Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	942,163	(A)6→5	intergenic (‑134/+115)	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	942,158	0	A	.	100.0%	151.7 / NA	31	intergenic (‑129/+120)	ptlE/mnhG1	Neopentalenolactone D synthase/Na(+)/H(+) antiporter subunit G1
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (20/11);  total (20/11)

TGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATCGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTGTGTCT  >  USA300TCH1516_ALE/942018‑942293                                                                                                                                             |                                                                                                                                        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                                                                                                                >  2:75522/1‑148 (MQ=255)                  aaCCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACa                                                                                                                >  2:75345/1‑148 (MQ=255)                  aaCCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACa                                                                                                                >  1:67090/1‑148 (MQ=255)                     ctctctctTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATg                                                                                                             <  2:58891/148‑1 (MQ=255)                     ctctctctTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATg                                                                                                             <  2:280012/148‑1 (MQ=255)                                  aaaCGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAAca                                                                                                >  2:48058/1‑148 (MQ=255)                                  aaaCGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAAca                                                                                                >  2:273308/1‑148 (MQ=255)                                                       taATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAAtt                                                                           <  1:114397/148‑1 (MQ=255)                                                       taATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAAtt                                                                           <  1:82185/148‑1 (MQ=255)                                                            attattatCATAATACATAACGACATGAAAGGCAATTACATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTACTAATTTGGaa                                                                      >  2:325540/1‑148 (MQ=255)                                                            attattatCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGaa                                                                      >  2:16010/1‑148 (MQ=255)                                                                ttatCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAatcat                                                                  <  1:92698/148‑1 (MQ=255)                                                                    cATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTa                                                              >  2:231424/1‑148 (MQ=255)                                                                                  aCATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTttgttgt                                                >  2:125363/1‑148 (MQ=255)                                                                                  aCATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTttgttgt                                                >  2:125330/1‑148 (MQ=255)                                                                                  aCATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTttgttgt                                                <  1:23422/148‑1 (MQ=255)                                                                                                     taaaGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGAttt                             <  1:166862/148‑1 (MQ=255)                                                                                                        agagATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGt                          <  2:370238/148‑1 (MQ=255)                                                                                                                   tAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTa               >  2:27878/1‑148 (MQ=255)                                                                                                                   tAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATAATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTa               >  2:168244/1‑148 (MQ=255)                                                                                                                   tAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAAGGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATAATCATGAGTTGGTTATATAATCTa               >  2:324139/1‑148 (MQ=255)                                                                                                                         gggCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAAttt         >  2:184900/1‑148 (MQ=255)                                                                                                                         gggCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAAttt         >  1:184734/1‑148 (MQ=255)                                                                                                                          ggCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAAtttt        >  1:120576/1‑148 (MQ=255)                                                                                                                                tCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTGTGTCt  >  1:355703/1‑148 (MQ=255)                                                                                                                                tCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTGTGTCt  >  1:165167/1‑148 (MQ=255)                                                                                                                                tCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTGTGTCt  >  1:184959/1‑148 (MQ=255)                                                                                                                                tCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTGTGTCt  >  1:81548/1‑148 (MQ=255)                                                                                                                                             |                                                                                                                                        TGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATCGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTGTGTCT  >  USA300TCH1516_ALE/942018‑942293

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: ‑