Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	1,087,670	A→T	L5I (TTA→ATA)	USA300HOU_1021 ←	hypothetical membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,087,670	0	A	T	100.0%	141.6 / NA	39	L5I (TTA→ATA)	USA300HOU_1021	hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (11/28);  total (11/28)

CCAAACCCCGTTTGTTAATTGTTCGAGGTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTAAACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGTATAGTAACACTTTCCTACGCTAGTTCAAGCTAGATCA  >  CP000730/1087536‑1087801                                                                                                                                       |                                                                                                                                    ccAAACCCCGTTTGTTAATTGTTCGAGGTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACAtt                                                                                                                        <  2:342574/148‑1 (MQ=255)  cAAACCCCGTTTGTTAATTGTTCGAGGTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACAttt                                                                                                                       <  2:56973/148‑1 (MQ=255)  cAAACCCCGTTTGTTAATTGTTCGAGGTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACAttt                                                                                                                       <  2:55552/148‑1 (MQ=255)  cAAACCCCGTTTGTTAATTGTTCGAGGTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACAttt                                                                                                                       <  2:4808/148‑1 (MQ=255)    aaCCCCGTTTGTTAATTGTTCGAGGTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACAttttt                                                                                                                     <  1:183647/148‑1 (MQ=255)    aaCCCCGTTTGTTAATTGTTCGAGGTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACAttttt                                                                                                                     <  1:184384/148‑1 (MQ=255)    aaCCCCGTTTGTTAATTGTTCGAGGTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACAttttt                                                                                                                     <  1:109611/148‑1 (MQ=255)            ttGTTAATTGTTCGAGGTGAAGGTCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACAtcctc                                                                                                             <  2:118035/148‑1 (MQ=255)            ttGTTAATTGTTCGAGGTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACAtcctc                                                                                                             >  2:29260/1‑148 (MQ=255)            ttGTTAATTGTTCGAGGTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACAtcctc                                                                                                             >  2:209532/1‑148 (MQ=255)                  aTTGTTCGAGGTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATGAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTANCNCAGATANCTTTATACCTTTTGACATTTTTACATCCTCCtaata                                                                                                       <  1:41030/148‑1 (MQ=255)                  aTTGTTCGAGGTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCtaata                                                                                                       <  1:343173/148‑1 (MQ=255)                       tCGAGGTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATaaaaaa                                                                                                  <  1:308862/148‑1 (MQ=255)                           ggTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAACAACGc                                                                                              >  1:181000/1‑148 (MQ=255)                           ggTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGc                                                                                              <  2:88218/148‑1 (MQ=255)                           ggTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGc                                                                                              >  1:224247/1‑148 (MQ=255)                            gTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGca                                                                                             <  1:263936/148‑1 (MQ=255)                                      gTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAAccatcca                                                                                   <  1:29985/148‑1 (MQ=255)                                           ttGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATACATAGGa                                                                              >  1:162160/1‑148 (MQ=255)                                                  ccATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTAt                                                                       <  1:266578/148‑1 (MQ=255)                                                      tGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGt                                                                   <  1:278549/148‑1 (MQ=255)                                                      tGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGt                                                                   <  1:351049/148‑1 (MQ=255)                                                         aaacaaacCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTca                                                                <  1:113771/148‑1 (MQ=255)                                                         aaacaaacCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTca                                                                <  1:220334/148‑1 (MQ=255)                                                             aaacCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAat                                                            <  2:229984/148‑1 (MQ=255)                                                                        aaTTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTa                                                 <  1:35637/148‑1 (MQ=255)                                                                        aaTTGTAAAAAGCCGCGATTACGACTGAAATAAGTACGGTGATTAGTATTTCAGATAGCTTTATACCTTTAGACATTTTTACATCTTCCTAATATTAAAACGCACAACCAGCCATAGGAAAGTTATGCGTTCAGAATCTATATGAGTa                                                 <  2:51492/148‑1 (MQ=255)                                                                                aTAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACatat                                         >  1:68686/1‑148 (MQ=255)                                                                                    cTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTGTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGtat                                     <  2:45533/148‑1 (MQ=255)                                                                                     tGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGtata                                    <  1:218952/148‑1 (MQ=255)                                                                                     tGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGtata                                    >  2:84007/1‑148 (MQ=255)                                                                                      gCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGTATAg                                   <  1:325391/148‑1 (MQ=255)                                                                                                             ggTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGTATAGTAACACTTTCCTACGCTAGTTCa            <  2:224247/148‑1 (MQ=255)                                                                                                             ggTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGTATAGTAACACTTTCCTACGCTAGTTCa            <  2:181000/148‑1 (MQ=255)                                                                                                                    aGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGTATAGTAACACTTTCCTACGCTAGTTCAAGCTAGa     <  1:210637/148‑1 (MQ=255)                                                                                                                     gTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGTATAGTAACACTTTCCTACGCTAGTTCAAGCTAGAt    >  2:320735/1‑148 (MQ=255)                                                                                                                       aTTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGTATAGTAACACTTTCCTACGCTAGTTCAAGCTAGATCa  >  2:52721/1‑148 (MQ=255)                                                                                                                       aTTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGTATAGTAACACTTTCCTACGCTAGTTCAAGCTAGATCa  >  2:298326/1‑148 (MQ=255)                                                                                                                       aTTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGTATAGTAACACTTTCCTACGCTAGTTCAAGCTAGATCa  >  2:109113/1‑148 (MQ=255)                                                                                                                                       |                                                                                                                                    CCAAACCCCGTTTGTTAATTGTTCGAGGTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTAAACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGTATAGTAACACTTTCCTACGCTAGTTCAAGCTAGATCA  >  CP000730/1087536‑1087801

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑