Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,102,618	T→C	intergenic (‑78/+238)	USA300HOU_RS10625 ← / ← USA300HOU_RS10630	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,102,618	0	T	C	100.0%	98.8 / NA	31	intergenic (‑78/+238)	USA300HOU_RS10625/USA300HOU_RS10630	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (14/17);  total (14/17)

ATTTGCTTTTGGATCTTCTACTAATTGAATAATGTTACGTTTTAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGTCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTC  >  USA300TCH1516_ALE/2102487‑2102754                                                                                                                                     |                                                                                                                                         aTTTGCTTTTGGATCTTCTACTAATTGAATAATGTTACGTCTTCTTTCCTCCCTTTTATCAAGCACTCCTTATTTTCAAATAAAATAGAGTGGTTGCCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCatat                                                                                                                                 >  2:201648/1‑141 (MQ=255)       ttttGGATCTTCTACTAATTGAATAATGTTACGTTTTAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCaa                                                                                                                           <  2:1401/141‑1 (MQ=255)                ttctACTAATTGAATAATGTTACGTTTTAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCtt                                                                                                                  <  1:66232/141‑1 (MQ=255)                       aaTTGAATAATGTTACGTTTTAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TCTGCTTCTACTTTGATTGTTATTGTGCCACTCATATTACCAACATATGCTTTAAACGt                                                                                                           >  1:53511/1‑141 (MQ=255)                         ttGAATAATGTTACGTTTTAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATTCTTTAACCGTgg                                                                                                         >  2:119023/1‑141 (MQ=255)                                  gTTACGTTTTAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCtt                                                                                                <  1:91837/141‑1 (MQ=255)                                      cGTTTTAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCCCCATATCCTATACACGTGGCAATACCTTGTGc                                                                                            <  1:282173/141‑1 (MQ=255)                                        ttttAATTTTGCTATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCtt                                                                                          <  2:152215/141‑1 (MQ=255)                                          ttAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATGGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCTACATCTGCTTTAACCGTGGCACTACCTTGTGCttgc                                                                                        >  1:221595/1‑139 (MQ=255)                                           tAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGATGAAACGATA‑GATACTTCTACATTTATTTTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGAAATAACTTGGGTTTCCg                                                                                       >  1:179079/1‑141 (MQ=255)                                            aaTTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGc                                                                                      >  1:10399/1‑141 (MQ=255)                                             aTTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCa                                                                                     >  1:183847/1‑141 (MQ=255)                                                      ttttATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCCTATTACAAACACATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGa                                                                            <  1:268989/141‑1 (MQ=255)                                                           taataCTCTCCTTATTTTCAAACAAAATAACGCGGGTGTGCCAGCTCGATAC‑GCATGAGTTATTGTTATAGTGCCATCCTCATTTCTAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATc                                                                       <  1:277994/141‑1 (MQ=255)                                                             ataCTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTACGCAGTGACTTGACCATCAc                                                                     >  1:254304/1‑141 (MQ=255)                                                                          tttCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGCCTTGACCATCACTATTGATTGATAc                                                        >  1:19390/1‑141 (MQ=255)                                                                            tCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACaa                                                      >  1:95652/1‑141 (MQ=255)                                                                               aataaaataGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAatat                                                   <  1:103965/141‑1 (MQ=255)                                                                                       agagGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGa                                           <  1:234244/141‑1 (MQ=255)                                                                                       agagGGGTTGTCCCCTAT‑TATGCTGCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGa                                           <  1:176245/141‑1 (MQ=255)                                                                                        gagGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGAt                                          >  2:89048/1‑141 (MQ=255)                                                                                         agGGGTTGTCCCCTCT‑TATGCTTCTAAAGTTATTGTTATAGTGCCACTCATATTACCAACGTATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATc                                         <  2:211129/141‑1 (MQ=255)                                                                                             gTTGGCCCCTCT‑TATGCTTCTACATGTATTGTTATAGTGCCACTCAGATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCGTCCGCAGTGACTTGAACATCACTATTGATTGATACAATATTCGTTTGATCtgtt                                     <  1:268580/141‑1 (MQ=255)                                                                                                 tCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTgtgt                                 >  1:7587/1‑141 (MQ=255)                                                                                                 tCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTgtgt                                 >  2:263317/1‑141 (MQ=255)                                                                                                 tCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTgtgt                                 >  1:139761/1‑141 (MQ=255)                                                                                                        t‑tATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCaa                          <  2:159218/141‑1 (MQ=255)                                                                                                             gCTTCTACATTTATTGTTATAGGGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAac                      <  1:30600/141‑1 (MQ=255)                                                                                                              cTTGTACATTTATTGTTATATTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAact                     <  2:268137/141‑1 (MQ=255)                                                                                                                      tttATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGa             <  1:93716/141‑1 (MQ=255)                                                                                                                                 aGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGctc  <  1:263317/141‑1 (MQ=255)                                                                                                                                     |                                                                                                                                         ATTTGCTTTTGGATCTTCTACTAATTGAATAATGTTACGTTTTAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGTCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTC  >  USA300TCH1516_ALE/2102487‑2102754

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑