGCCTTATTGTCATATTCGGTAAATTTTGATTTTTCTTCTTTGgaaa                                                                             >  1:17759/1‑141 (MQ=255)                    cTTTTTTAAATCTTCTTCAGTGACGATACGTAAATTATTATTTGGTGCTGCGCCACCTTCATCATCAAATTTACCTTTTTCAATACTTTCGTCAGCCTTATTGTCATATTCGGTAAATTTTGATTTTTCTTCTTTGaaaaa                                                                            <  1:74439/141‑1 (MQ=255)                    cTTTTTTAAATCTTCTTCAGTGACGATACGTAAATTATTATTTGGTGCTGCGCCACCTTCATCATCAAATTTACCTTTTTCAATACTTTCGTCAGCCTTATTATCATATTCTGTAAATTTTGATTCTTCTTCTTTGaataa                                                                            >  2:151771/1‑141 (MQ=255)                                    tcAGTGACGATACGTAAATTATTATTTGGTGCTGCGCCACCTTCATCATCAAATTTACCTTTTTCGATACTTTCGTCAGCCTTATTGTCATATTCGGTAAATTTTGATTTTTCTTCTTTGATAAATGCTTTTGGATTAttt                                                            >  2:139695/1‑141 (MQ=255)                                            gATACGTAAATTATTATTTGGTGCTGCGCCACCTTCATCATCAAATTTACCTTTTTCAATACTTTCGTCAGCCTTATTGTCATATTCGGTAAATTTTGATTTTTCTTCTTTGAAAAATGCTTTTGGATTATTTTTTAATCt                                                    <  1:155560/141‑1 (MQ=255)                                                   aaaTTATTATTTGGTGCTGCGCCACCTTCATCATCAAATTTACCTTTTTCAATACTTTCGTCAGCCTTATTGTCATATTCGGTAAATTTTGATTTTTCTTCTTTGAAAAATGCTTTTGGATTATTTTTTAATCTATTAGCa                                             <  1:223713/141‑1 (MQ=255)                                                                 tgctgcGCCACCTTCATCATCAAATTTACCTTTTTCAATACTTTCGTCAGCCTTATTGTCATATTCGGTAAATTTTGATTTTTCTTCTTTGAAAAATGCTTTTGGATTATTTTTTAATCTATTAGCATATTCTTTCGGAtt                               <  1:247993/141‑1 (MQ=255)                                                                 tgctgcGCCACCTTCATCATCAAATTTACCTTTTTCAATACTTTCGTCAGCCTTATTGTCATATTCGGTAAATTTTGATTTTTCTTCTTTGAAAAATGCTTTTGGATTATTTTTTAATCTATTAGCATATTCTTTCGGAtt                               <  1:247994/141‑1 (MQ=255)                                                                             ttCATCATCAAATTTACCTTTTTCAATACTTTCGTCAGCCTTATTGTCATATTCGGTAAATTTTGATTTTTCTTCTTTGAAAAATGCTTTTGGATTATTTTTTAATCTATTAGCATATTCTTTCGGATTTGTTTTTActtc                   <  1:93417/141‑1 (MQ=255)                                                                                atcatcaAATTTACCTTTTTCAATACTTTCGTCAGCCTTATTGTCATATTCGGTCCCTTGCCACGATTCTTCTTTGAAAAATGCTTTTGGATTATTTTTTAATCTATTAGCATATTCTTTCGGATTTGTTTTTACTTCttt                <  1:133044/141‑1 (MQ=255)                                                                                              ttttttCAATACTTTCGTCAGCCTTATTGTCATATTCGGTAAATTTTGATTTTTCTTCTTTGAAAAATGCTTTTGGATTATTTTTTAATCTATTAGCATATTCTTTCGGATTTGTTTTTACTTCTTTAATTGTTTCATTAg  <  2:121255/140‑1 (MQ=255)                                                                                                                   |                                                                                                                        CAGATAATGCATTTTTATTCTTTTTTAAATCTTCTTCAGTGACGATACGTAAATTATTATTTGGTGCTGCGCCACCTTCATCATCAAATTTACCTTTTTCAATACTTTCGTCAGTCTTATTGTCATATTCGGTAAATTTTGATTTTTCTTCTTTGAAAAATGCTTTTGGATTATTTTTTAATCTATTAGCATATTCTTTCGGATTTGTTTTTACTTCTTTAATTGTTTCATTAG  >  USA300TCH1516_ALE/1874085‑1874318

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: ‑