Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,035,886	T→C	intergenic (+386/‑3)	ftnA → / → polC_2	Bacterial non‑heme ferritin/DNA polymerase III PolC‑type

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,035,886	0	T	C	100.0%	113.9 / NA	30	intergenic (+386/‑3)	ftnA/polC_2	Bacterial non‑heme ferritin/DNA polymerase III PolC‑type
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (17/13);  total (17/13)

ATATCATCATTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACTACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATCCGCAAGAC  >  USA300TCH1516_ALE/2035743‑2036026                                                                                                                                                |                                                                                                                                             atatCATCATTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACAt                                                                                                                                          <  1:106764/148‑1 (MQ=255) atatCATCATTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACAt                                                                                                                                          <  2:23835/148‑1 (MQ=255)      atcatTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATAc                                                                                                                                     <  1:314915/148‑1 (MQ=255)         atTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAg                                                                                                                                  >  2:152475/1‑148 (MQ=255)         atTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAg                                                                                                                                  >  2:103414/1‑148 (MQ=255)                      tCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGc                                                                                                                     <  1:228480/148‑1 (MQ=255)                            ttACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGa                                                                                                               <  1:10813/148‑1 (MQ=255)                                  ccAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGa                                                                                                         <  2:45432/148‑1 (MQ=255)                                          tAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCaa                                                                                                 >  1:127402/1‑148 (MQ=255)                                                tCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGTTTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTa                                                                                           >  1:290390/1‑148 (MQ=255)                                                tCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTa                                                                                           <  2:42970/148‑1 (MQ=255)                                                tCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTa                                                                                           <  2:42949/148‑1 (MQ=255)                                                tCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTa                                                                                           >  2:179083/1‑148 (MQ=255)                                                tCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTa                                                                                           <  2:174315/148‑1 (MQ=255)                                                           cTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGt                                                                                >  1:86254/1‑148 (MQ=255)                                                           cTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGt                                                                                >  1:86769/1‑148 (MQ=255)                                                                   ataataTTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTc                                                                        >  1:376804/1‑148 (MQ=255)                                                                   ataataTTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTc                                                                        >  1:89970/1‑148 (MQ=255)                                                                               aTCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGt                                                            >  1:271497/1‑148 (MQ=255)                                                                                        aaGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCAt                                                   <  2:334340/148‑1 (MQ=255)                                                                                           cAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGa                                                >  2:265258/1‑148 (MQ=255)                                                                                            aaaTGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGAt                                               >  2:120606/1‑148 (MQ=255)                                                                                                             ttAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAAc                              <  2:65524/148‑1 (MQ=255)                                                                                                                atatatACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACAtt                           <  1:230762/148‑1 (MQ=255)                                                                                                                       cATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATAct                    >  1:150309/1‑148 (MQ=255)                                                                                                                                aattGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAAt           >  2:18699/1‑148 (MQ=255)                                                                                                                                  ttGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATcc         <  2:310058/148‑1 (MQ=255)                                                                                                                                        ggATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATCCGCAAGa   >  1:31138/1‑148 (MQ=255)                                                                                                                                         gATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATCCGCAAGAc  >  1:190700/1‑148 (MQ=255)                                                                                                                                         gATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATCCGCAAGAc  >  1:107491/1‑148 (MQ=255)                                                                                                                                                |                                                                                                                                             ATATCATCATTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACTACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATCCGCAAGAC  >  USA300TCH1516_ALE/2035743‑2036026

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑