Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	942,060	C→G	intergenic (‑31/+218)	ptlE ← / ← mnhG1	Neopentalenolactone D synthase/Na(+)/H(+) antiporter subunit G1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	942,060	0	C	G	100.0%	133.0 / NA	35	intergenic (‑31/+218)	ptlE/mnhG1	Neopentalenolactone D synthase/Na(+)/H(+) antiporter subunit G1
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base G (19/16);  total (19/16)

AAAAAGTTTCGTGTGGGTCAATGATTGTTAATCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATCGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACA  >  USA300TCH1516_ALE/941915‑942199                                                                                                                                                  |                                                                                                                                            aaaaaGTTTCGTGTGGGTCAATGATTGTTAATCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGt                                                                                                                                           <  1:102021/148‑1 (MQ=255)   aaaGTTTCGTGTGGGTCAATGATTGTTAATCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTa                                                                                                                                         >  1:211652/1‑148 (MQ=255)   aaaGTTTCGTGTGGGTCAATGATTGTTAATCGGTCTGTTGTTAAGCCGCTTGATAATAGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTa                                                                                                                                         >  1:276596/1‑148 (MQ=255)               gggTCAATGATTGTTAATCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAatt                                                                                                                             <  1:62532/148‑1 (MQ=255)                         ttGTTAATCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCa                                                                                                                   >  1:280012/1‑148 (MQ=255)                         ttGTTAATCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCa                                                                                                                   >  1:58891/1‑148 (MQ=255)                            ttAATCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAGCCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCataa                                                                                                                <  1:176614/148‑1 (MQ=255)                            ttAATCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCataa                                                                                                                <  2:241097/148‑1 (MQ=255)                            ttAATCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCataa                                                                                                                <  1:88337/148‑1 (MQ=255)                                 cGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACAt                                                                                                           >  2:166862/1‑148 (MQ=255)                                          gttAATCCGCTTGATAATAGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATg                                                                                                  >  2:23422/1‑148 (MQ=255)                                                 cGCTTGATAATAGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCa                                                                                           <  2:353229/148‑1 (MQ=255)                                                 cGCTTGATAATAGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCa                                                                                           <  1:129229/148‑1 (MQ=255)                                                 cGCTTGATAATAGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCa                                                                                           <  2:175914/148‑1 (MQ=255)                                                  gCTTGATAATAGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCaa                                                                                          <  2:60275/148‑1 (MQ=255)                                                      gATAATAGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCaattaa                                                                                      <  1:23424/148‑1 (MQ=255)                                                        taataGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCaattaaat                                                                                    >  1:336998/1‑148 (MQ=255)                                                         aataGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCaattaaatt                                                                                   <  2:51314/148‑1 (MQ=255)                                                                      cGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATg                                                                      >  1:74333/1‑148 (MQ=255)                                                                      cGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATg                                                                      >  2:346795/1‑148 (MQ=255)                                                                      cGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATGTAATTAAAGAGATATATg                                                                      >  1:3188/1‑148 (MQ=255)                                                                                        tGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGt                                                    >  1:370238/1‑148 (MQ=255)                                                                                             ccgccgATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTATGATTTATAATTATTACTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCGGTAGTCa                                               >  2:11456/1‑148 (MQ=255)                                                                                                        tGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGaaaaatca                                    >  2:311369/1‑145 (MQ=255)                                                                                                         gTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGaaaaatcat                                   >  2:45040/1‑144 (MQ=255)                                                                                                                gCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGaaaaa                           <  1:263446/148‑1 (MQ=255)                                                                                                                  ataataAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAaga                         <  2:101365/148‑1 (MQ=255)                                                                                                                    aataaAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAgg                       <  2:140806/148‑1 (MQ=255)                                                                                                                         aaCCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACa                  >  1:67090/1‑148 (MQ=255)                                                                                                                         aaCCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACa                  >  2:75345/1‑148 (MQ=255)                                                                                                                         aaCCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACa                  >  2:75522/1‑148 (MQ=255)                                                                                                                            ctctctctTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATg               <  2:280012/148‑1 (MQ=255)                                                                                                                            ctctctctTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATg               <  2:58891/148‑1 (MQ=255)                                                                                                                                         aaaCGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAAca  >  2:273308/1‑148 (MQ=255)                                                                                                                                         aaaCGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAAca  >  2:48058/1‑148 (MQ=255)                                                                                                                                                  |                                                                                                                                            AAAAAGTTTCGTGTGGGTCAATGATTGTTAATCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTGCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATCGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACA  >  USA300TCH1516_ALE/941915‑942199

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑