Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	1,607,132	C→T	intergenic (+1247/+815)	USA300HOU_1490 → / ← USA300HOU_1492	integrase/possible lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,607,132	0	C	T	100.0%	69.9 / NA	20	intergenic (+1247/+815)	USA300HOU_1490/USA300HOU_1492	integrase/possible lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (7/13);  total (7/13)

AAGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGCACACCATCATTAATGTTAAC  >  CP000730/1607005‑1607267                                                                                                                                |                                                                                                                                        aaGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTAcc                                                                                                                            <  1:343618/141‑1 (MQ=255)  aGTTTAATTAGAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCg                                                                                                                           <  2:218622/141‑1 (MQ=255)                         aGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACa                                                                                                    <  1:248108/141‑1 (MQ=255)                                gCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGt                                                                                             >  1:295144/1‑141 (MQ=255)                                       aaTCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGtt                                                                                      <  2:145629/141‑1 (MQ=255)                                            ccTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCGTTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCtt                                                                                 >  2:245650/1‑141 (MQ=255)                                                    aaCATTTATTGTTTTTCTTCCTTCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTTCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCtttttaaatg                                                                         <  2:361015/141‑7 (MQ=255)                                                    aaCATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTAttt                                                                         <  1:31715/141‑1 (MQ=255)                                                      cATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTaa                                                                       >  1:42570/1‑141 (MQ=255)                                                       aTTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAAc                                                                      <  1:380798/141‑1 (MQ=255)                                                         ttATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACtt                                                                    <  1:348106/141‑1 (MQ=255)                                                                aaTTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTta                                                             <  1:352130/141‑1 (MQ=255)                                                                          tccatATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTTCTTTTTTAATCTTTGTATCTTTTACCGACTTTATTTTGCTTAGTGGTACATCATCGTATGTGTTTTCTTTTCTTTTTTACTTCCTTTTATATCCtcatt                                                   >  2:218625/1‑137 (MQ=255)                                                                                          tgttaATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGt                                   >  1:242794/1‑141 (MQ=255)                                                                                           gttaATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTa                                  <  2:89770/141‑1 (MQ=255)                                                                                                   tCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCt                          <  2:193045/141‑1 (MQ=255)                                                                                                            cTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGCACAcc                 <  2:128294/141‑1 (MQ=255)                                                                                                            cTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGCACAcc                 <  2:391232/141‑1 (MQ=255)                                                                                                                          tAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGCACACCATCATTAATGTTaa   >  1:165353/1‑141 (MQ=255)                                                                                                                           aaTTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCCTTTATCAAATACATCGCTGTCTATTAATGTATCTAACATGGGCCCACCATCATTAATGTTAAc  >  1:37217/1‑141 (MQ=255)                                                                                                                                |                                                                                                                                        AAGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGCACACCATCATTAATGTTAAC  >  CP000730/1607005‑1607267

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