Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,478,559	C→T	L33L (CTA→TTA)	unknown →	Flp pilus assembly protein, pilin Flp

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,478,559	0	C	T	100.0%	87.2 / NA	33	L33L (CTA→TTA)	unknown	Flp pilus assembly protein, pilin Flp
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (19/14);  total (19/14)

GAGCTATTCTACACTCTATATTAGAATTAATTATGATGGATTTACTGGATTACTTTTATCGTCAAGTAGTCTTTTTTTCGTGTAAGTTTTACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGCTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGAGGATAACAGCTTTATTAAGGCGTTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCTCTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGATAAAAAAATGAACTGGCTTATTAATACTTTAGTAGTCATAACGATCTTACTGCTGACTACTTTATCTGTAACTGACATTCGTTCTCGGATTATTAGTAAC  >  1/1478431‑1478802                                                                                                                                 |                                                                                                                                                                                                                                                    gggctattctttgcttcattttgaaattaattATGATGGATTTACTGGATTACTTTTATCATCAAGTAGTCTTTTCTTCGTATAGGTTTTACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAg                                                                                                                            >  1:880613/25‑250 (MQ=255)  ggctattctttgcttcattttgaaattaattATGATGGATTTACTGGATTACTTTTATCATCAAGTAGTCTTTTCTTCGTATAGGTTTTACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGc                                                                                                                           <  1:62568/227‑1 (MQ=255)    ctattctttgcttcattttgaaattaattATGATGGATTTACTGGATTACTTTTATCATCAAGTAGTCTTTTCTTCGTATAGGTTTTACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCaaa                                                                                                                        <  1:392439/230‑1 (MQ=255)                      tgaaattaattATGATGGATTTACTGGATTACTTTTATCATCAAGTAGTCTTTTCTTCGTATAGGTTTTACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGa                                                                                                      <  1:159307/248‑1 (MQ=255)                                       gATTTACTGGATTACTTTTATCATCAAGTAGTCTTTTCTTCGTATAGGTTTTACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTgg                                                                                      >  1:886480/1‑249 (MQ=255)                                         tttACTGGATTACTTTTATCATCAAGTAGTCTTTTCTTCGTATAGGTTTTACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCtta                                                                                  >  1:599507/1‑251 (MQ=255)                                               ggATTACTTTTATCATCAAGTAGTCTTTTCTTCGTATAGGTTTTACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCTTATTaacg                                                                            >  1:230394/1‑249 (MQ=255)                                               ggATTACTTTTATCATCAAGTAGTCTTTTCTTCGTATAGGTTTTACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGAATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCTTATTaacg                                                                            >  1:452470/1‑249 (MQ=255)                                                     cTTTTATCATCAAGTAGTCTTTTCTTCGTATAGGTTTTACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTg                                                                                                                                                                                                                                               <  1:371830/83‑1 (MQ=255)                                                     cTTTTATCATCAAGTAGTCTTTTCTTCGTATAGGTTTTACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTttatta                                                                                                                                                                                      <  1:214149/140‑1 (MQ=255)                                                          atcatCAAGTAGTCTTTTCTTCGTATAGGTTTTACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCTTATTAACGCTTtagtaatc                                                                 <  1:835872/247‑4 (MQ=255)                                                           tcatCAAGTAGTCTTTTCTTCGTATAGGTTTTACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCTTATTAACGCTTtagt                                                                     >  1:190674/4‑246 (MQ=255)                                                               cAAGTAGTCTTTTCTTCGTATAGGTTTTACAGAAATCGACAAGGGATTACTTCTGTTGATTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCttatta                                                                               <  1:757379/232‑1 (MQ=255)                                                               cAAGTAGTCTTTTCTTCGTATAGGTTTTACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCttatta                                                                               >  1:263358/1‑232 (MQ=255)                                                                    agtCTTTTCTTCGTATAGGTTTTACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCTTATTAACGCTTtagtaa                                                                   >  1:149626/1‑238 (MQ=255)                                                                          ttcttCGTATAGGTTTTACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCTTATTAACGCTTTAGTAATCATAACGctctcgctgc                                                 <  1:2621/248‑7 (MQ=255)                                                                                gtataggTTTTACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCTTATTAACGCTTTAGTAATCATAACGCTCTCGctgctggtta                                           >  1:482912/7‑247 (MQ=255)                                                                                      gTTTTACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCTTATTAACGCTTTAGTAATCATAACGCTCTCGCTGCTGGTTACTTTAt                                     >  1:366220/1‑251 (MQ=255)                                                                                        tttACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCTTATTAACGCTTTAGTAATCATAACGCTCTCGCTGCTGGTTACTTTATCt                                   <  1:858182/251‑1 (MQ=255)                                                                                         ttACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCTTATTAACGCTTTAGTAATCATAACGCTCTCGCTGCTGGTTACTTTATCta                                  <  1:291182/251‑2 (MQ=255)                                                                                                 aTCGACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCTTATTAACGCTTTAGTAATCATAACGCTCTCGCTGCTGGTTACTTTATCTATAACTGa                           >  1:311721/1‑250 (MQ=255)                                                                                                    gACAAGGGATTACTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCTTATTAACGCTTtagtaa                                                                   <  1:281763/207‑2 (MQ=255)                                                                                                                cTTCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCTTATTAACGCTTTAGTAATCATAACGCTCTCGCTGCTGGTTACTTTATCTATAACTGACATTCGTTTTCggctt           >  1:674379/1‑248 (MQ=255)                                                                                                                  tCTGTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGACCTGGCTTATTAACGCTTTAGTAATCATAACGCTCTCGCTGCTGGTTACTTTATCTATAACTGACATTCGTTTTCGGcttat         >  1:430098/1‑251 (MQ=255)                                                                                                                     gTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAg                                                                                                                                                                                                                       >  1:209814/1‑43 (MQ=255)                                                                                                                     gTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGc                                                                                                                                                                                             <  1:519820/69‑1 (MQ=255)                                                                                                                     gTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCttatta                                                                               >  1:869767/1‑178 (MQ=255)                                                                                                                     gTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCTTATTAACGCTTtag                                                                      >  1:583085/1‑187 (MQ=255)                                                                                                                     gTTGAGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCTTATTAACGCTTTAGTAATCATAACGCTCTCGCTGCTGGTTACTTTATCTATAAc                              <  1:462671/227‑1 (MQ=255)                                                                                                                         aGTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGt                                                                                                                                                                        >  1:864982/1‑86 (MQ=255)                                                                                                                          gTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCTTATTAACGCTTTAGTAATCATAACGCTCTCGCTGCTGGTTACTTTATCta                                  >  1:857845/1‑217 (MQ=255)                                                                                                                          gTATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCTTATTAACGCTTTAGTAATCATAACGCTCTCGCTGCTGGTTACTTTATCTATAACTGACATTCGTTTTCGGCTTATTAGTAAc  >  1:359386/1‑250 (MQ=255)                                                                                                                           tATGGGTTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGGGGATAACAGCTTTATTAAGGCAGTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCACTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGAT‑AAAAAATGAACTGGCTTATTAACGCTTTAGTAATCATAACGCTCTCGCTGCTGGTTACTTTATCTATAACTGACATTCGTTTTCGGCTTATTAGTAAc  <  1:724868/249‑1 (MQ=255)                                                                                                                                 |                                                                                                                                                                                                                                                    GAGCTATTCTACACTCTATATTAGAATTAATTATGATGGATTTACTGGATTACTTTTATCGTCAAGTAGTCTTTTTTTCGTGTAAGTTTTACAGAAATCGACAAGGGATTACTTCTGTTGAGTATGGGCTAATTGCTGTGGCTATTGCTGTTTTTGTAGTCGCCGTTTTAGTCGAGGATAACAGCTTTATTAAGGCGTTGTCAGGTAAGTTCTCGGATTTAACGACCACTGTCTCTGACGCCATAGTTAGCAAAAGTAGCTAAGAAAAATGATAAAAAAATGAACTGGCTTATTAATACTTTAGTAGTCATAACGATCTTACTGCTGACTACTTTATCTGTAACTGACATTCGTTCTCGGATTATTAGTAAC  >  1/1478431‑1478802

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: ‑