Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,996,168	A→G	noncoding (47/75 nt)	USA300TCH1516_01859 ←	tRNA‑Gly

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,996,168	0	A	G	100.0%	49.7 / NA	19	noncoding (47/75 nt)	USA300TCH1516_01859	tRNA‑Gly
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (6/13);  total (6/13)

CGCAAATATTAAATTATGGAGCGGAAGATAGGATTTACACCTATACCTCATTCCAGGAAGGAATGTATTCTAAGAGTTGAAATACTCCCGCATTATTATTAAATTATGGAGCGGAAGATAGGATTTGCACCTATACCTCGTTCCGGGAAGGAACGTGTTCTAAAAGTTGAACTACTCCCGCATAAACCTGGAGGCGGCAACCGGATTTGAACCGGTGATAAAGGTTTTGCAGACCTCTGCCTTACCACTTGGCTATGCCGCC  >  USA300TCH1516_ALE/1996034‑1996295                                                                                                                                       |                                                                                                                                cGCAAATATTAAATTATGGAGCGGAAGATAGGATTTACACCTATACCTCATTCCAGGAAGGAATGTATTCTAAGAGTTGAAATACTCCCGCATTATTATTAAATTATGGAGCGGAAGATAGGATTTGCACCTATGCCTCGt                                                                                                                           >  1:164787/1‑141 (MQ=255) cGCAAATATTAAATTATGGAGCGGAAGATAGGATTTACACCTATACCTCATTCCAGGAAGGAATGTATTCTAAGAGTTGAAATACTCCCGCATTATTATTAAATTATGGAGCGGAAGATAGGATTTGCACCTATGCCTCGt                                                                                                                           >  1:187968/1‑141 (MQ=255) cGCAAATATTAAATTATGGAGCGGAAGATAGGATTTACACCTATACCTCATTCCAGGAACGAATGTATTCTAAGAGTTGAAATACTCCCGCATTATTATTAAATTATGGAGCGGAAGATAGGATTTGCACCTATGCCTCGt                                                                                                                           <  1:78095/141‑1 (MQ=255)  gCAAATATTAAATTATGGAGCGGAAGATAGGATTTACACCTATACCTCATTCCAGGAAGGAATGTATTCTAAGAGTTGAAATACTCCCGCATTATTATTAAATTATGGAGCGGAAGATAGGATTTGCACCTATGCCTCGtt                                                                                                                          >  1:97552/1‑141 (MQ=255)                aTGGAGCGTAAGATAGGAGTTACACCTATACCTCATTCCAGGAAGGAAAGTATTTTAAGGGTTGAAATACTCCCGCATTATTAGTAAATTATGGAGCGGAAGATAGGATTTGCACCTATGCCTCGTTCCGGGAAGGAACgt                                                                                                            <  2:85065/141‑1 (MQ=18)                                    tACACCTATACCTCATTCCAGGAAGGAATGTATTCTAAGAGTTGAAATACTCCCGCATTATTCTTCAATTATGAACACGGCGAGAGAATTTGCACCTATGCCTCGTTCCGGCGACGAACGTGTTCTCAAAGTTGAaccact                                                                                        >  2:273829/1‑141 (MQ=255)                                      cacCTATACCCCATTGCAGAAAGGCATGTATTATAAGAGGTGAAATACACCCGCATTATTATTAAATTATGGAGCGGAAGATAGGATTTGCACCTATGCCTCGTTCCGGGAAGGAACGTGTTCTAAAAGTTGAACTACTcc                                                                                      <  2:79790/141‑1 (MQ=21)                                        ccTATACCTCATTCCAGGAAGGAATGTATTCTAAGAGTTGAAATACTCCCGCATTATTATTAAATTATGGAGCGGAAGATAGGATTTGCACCTATGCCTCGTTCCGGGAAGGAACGTGTTCTAAAAGTTGAACTACTCCCg                                                                                    <  1:170837/141‑1 (MQ=255)                                                       aggaaggaATGTATTCTAAGAGTTGAAATACTCCCGCATTATTCTTAAATTATGGAGCGGACGATAGGATTTGCACCTATGCCTCGTTCCGGGAAGGAACGTGTTCTAAACGATCAACTACTGCCGCATCAACCTGCAgac                                                                     >  2:193645/1‑139 (MQ=21)                                                             aaaTGTATTCTAAGAGTTGAAATACTCCCGCATTATTATTAAATTATGGAGCGGAAGATAGGATTTGCACCTATGCCTCGTTCCGGGAAGGAACGTGTTCTAAAAGTTGAACTACTCCCGCATAAACCTGGAGGCGGCAAc                                                               <  1:140514/140‑1 (MQ=255)                                                                               gAAATACTCCCGCATTATTATTAAATTATGGAGCGGAAGATAGGATTTGCACCTATGCCTCGTTCCGGGAAGGAACGTGTTCTAAAAGTTGAACTACTCCCGCATAAACCTGGAGGCGGCAACCGGATTTGAACCGGTGAt                                             <  1:156958/141‑1 (MQ=255)                                                                                aaaTACTCCCGCATTATGATTAAATTATGGAGCGGAAGATAGGATTTGCACCTATGCCTCGTTCCGGGAAGGAACGTGTTCTAAAAGTTGAACTACTCCCGCATAAACCTGGAGGCGGCAACCGGATTTGAACCGGTGATa                                            <  1:86097/141‑1 (MQ=255)                                                                                        ccGCATTATTATTAAATTATGGAGCGGAAGATAGGATTTGCACCTATGCCTCGTTCCGGGAAGGAACGTGTTCTAAAAGTTGAACTACTCCCGCATAAACCTGGAGGCGGCAACCGGATTTGAACCGGTGATAAAGGtttt                                    <  2:279204/141‑1 (MQ=255)                                                                                                   ttaAATTATGGAGCGGAAGATAGGATTTGCACCTATGCCTCGTTCCGGGAAGGAACGTGTTCTAAAAGTTGAACTACTCCCGCATAAACCTGGAGGCGGCAACCGGATTTGAACCGGTGATAAAGGTTTTGCAGACCTCTg                         <  2:8985/141‑1 (MQ=255)                                                                                                            ggAGGGGAAGATAGGATTTGCACCTATGCCTCGTTCCGGGAAGGAACGTGTTCTAAAAGTTGAACTACTCCCGCATAAACCTGGAGGCGGCAACCGGATTTGAACCGGTGATAAAGGTTTTGCAGACCTCTGCCTTACCAc                <  2:97552/141‑1 (MQ=255)                                                                                                                     gATAGGATTTGCACCTATGCCTCGTTCCGCGAAGGAACGTGTTCTAAAAGTTGAACTACCCCCGCCTAAACCTGTAGCCCGCAACCGGATTTCAACCCCTCATAAACCTTTTACATACCTCTGCCCTCCCCCttccctaca       >  2:33759/1‑134 (MQ=12)                                                                                                                       tAGGATTTGCACCTATGCCTCGTTCCGGGAAGGAACGTGTTCTAAAAGTTGAACTACTCCCGCATAAACCTGGAGGCGGCAACCGGATTTGAACCGGTGATAAAGGTTTTGCAGACCTCTGCCTTACCACTTGGCTATgcc     <  1:215311/141‑1 (MQ=255)                                                                                                                          gATTTGCACCTATGCCTCGTTCCGGGAAGTAACGTGTTCTAAAAGTTGAACTACTCCCGCATAAACCTGGAGGCGGCAACCGGATTTGAACCGGTGATAAAGGTTTTGCGGACCTCTGCCTTACCACTTGGCTATgccgcc  <  2:12478/141‑1 (MQ=255)                                                                                                                          gATTTGCACCTATGCCTCGTTCCGGGAAGGAACGTGTTCTAAAAGTTGAACTACTCCCGCATAAACCTGGAGGCGGCAACCGGATTTGAACCGGTGATAAAGGTTTTGCAGACCTCTGCCTTACCACTTGGCTATgccgcc  <  1:273829/141‑1 (MQ=255)                                                                                                                                       |                                                                                                                                CGCAAATATTAAATTATGGAGCGGAAGATAGGATTTACACCTATACCTCATTCCAGGAAGGAATGTATTCTAAGAGTTGAAATACTCCCGCATTATTATTAAATTATGGAGCGGAAGATAGGATTTGCACCTATACCTCGTTCCGGGAAGGAACGTGTTCTAAAAGTTGAACTACTCCCGCATAAACCTGGAGGCGGCAACCGGATTTGAACCGGTGATAAAGGTTTTGCAGACCTCTGCCTTACCACTTGGCTATGCCGCC  >  USA300TCH1516_ALE/1996034‑1996295

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑