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%	123.9 / NA	33	intergenic (+1247/+815)	USA300HOU_1490/USA300HOU_1492	integrase/possible lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (4/29);  total (4/29)

CGCATCAAGATTTTCTAAATTAAGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGCACACCATCATTAATGTTAACG  >  CP000730/1606984‑1607268                                                                                                                                                     |                                                                                                                                         cGCATCAAGATTTTCTAAATTAAGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTg                                                                                                                                        <  2:382332/151‑1 (MQ=255)  gCATCAAGATTTTCTAAATTAAGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGt                                                                                                                                       <  2:422712/151‑1 (MQ=255)       aaGATTTTCTAAATTAAGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCtt                                                                                                                                  <  2:131856/151‑1 (MQ=255)                  aaTTAAGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACttt                                                                                                                       <  1:293120/151‑1 (MQ=255)                     tAAGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTAtt                                                                                                                    <  2:224831/151‑1 (MQ=255)                     tAAGTCTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTAtt                                                                                                                    <  1:387938/151‑1 (MQ=255)                      aaGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTAttt                                                                                                                   <  2:171912/151‑1 (MQ=255)                            aattaaAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTATTGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTa                                                                                                             <  2:349621/151‑1 (MQ=255)                             attaaAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAg                                                                                                            >  1:218883/1‑151 (MQ=255)                                  aGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTa                                                                                                       <  2:256139/151‑1 (MQ=255)                                   gTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTAc                                                                                                      >  1:308440/1‑151 (MQ=255)                                    ttCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACa                                                                                                     <  1:142735/151‑1 (MQ=255)                                          ttCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCg                                                                                               <  1:419861/151‑1 (MQ=255)                                            ccAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTa                                                                                             <  2:309030/151‑1 (MQ=255)                                                aaCGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTAtgtg                                                                                         <  1:354939/151‑1 (MQ=255)                                                aaCGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTAtgtg                                                                                         <  2:15069/151‑1 (MQ=255)                                                  cGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGtt                                                                                       <  1:151136/151‑1 (MQ=255)                                                           gAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCt                                                                              <  2:191633/151‑1 (MQ=255)                                                                       cAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCt                                                                  <  2:451868/151‑1 (MQ=255)                                                                       cAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCt                                                                  <  1:112983/151‑1 (MQ=255)                                                                         aaCATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATATTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCttt                                                                <  2:337870/151‑1 (MQ=255)                                                                               tATTGGAATTCGCCCATCCATATCTAATGTTATGTTCATAGTCTTTTTTACTCTTTTCCACTTCTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAAc                                                          <  1:160530/151‑1 (MQ=255)                                                                               tATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAAc                                                          <  1:63050/151‑1 (MQ=255)                                                                               tATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAAc                                                          <  2:201634/151‑1 (MQ=255)                                                                               cgtttcaaTTCGCCCACCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAAc                                                          <  1:117382/145‑1 (MQ=255)                                                                                      aTTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTTTCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATg                                                   <  1:334438/151‑1 (MQ=255)                                                                                           cccATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTTCTTTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGt                                              >  2:255574/1‑151 (MQ=255)                                                                                                                     tAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGcaca                    >  1:350013/1‑151 (MQ=255)                                                                                                                           tttttACTGGTTTCCAGTTTTATTGTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTGTATAACCTACATGTCTGGCTATTAAAGTATCTAATCTGGGCACACcatca              <  2:184140/151‑1 (MQ=255)                                                                                                                                       tCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGCACACCATCATTAATGTTAAcg  <  2:13914/151‑1 (MQ=255)                                                                                                                                       tCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGCACACCATCATTAATGTTAAcg  <  1:325781/151‑1 (MQ=255)                                                                                                                                       tCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGCACACCATCATTAATGTTAAcg  <  1:54511/151‑1 (MQ=255)                                                                                                                                       tCCATTTTCAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTAGATGGCTCTCTATTAAAGTATCTAACCTGGGCACACCATCATTAATGTTAAcg  <  1:398894/151‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                         CGCATCAAGATTTTCTAAATTAAGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGCACACCATCATTAATGTTAACG  >  CP000730/1606984‑1607268

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑