Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006584	1,588,241	A→C	E403D (GAA→GAC)	LY180_07560 →	type IV secretion protein Rhs

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006584	1,588,241	0	A	C	100.0%	52.9 / NA	19	E403D (GAA→GAC)	LY180_07560	type IV secretion protein Rhs
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (10/9);  total (10/9)

CGCAGGCGAACCTGAACCGGGAATGGCAGGTGGTGGCGAGCGATCTTCACGGCGAACAGCCGCAGGCGGTACCGGGACGCAGGGGTTCAGGCACCACGCTGGATAACCATTTTGCGGTAATACCGGCAGACAGAACATGGCGACCACAGCCGTTGCTGAAACCGCTGGTGGACGGCCCGCAGAGCGCCGTCGTGACGGGACCGGCAGGCGAGGAAATCTTCTGTGATGAACATGGCCGCGTGCGGGTGAAATTTAACTGGGACCGCTATAACCCGTCAAACCAGGAAAGTTCATGCTGGATCCGTGTGGCACAGGCGTGGGCAGGCACCGGCTTTGGCAACCTGGCGATACCGCGAGTGGGTCAGGAGGTGATTGTGGACTTCCTCAACGGCGACCCGGACCAGCCGATTATTATGGGGCGTACCTACCACCATGAAAACCGC‑ACACCCGGCAGCCTGCCGGGGACGAAGACGCAGATGACGATCCGCTCGAAAACCTATAAGGGCAGCGGGTTTAATGAACTGAAGTTTGACGATGCGACAGGGAAAGAACAGGTCTACATCCACGCGCAGAAGAACA  >  CP006584/1587955‑1588533                                                                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                                                                      cGCAGGCGAACCTGAACCGGGAATGGCAGGTGGTGGCGAGCGATCTTCACGGCGAACAGCCGCAGGCGGTACCGGGACGCAGGGGTTCAGGCACCACGCTGGATAACCATTTTGCGGTAATACCGGCAGACAGAACATGGCGACCACAGCCGTTGCTGAAACCGCTGGTGGACGGCCCGCAGAGCGCCGTCGTGACGGGACCGGCAGGCGAGGAAATCTTCTGTGATGAACATGGCCGCGTGCGGGTGAAATTTAACTGGGACCGCTATAACCCGTCAAACCAGGACAGTTCATGCTg                                                                                                                                                                                                                                                                                            <  1:31884/298‑1 (MQ=25)    aGGCGAACCTGAACCGGGAATGGCAGGTGGTGGCGAGCGATCTTCACGGCGAACAGCCGCAGGCGGTACCGGGACGCAGGGGTTCAGGCACCACGCTGGATAACCATTTTGCGGTAATACCGGCAGACAGAACATGGCGACCACAGCCGTTGCTGAAACCGCTGGTGGACGGCCCGCAGAGCGCCGTCGTGACGGGACCGGCAGGCGAGGAAATCTTCTGTGATGAACATGGCCGCGGGCGGGTGAAATTTAACTGGGACCGCTATAACCCGTCAAACCAGGACAGTTCATGCTGGAt                                                                                                                                                                                                                                                                                         >  1:7917/1‑298 (MQ=25)    aGGCGAACCTGAACCGGGAATGGCAGGTGGTGGCGAGCGATCTGCACGGCGAACAGCCGCAGGCGGTACCGGGACGCAGGGGTTCAGGCACCACGCTGGATAACCATTTTGCGGTAATACCGGCAGACAGAACATGGCGACCACAGCCGTTGCTGAAACCGCTGGTGGACGGCCCGCAGAGCGCCGTCGTGACGGGACCGGCAGGCGAGGAAATCTTCTGTGATGAACATGGCCGCGTGCGGGTGAAATTTAACTGGGACCGCTATAACCCGTCAAACCAGGACAGTTCATGCTGGAt                                                                                                                                                                                                                                                                                         <  1:273970/298‑1 (MQ=25)          aCCTGAACCGGGAATGGCAGGTGGTGGCGAGCGATCTTCACGGCGAACAGCCGCAGGCGGTACCGGGACGCAGGGGTTCAGGCACCACGCTGGATAACCATTTTGCGGTAATACCGGCAGACAGAACATGGCGACCACAGCCGTTGCTGAAACCGCTGGTGGACGGCCCGCAGAGCGCCGTCGTGACGGGACCGGCAGGCGAGGAAATCTTCTGTGATGAACATGGCCGCGTGCGGGTGAAATTTAACTGGGACCGCTATAACCCGTCAAACCAGGACAGTTCATGCTGGATCCgtgt                                                                                                                                                                                                                                                                                   <  1:169096/298‑1 (MQ=25)                                            tCTTCACGGCGAACAGCCGCAGGCGGTACCGGGACGCAGGGGTTCAGGCACCACGCTGGATAACCATTTTGCGGTAATACCGGCAGACAGAACATGGCGACCACAGCCGTTGCTGAAACCGCTGGTGGACGGCCCGCAGAGCGCCGTCGTGACGGGACCGGCAGGCGAGGAAATCTTCTGTGATGAACATGGCCGCGTGCGGGTGAAATTTAACTGGGACCGCTATAACCCGTCAAACCAGGACAGTTCATGCTGGATCCGTGTGGCACAGGCGTGGGCAGGCACCGGCTTTGGCAAc                                                                                                                                                                                                                                                 >  1:11430/1‑298 (MQ=37)                                                           gCCGCAGGCGGTACCGGGACGCAGGGGTTCAGGCACCACGCTGGATAACCATTTTGCGGTAATACCGGCAGACAGAACATGGCGACCACAGCCGTTGCTGAAACCGCTGGTGGACGGCCCGCAGAGCGCCGTCGTGACGGGACCGGCAGGCGAGGAAATCTTCTGTGATGAACATGGCCGCGTGCGGGTGAAATTTAACTGGGACCGCTATAACCCGTCAAACCAGGACAGTTCATGCTGGATCCGTGTGGCACAGGCGTGGGCAGGCACCGGCTTTGGCCACCTGGCGATACcgcgc                                                                                                                                                                                                                                  >  1:58414/1‑297 (MQ=37)                                                                                         aGGCACCACGCTGGATAACCATTTTGCGGTAATACCGGCAGCCAGAACATGGCGACCACAGCCGTTGCTGAAACCCCTGGTGGACGGCCCGCCGAGCGCCGTCGTGACGGACCCGGCAGGCGCGGAAATCTACTGTGACGAACCTGCCCGCGTGCGGGCGAAATTTAACTGGTCCCGCCATCAACCGTCAAACCAGGCCGCCTCATGCGGGATCCGCGCGGCCCAGGAGTGCGCCGCCCCCCGCGTTGGCAACATGGCTATACCCCGACGGGTGCAGGAGGTGagcgcggtcgtaccc                                                                                                                                                                                                    >  2:103475/1‑284 (MQ=255)                                                                                            caccaaGCTGGATAACCATGTTGCTGTAATACCGGCAGACAGAACATGGCGACCACCGCCGTTGCGGAAGCCGCTGGTGGACGGCCCGCAGAGCGCCGTCGTGACGGGACCGGCAGGCGAGGAAATCTTCTGTGATGATCATGGCCGCGTGCGGGTGAAATTTAACTGGGAACGCTATAACCCGTCAAACCAGGACAGTTCATGCTGGATCCGTGTGGGACAGGCGTGGGCAGGCACCGGCTTTGGCAACCTGGCGATACCGCGAGTGGGTCAGGAGGTGATTGTGGACTTCCTCAAc                                                                                                                                                                                                 <  1:85282/298‑1 (MQ=14)                                                                                                                                       aCATGGCGACCACAGCCGTCGCTGTAACCGCGGGTGGACGGTCCGCAGAGCGCCGTCGTGACGGGACCGGCAGGCGAGGAAATCTTCTGTGATGAACATGGCCGCGTGCGGGTGAAATTTAACTGGGACCGCTATAACTCGTCAAACCAGGACAGTTCATGCTGGATCCGTGTGGCACAGGCGTGGGCAGGCACCGGCTTTGGCAACCTGGCGATACCGCGAGTGGGTCAGGAGGTGATTGTGGACTTCCTCAACGGCGACCCGGACAAGCCGATTATTATGGGGCGTACCTaccacc                                                                                                                                                      <  1:298806/298‑1 (MQ=255)                                                                                                                                                                    gCTGGTGGACGGCCCGCAGAGCGCCGTCGTGACGGGACCGGCAGGCGAGGAAATCTTCTGTGATGAACCTGGCCGCGTGCGGGTGAAATTTAACTGGGACCGCTATAACCCGTCAAACCAGGACAGTTCATGCTGGATCCGGGTGGCACAGGCGTGGGCCGGCCACGGCTTTGGCAACCCGGCGACACCGCGAGTGGGTGAGGAGGCTATGGTGGACTTCCTAAACGGCGACCCGGACCAGCCGATGATTCTGGGGCGGAACTAACAACCTCAACACCCCAACACCCgcaccaccccg                                                                                                                         >  2:73855/1‑288 (MQ=11)                                                                                                                                                                                                         ccGGCAGGCGAGGAAATCTTCGGTGATGAACATGGCCGCGTGCGGGTGAAATTTAACTGGGACCGCTATACCCCGTCAAACCAGGACAGTTCATGCTGGTTCCGTGTGGCACAGGCGTGGGCAGGCACCGGCTTTGGCAACCTGGCGATACCGCGAGTGGGTCAGGAGGTGATTGGGGACTTCCTCAACGGCGACCCGAACCAGCCGATTATTATGGGGCGTACCTACCACCATGAAAACCGC‑ACACCCGGCAGCCTGCCGGGTACGAAGACGCAGATGACGATCCGCTCGAAAACCt                                                                                   <  1:124655/298‑1 (MQ=255)                                                                                                                                                                                                                        aTCTTCTGTGATGAACATGGCCGCGTGCGGGTGAAATTTAACTGGGACCGCTATAACCCGTCAAACCAGGACAGTTCATGCTGGATCCGTGTGGCACAGGCGTGGGCAGGCACCGGCTTTGGCAACCTGGCGATACCGCGAGTGGGTCAGGAGGTGATTGTGGACTTCCTCAACGGCGACCCGGACCAGCCGATTATTATGGGGCGTACCTACCACCATGAAAACCGC‑ACACCCGGCAGCCTGCCGGGGACGAAGACGCAGATGACGATCCGCTCGAAAACCTATAAGGGCAGCGGGt                                                                    <  1:73855/298‑1 (MQ=37)                                                                                                                                                                                                                        aTCTTCTGTGATGAACATGGCCGCGTGCGGGTGAAATTTAACTGGGACCGCTATAACCCGTCAAACCAGGACAGTTCATGCTGGATCCGTGTGGCACAGGCGTGGGCAGGCACCGGCTTTGGCAACCTGGCGATACCGCGAGTGGGTCAGGAGGTGATTGTGGACTTCCTCAACGGCGACCCGGACCAGCCGATTATTATGGGGCGTACCTACCACCATGAAAACCGC‑ACACCCGGCAGCCTGCCGGGGAAGAAGACGCAGATGACGATCCGCTCGAAAACCTATAAGGGCAGCGGGt                                                                    >  1:336168/1‑298 (MQ=37)                                                                                                                                                                                                                                tgatgaACATGGCCGCGTGCGGGTGAAATTTAACTGGGACCGCTATAACCCGTCAAACCAGGACAGTTCATGCTGGATCCGTGTGGCACAGGCGTGGGCAGGCACCGGCTTTGGCAACCTGGCGATACCGCGAGTGGGTCAGGAGGTGATTGTGGACTTCCTCAACGGCGACCCGGACCAGCCGATTATTATGGGGCGTACCTACCACCATGAAAACCGC‑ACACCCGGCAGCCTGCCGGGGACGAAGACGCAGATGACGATCCGCTCGAAAACCTATAAGGGCAGCGGGTTTAATGaa                                                            <  1:129245/298‑1 (MQ=37)                                                                                                                                                                                                                                     aaCATGGCCGCGAGCGGGTGAAATTTAAATGGGACCGCTATAACCCGTCAAACCAAGACAGTTCATGCTGGATCCGAGTGGCACAGGCGTGGGCAGGCACCGGCTTTGGCAACCTGGCGATACCGCGAGTGGGTCAGGAGGTGATTGTGGACTTCCTCAACGGAGACCCGGACCAGCCGATTATTATGGGGCGTACCTACCACCATGAAAACCGC‑ACACCCGGCAGCCTGCCGGGGACGAAGACGCAGATGACGATCCGCTCGAAAAACTATAAGGGCAGCGGGTGTAATGAACGGaa                                                       >  1:86324/1‑298 (MQ=255)                                                                                                                                                                                                                                        aTGGCCGCGTGCGGGTGAAATTTAACTGGGACCGCTCTAACCCGTCAACCCAGGACAGTTCATGCTGGATCCGTGTGGCACAGGCGTGGGCAGGCACCGGCTTTGGCAACCTGGCGATACCGCGAGTGGGTCAGGAGGTGATTGTGGACTTCCTCAACGGCGACCCGGACCAGCCGATTATTATGGGGCGTACCTACCACCATGAAAACCGC‑ACACCCGGCAGCCTGCCGGGGACGAAGACGCAGATGACGATCCGCTCGAAAACCTATAAGGGCAGCGGGTTTAATGAACTGAAGtt                                                    <  1:179504/298‑1 (MQ=37)                                                                                                                                                                                                                                             cgcgTGCGGGTGAAATTTAACTGGGACCGCTATAACCCGTCAAACCAGGACAGTTCATGCTGGATCCGTGTGGCACAGGCGTGGGCAGGCACCGGCTTTGGCAACCTGGCGATACCGCGAGTGGGTCAGGAGGTGATTGTGGACTTCCTCAACGGCGACCCGGACCAGCCGATTATTATGGGGCGTACCTACCACCATGAAAACCGC‑ACACCCGGCAGCCTGCCGGGGACGAAGACGCAGATGACGATCCGCTCGAAAACCTATAAGGGCAGCGGGTTTAATGAACTGAAGTTTGACg                                               >  1:217519/1‑298 (MQ=37)                                                                                                                                                                                                                                                                         gCTATAACCCGTCAAACCAGGACAGTTCATGCTGGATCCGTGTGGCACAGGCGTGGGCAGGCACCGGCTTTGGCAACCTGGCGATACCGCGAGTGGGTCAGGAGGTGATTGTGGACTTCCTCAACGGCGACCCGGACCAGCCGATTATTATGGGGCGTACCTACCACCATGAAAACCGC‑ACACCCGGCAGCCTGCCGGGGACGAAGACGCAGATGACGATCCGCTCGAAAACCTATAAGGGCAGCGGGTTTAATGAACTGAAGTTTGACGATGCGACAGGGAAAGAACAGGTCTACAt                   >  1:108555/1‑298 (MQ=37)                                                                                                                                                                                                                                                                                          cAGGACAGTTCATGCTGGATCCGTGTGGCACAGGCGTGGGCAGGCACCGGCTTTGGCAACCTGGCGATACCGCGAGTGGGTCAGGAGGTGATTGTGGACTTCCTCAACGGCGACCCGGACCAGCCGATTATTATGGGGCGTACCTACCACCATGAAAACCGC‑ACACCCGGCAGCCTGCCGGGGACGAAGACGCAGATGACGATCCGCTCGAAAACCTATAAGGGCAGCGGGTTTAATGAACTGAAGTTTGACGATGCGACAGGGAAAGAACAGGTCTACATCCACGCGCAGAAGAACa  >  1:332052/1‑298 (MQ=37)                                                                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                                                                      CGCAGGCGAACCTGAACCGGGAATGGCAGGTGGTGGCGAGCGATCTTCACGGCGAACAGCCGCAGGCGGTACCGGGACGCAGGGGTTCAGGCACCACGCTGGATAACCATTTTGCGGTAATACCGGCAGACAGAACATGGCGACCACAGCCGTTGCTGAAACCGCTGGTGGACGGCCCGCAGAGCGCCGTCGTGACGGGACCGGCAGGCGAGGAAATCTTCTGTGATGAACATGGCCGCGTGCGGGTGAAATTTAACTGGGACCGCTATAACCCGTCAAACCAGGAAAGTTCATGCTGGATCCGTGTGGCACAGGCGTGGGCAGGCACCGGCTTTGGCAACCTGGCGATACCGCGAGTGGGTCAGGAGGTGATTGTGGACTTCCTCAACGGCGACCCGGACCAGCCGATTATTATGGGGCGTACCTACCACCATGAAAACCGC‑ACACCCGGCAGCCTGCCGGGGACGAAGACGCAGATGACGATCCGCTCGAAAACCTATAAGGGCAGCGGGTTTAATGAACTGAAGTTTGACGATGCGACAGGGAAAGAACAGGTCTACATCCACGCGCAGAAGAACA  >  CP006584/1587955‑1588533

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑