Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,539,574	Δ1 bp	intergenic (‑111/‑403)	unknown ← / → unknown	Flp pilus assembly protein, pilin Flp/Phosphate starvation‑inducible protein PhoH, predicted ATPase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,539,573	0	T	.	100.0%	106.5 / NA	25	intergenic (‑110/‑404)	unknown/unknown	Flp pilus assembly protein, pilin Flp/Phosphate starvation‑inducible protein PhoH, predicted ATPase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (10/15);  total (10/15)

GAATACTGCAACGATTAACACGGCAACAGCAATAGCGATCAAACCATATTCAATTGCAGTCACACCTGCTTGATTTTCTCTGAAAGAACGGATTGCTTCAGCTGCTTTGATGTATGCTTTAGTAGTTAAAGTATTTAACATTGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTATTATAGTCCTGAAAAATTAAAATGCAAGTTTTTTTAGAATAATAAATTCACTATGTATATGTACGTATTGTGATTGCGAAAACTTTTTAATTAACAGTATGTTAAGGGTTATTGTAAATGAGCTATTTCTACTTTCTCTATTGATTTTACAGTAAATTTACAACTTTTAACTTTAATTACAAAAACACTTAAATATGTGTGGATTTAGAGATATCGCGATTTATTTCTTTTTTCTTTGTAGGAA  >  1/1539323‑1539816                                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                    gAATACTGCAACGATTAACACGGCAACAGCAATAGCGATCAAACCATATTCAATTGCAGTCACACCTGCTTGATTTTCTCTGAAAGAACGGATTGCTTCAGCTGCTTTGATGTATGCTTTAGTAGTTAAAGTATTTAACATTGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGtat                                                                                                                                                                                                                                                     >  1:28335/1‑251 (MQ=255)   aTACTGCAACGATTAACACGGCAACAGCAATAGCGATCAAACCATATTCAATTGCAGTCACACCTGCTTGATTTTCTCTGAAAGAACGGATTGCTTCAGCTGCTTTGATGTATGCTTTAGTAGTTAAAGTATTTAACATTGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGtatat                                                                                                                                                                                                                                                   <  1:884156/251‑3 (MQ=255)   aTACTGCAACGATTAACACGGCAACAGCAATAGCGATCAAACCATATTCAATTGCAGTCACACCTGCTTGATTTTCTCTGAAAGAACGGATTGCTTCAGCTGCTTTGATGTATGCTTTAGTAGTTAAAGTATTTAACATTGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGtatat                                                                                                                                                                                                                                                   <  1:706114/251‑3 (MQ=255)   aTACTGCAACGATTAACACGGCAACAGCAATAGCGATCAAACCATATTCAATTGCAGTCACACCTGCTTGATTTTCTCTGAAAGAACGGATTGCTTCAGCTGCTTTGATGTATGCTTTAGTAGTTAAAGTATTTAACATTGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGtatat                                                                                                                                                                                                                                                   <  1:627293/251‑3 (MQ=255)      cTGCAACGATTAACACGGCAACAGCAATAGCGATCAAACCATATTCAATTGCAGTCACACCTGCTTGATTTTCTCTGAAAGAACGGATTGCTTCAGCTGCTTTGATGTATGCTTTAGTAGTTAAAGTATTTAACATTGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGt                                                                                                                                                                                                                                               <  1:468214/251‑1 (MQ=255)             gATTAACACGGCAACAGCAATAGCGATCAAACCATATTCAATTGCAGTCACACCTGCTTGATTTTCTCTGAAAGAACGGATTGCTTCAGCTGCTTTGATGTATGCTTTAGTAGTTAAAGTATTTAACATTGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGTCCTGaaa                                                                                                                                                                                                                                        >  1:625438/1‑251 (MQ=255)                           cAGCAATAGCGATCAAACCATATTCAATTGCAGTCACACCTGCTTGATTTTCTCTGAAAGAACGGATTGCTTCAGCTGCTTTGATGTATGCTTTAGTAGTTAAAGTATTTAACATTGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGt                                                                                                                                                                                                                                               <  1:253314/230‑1 (MQ=255)                           cAGCAATAGCGATCAAACCATATTCAATTGCAGTCACACCTGCTTGATTTTCTCTGAAAGAACGGATTGCTTCAGCTGCTTTGATGTATGCTTTAGTAGTTAAAGTATTTAACATTGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGt                                                                                                                                                                                                                                               <  1:664083/230‑1 (MQ=255)                                      aTCAAACCATATTCAATTGCAGTCACACCTGCTTGATTTTCTCTGAAAGAACGGATTGCTTCAGCTGCTTTGATGTATGCTTTAGTAGTTAAAGTATTTAACATTGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGtatat                                                                                                                                                                                                                                                   >  1:318791/1‑214 (MQ=255)                                                         cAGTCACACCTGCTTGATTTTCTCTGAAAGAACGGATTGCTTCAGCTGCTTTGATGTATGCTTTAGTAGTTAAAGTATTTAACATTGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGt                                                                                                                                                                                                                                               <  1:17186/200‑1 (MQ=255)                                                            tCACACCTGCTTGATTTTCTCTGAAAGAACGGATTGCTTCAGCTGCTTTGATGTATGCTTTAGTAGTTAAAGTATTTAACATTGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGTCCTGAAAAATTAAAATGCAAGTTTTTTTAGAATAATAAATTCACtatgtatatg                                                                                                                                                                                         <  1:110562/251‑1 (MQ=255)                                                                                               gCTTCAGCTGCTTTGATGTATGCTTTAGTAGTTAAAGTATTTAACATTGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGTCCTGaaa                                                                                                                                                                                                                                        >  1:424453/1‑169 (MQ=255)                                                                                                        gctTTGATGTATGCTTTAGTAGTTAAAGTATTTAACATTGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGtatatag                                                                                                                                                                                                                                                 <  1:411900/152‑5 (MQ=255)                                                                                                                   tGCTTTAGTAGTTAAAGTATTTAACATTGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGTCCTGAAAAATTAAAATGCAAGTTTTTTTAGAATAATAAATTCACTATGTATATGTACGTATTGTGATTGCGAAAACTTTTTAATTAACAGTATGTTAAGGGTTATTGTa                                                                                                                                  <  1:484344/251‑1 (MQ=255)                                                                                                                                   gTATTTAACATTGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGTc                                                                                                                                                                                                                                              <  1:757877/127‑1 (MQ=255)                                                                                                                                   gTATTTAACATTGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGTCCTGAAAAATTAAAATGCAAGTTTTTTTAGAATAATAAATTCACtatgtatatgta                                                                                                                                                                                       <  1:382401/182‑1 (MQ=255)                                                                                                                                     aTTTAACATTGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGt                                                                                                                                                                                                                                               >  1:497720/1‑124 (MQ=255)                                                                                                                                             ttGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGTCCTGAAAAATTAAAATGCAAGTTTTTTTAGaat                                                                                                                                                                                                              >  1:568183/1‑149 (MQ=255)                                                                                                                                               gTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGTCCTGAAAAATTAAAATGCAAGTTTTTTTAGAATAATAAATTCACtatgtatatg                                                                                                                                                                                         <  1:566836/168‑1 (MQ=255)                                                                                                                                               gTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGTCCTGAAAAATTAAAATGCAAGTTTTTTTAGAATAATAAATTCACTATGTATATGTACGTATTGTGATTGCGAAAACTTTTTAATTAACAGTATGtt                                                                                                                                               <  1:199993/210‑1 (MQ=255)                                                                                                                                               gTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGTCCTGAAAAATTAAAATGCAAGTTTTTTTAGAATAATAAATTCACTATGTATATGTACGTATTGTGATTGCGAAAACTTTTTAATTAACAGTATGTTAAGGGTTATTGTAAATGAGCTATTTCTACTTTCTCTATTGa                                                                                                      >  1:225005/1‑251 (MQ=255)                                                                                                                                                 cTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGTCCTGAAAAATTAAAATGCAAGTTTTTTTAGAATAATAAATTCACTATGTATATGTACGTATTGTGATTGCGAAAACTTTTTAATTAACAGTATGTTAAggg                                                                                                                                          >  1:497732/1‑213 (MQ=255)                                                                                                                                                                                                gAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGt                                                                                                                                                                                                                                               <  1:408451/65‑1 (MQ=255)                                                                                                                                                                                                             gtgtCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGTCCTGAAAAATTAAAATGCAAGTTTTTTTAGAATAATAAATTCACtatgtatatg                                                                                                                                                                                         >  1:693226/1‑106 (MQ=255)                                                                                                                                                                                                             gtgtCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGTCCTGAAAAATTAAAATGCAAGTTTTTTTAGAATAATAAATTCACtatgtata                                                                                                                                                                                           <  1:666090/104‑1 (MQ=255)                                                                                                                                                                                                                       tttaATAAGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGTCCTGaaa                                                                                                                                                                                                                                        <  1:498269/49‑1 (MQ=255)                                                                                                                                                                                                                         taataaGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGt                                                                                                                                                                                                                                               >  1:3041/1‑40 (MQ=255)                                                                                                                                                                                                                         taataaGCTTGTGGAATTAAATAAACGACCGGTA‑TATAGTCCTGAAAAATTAAAATGCAAGTTTTTTTAGAATAATAAATTCACTATGTATATGTACGTATTGTGATTGCGAAAACTTTTTAATTAACAGTATGTTAAGGGTTATTGTAAATGAGCTATTTCTACTTTCTCTATTGATTTTACAGTAAATTTACAACTTTTAACTTTAATTACAAAAACACTTAAATATGTGTGGATTTAGAGATATcgcg                            >  1:354355/1‑251 (MQ=255)                                                                                                                                                                                                                                cTTGTGGAATTAAATAAACGACCGGTA‑TATAGTCCTGAAAAATTAAAATGCAAGTTTTTTTAGAATAATAAATTCACTATGTATATGTACGTATTGTGATTGCGAAAACTTTTTAATTAACAGTATGTTAAGGGTTATTg                                                                                                                                    >  1:151415/1‑140 (MQ=255)                                                                                                                                                                                                                                  tgtgGAATTAAATAAACGACCGGTA‑TATAGTCCTGAAAAATTAAAATGCAAGTTTTTTTAGAATAATAAATTCACtatgtatatg                                                                                                                                                                                         <  1:744965/85‑1 (MQ=255)                                                                                                                                                                                                                                                    aCCGGTA‑TATAGTCCTGAAAAATTAAAATGCAAGTTTTTTTAGAATAATAAATTCACTATGTATATGTACGTATTGTGATTGCGAAAACTTTTTAATTAACAGTATGTTAAGGGTTATTGTAAATGAGCTATTTCTACTTTCTCTATTGATTTTACAGTAAATTTACAACTTTTAACTTTAATTACAAAAACACTTAAATATGTGTGGATTTAGAGATATCGCGATTTATTTCTTTTTTCTTTGTAGGaa  <  1:232544/250‑1 (MQ=255)                                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                    GAATACTGCAACGATTAACACGGCAACAGCAATAGCGATCAAACCATATTCAATTGCAGTCACACCTGCTTGATTTTCTCTGAAAGAACGGATTGCTTCAGCTGCTTTGATGTATGCTTTAGTAGTTAAAGTATTTAACATTGTCTTAATGCTCCTTTGTTGTTTATAGAAAATAAAATTCAAGAATCCTTGAGTTTGAACTTAGTGTCATTTATTTAATAAGCTTGTGGAATTAAATAAACGACCGGTATTATAGTCCTGAAAAATTAAAATGCAAGTTTTTTTAGAATAATAAATTCACTATGTATATGTACGTATTGTGATTGCGAAAACTTTTTAATTAACAGTATGTTAAGGGTTATTGTAAATGAGCTATTTCTACTTTCTCTATTGATTTTACAGTAAATTTACAACTTTTAACTTTAATTACAAAAACACTTAAATATGTGTGGATTTAGAGATATCGCGATTTATTTCTTTTTTCTTTGTAGGAA  >  1/1539323‑1539816

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑