Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,298,108	T→A	intergenic (+4/‑232)	pnp → / → rnj2	Polyribonucleotide nucleotidyltransferase/Ribonuclease J 2

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,298,108	0	T	A	100.0%	86.0 / NA	26	intergenic (+4/‑232)	pnp/rnj2	Polyribonucleotide nucleotidyltransferase/Ribonuclease J 2
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (11/15);  total (11/15)

ACATTTCACAAATTTCAAAAAATAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATTTAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTATCCTGTAT  >  USA300TCH1516_ALE/1297968‑1298245                                                                                                                                             |                                                                                                                                          acaTTTCACAAATTTCAAAAAATATAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTc                                                                                                                                    <  3:111215/148‑1 (MQ=255)   aTTTCACAAATTTCAAAAAATAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCat                                                                                                                                  <  3:69343/148‑1 (MQ=255)         caAATTTCAAAAAATAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATgacg                                                                                                                            >  4:276827/1‑148 (MQ=255)               tCAAAAAATAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATgac                                                                                                                             >  1:48851/1‑141 (MQ=255)                                         aGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCa                                                                                            >  4:387384/1‑148 (MQ=255)                                                       tCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTg                                                                              >  3:131195/1‑148 (MQ=255)                                                       tCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTg                                                                              >  3:131200/1‑148 (MQ=255)                                                            gACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAg                                                                                <  2:39358/141‑1 (MQ=255)                                                                   agtaaGTTAAAATTACAGAAATTGATAAACAAGGTTGAGTAAATCCTTCACAAAGAACATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCg                                                                         <  2:39974/138‑1 (MQ=255)                                                                    tGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGGAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGt                                                                        <  2:35189/141‑1 (MQ=255)                                                                                              aaCAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATATTAGATAACGTCATATGATGACAATGGATCGTCATGTGATTTTTTTATGCCACTTCTTACGATGTGACCCGTTTTGAATTTGTTGTATTGTACATTTTaatccgc                                       <  4:97796/148‑6 (MQ=255)                                                                                              aaCAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGc                                       <  3:259472/148‑1 (MQ=255)                                                                                              aaCAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGc                                       <  3:130921/148‑1 (MQ=255)                                                                                                 aaGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCttt                                    >  4:404153/1‑148 (MQ=255)                                                                                                     tCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTttatta                                <  3:412983/148‑1 (MQ=255)                                                                                                                cTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTTTGTTTTTTTTTACGAAGTGACCCGTTTTGTATTTGTTGTATTGAACATTTTAAAACGCTTTCTTATTTTGTGTGCa                     >  4:237226/1‑148 (MQ=255)                                                                                                                   cacaTAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACt                  >  3:328181/1‑148 (MQ=255)                                                                                                                   cacaTAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACt                  >  3:72437/1‑148 (MQ=255)                                                                                                                   cacaTAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACt                  >  3:79338/1‑148 (MQ=255)                                                                                                                      aTAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGc                      <  1:39094/141‑1 (MQ=255)                                                                                                                              ttAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTATcc       <  3:404153/148‑1 (MQ=255)                                                                                                                              ttAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTATcc       <  3:227685/148‑1 (MQ=255)                                                                                                                                agaagaATAATATATAAAGTCAGATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTTAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTATCCtg     <  4:247245/148‑1 (MQ=255)                                                                                                                                 gaagaaTAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAAtt           <  2:48851/141‑1 (MQ=255)                                                                                                                                 gaagaaTAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTATCCtgt    <  3:276827/148‑1 (MQ=255)                                                                                                                                   agaaTAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTTACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTTTGTGCAACTGTTAATTATCCtgtat  >  4:240820/1‑148 (MQ=255)                                                                                                                                             |                                                                                                                                          ACATTTCACAAATTTCAAAAAATAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATTTAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTATCCTGTAT  >  USA300TCH1516_ALE/1297968‑1298245

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑