Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,668,658	(T)8→7	intergenic (‑467/‑84)	USA300HOU_RS13735 ← / → USA300TCH1516_02539	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,668,651	0	T	.	100.0%	74.5 / NA	16	intergenic (‑460/‑91)	USA300HOU_RS13735/USA300TCH1516_02539	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (10/6);  total (10/6)

TGTTTTTGTGCTGTGTTTATAAAACCGCACACTATATTCAAAAATAACTTATTACACATATATTTGCAATAAGATAATTAAAGTAGGATATTATTTTTAGTTTTCTGATAGGAATGATGATAGTCTATAGGTTGAATCTTTACTTTTTTTTAAAGCTAAATTTACATCAACTTAACAATGGTTGGTTATACTGAAGATGAAAATATTTAGTATAACTTAGTGGAGGCGATAAAGGTGCAATTGAGTCATTCCGTTAAAGTTGCAATTTCTATCTATTTAG  >  USA300TCH1516_ALE/2668508‑2668787                                                                                                                                                |                                                                                                                                         tgtttttgtGCTGTGTTTATAAAACCGCACACTATATTCAAAAATAACTTATTACACATATATTTGCAATAAGATAATTAAAGTAGGATATTATTTTTAGTTTTCTGATAGGAATGATGATAGTCTATAGGTTGAATCTTTACttttttta                                                                                                                                   >  1:40218/1‑150 (MQ=255)       tgtgCTGTGTTTATAAAACCGCACACTATATTCAAAAATAACTTATTACACATATATTTGCAATAAGATAATTAAAGTAGGATATTATTTTTAGTTTTCTGATAGGAATGATGATAGTCTATAGGTTGAATCTTTAC‑TTTTTTTAAAGCTa                                                                                                                            <  1:39799/151‑1 (MQ=255)                   ataAAACCGCACACTATATTCAAAAATAACTTATTACACATATATTTGCAATAAGATAATTAAAGTAGGATATTATTTTTAGTTTTCTGATAGGAATGATGATAGTCTATAGGTTGAATCTTTAC‑TTTTTTTAAAGCTAAATTTACATCaa                                                                                                                >  2:1993/1‑151 (MQ=255)                   ataAAACCGCACACTATATTCAAAAATAACTTATTACACATATATTTGCAATAAGATAATTAAAGTAGGATATTATTTTTAGTTTTCTGATAGGAATGATGATAGTCTATAGGTTGAATCTTTAC‑TTTTTTTAAAGCTAAATTTACATCaa                                                                                                                >  2:233784/1‑151 (MQ=255)                   ataAAACCGCACACTATATTCAAAAATAACTTATTACACATATATTTGCAATAAGATAATTAAAGTAGGATATTATTTTTAGTTTTCTGATAGGAATGATGATAGTCTATAGGTTGAATCTTTAC‑TTTTTTTAAAGCTAAATTTACATCaa                                                                                                                >  2:300030/1‑151 (MQ=255)                      aaaCCGCACACTATATTCAAAAATAACTTATTACACATATATTTGCAATAAGATAATTAAAGTAGGATATTATTTTTAGTTTTCTAATATGAATGATGATAGTCTATAGGTTGAATCTTTAC‑TTTTTTTAAAGCTAAATTTACATCAACtt                                                                                                             <  1:168284/151‑1 (MQ=255)                                   tatTCAAAAATAACTTATTACACATATATTTGCAATAAGATAATTAAAGTAGGATATTATTTTTAGTTTTCTGATAGGAATGATGATAGTCTATAGGTTGAATCTTTAC‑TTTTTTTAAAGCTAAATTTACATCAACTTAACAAtgtttggt                                                                                                >  2:272565/1‑151 (MQ=255)                                                   attaCACATATATTTGCAATAAGATAATTAAAGTAGGATATTATTTTTAGTTTTCTGATAGGAATGATGATAGTCTATAGGTTGAATCTTTAC‑TTTTTTTAAAGCTAAATTTACATCAACTTAACAATGGTTGGTTATACTGAAGATGaaa                                                                                >  1:31445/1‑151 (MQ=255)                                                         caTATATTTGCAATAAGATAATTAAAGTAGGATATTATTTTTAGTTTTCTGATAGGAATGATGATAGTCTATAGGTTGAATCTTTAC‑TTTTTTTAAAGCTAAATTTACATCAACTTAACAATGGTTGGTTATACTGAAGATGAAAATAttt                                                                          >  2:86626/1‑151 (MQ=255)                                                                               tAAAGTAGGATATTATTTTTAGTTTTCTGATAGGAATGATGATAGTCTATAGGTTGAATCTTTAC‑TTTTTTTAAAGCTAAATTTACATCAACTTAACAATGGTTGGTTATACTGAAGATGAAAATATTTAGTATAACTTAGTGGAGGCGAt                                                    <  2:286604/151‑1 (MQ=255)                                                                                       natatTATTTTTAGTTTTCTGATAGGAATGATGATAGTCTATAGGTTGAATCTTTAC‑TTTTTTTAAAGCTAAATTTACATCAACTTAACAATGGTTGGTTATACTGAAGATGAAAATATTTAGTATAACTTAGTGGAGGCGATAAAGGTGc                                            >  2:53585/2‑151 (MQ=255)                                                                                                tttAGTTTTCTGATAGGAATGATGATAGTCTATAGGTTGAATCTTTAC‑TTTTTTTAAAGCTAAATTTACATCAACTTAACAATGGTTGGTTATACTGAAGATGAAAATATTTAGTATAACTTAGTGGAGGCGATAAAGGTGCAATTGAGTc                                   >  1:173806/1‑151 (MQ=255)                                                                                                            aTAGGAATGATGATAGTCTATAGGTTGAATCTTTAC‑TTTTTTTAAAGCTAAATTTACATCAACTTAACAATGGTTGGTTATACTGAAGATGAAAATATTTAGTATAACTTAGTGGAGGCGATAAAGGTGCAATTGAGTCATTCCGTTAAAg                       <  2:150486/151‑1 (MQ=255)                                                                                                            aTAGGAATGATGATAGTCTATAGGTTGAATCTTTAC‑TTTTTTTAAAGCTAAATTTACATCAACTTAACAATGGTTGGTTATACTGAAGATGAAAATATTTAGTATAACTTAGTGGAGGCGATAAAGGTGCAATTGAGTCATTCCGTTAAAg                       >  2:93663/1‑151 (MQ=255)                                                                                                             tAGGAATGATGATAGTCTATAGGTTGAATCTTTAC‑TTTTTTTAAAGCTAAATTTACATCAACTTAACAATGGTTGGTTATACTGAAGATGAAAATATTTAGTATAACTTAGTGGAGGCGATAAAGGTGCAATTGAGTCATTCCGTTAAAGt                      <  2:40218/151‑1 (MQ=255)                                                                                                                           gTCTATAGGTTGAATCTTTAC‑TTTTTTTAAAGCTAAATTTACATCAACTTAACAATGGTTGGTTATACTGAAGATGAAAATATTTAGTATAACTTAGTGGAGGCGATAAAGGTGCAATTGAGTCATTCCGTTAAAGTTGCAATTtctatct        <  1:258894/151‑1 (MQ=255)                                                                                                                                 aGGTTGAATCTTTAC‑TTTTTTTAAAGCTAAATTTACATCAACTTAACAATGGTTGGTTATACTGAAGATGAAAATATTTAGTATAACTTAGTGGAGGCGATAAAGGTGCAATTGAGTCATTCCGTTAAAGTTGCAATTTCTATCTATTTAg  >  2:256669/1‑151 (MQ=255)                                                                                                                                                |                                                                                                                                         TGTTTTTGTGCTGTGTTTATAAAACCGCACACTATATTCAAAAATAACTTATTACACATATATTTGCAATAAGATAATTAAAGTAGGATATTATTTTTAGTTTTCTGATAGGAATGATGATAGTCTATAGGTTGAATCTTTACTTTTTTTTAAAGCTAAATTTACATCAACTTAACAATGGTTGGTTATACTGAAGATGAAAATATTTAGTATAACTTAGTGGAGGCGATAAAGGTGCAATTGAGTCATTCCGTTAAAGTTGCAATTTCTATCTATTTAG  >  USA300TCH1516_ALE/2668508‑2668787

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