Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,844,458	A→G	I6I (ATT→ATC)	unknown ←	O antigen biosynthesis rhamnosyltransferase rfbN (EC 2.4.1.‑)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,844,458	0	A	G	100.0%	93.9 / NA	32	I6I (ATT→ATC)	unknown	O antigen biosynthesis rhamnosyltransferase rfbN (EC 2.4.1.‑)
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (15/17);  total (15/17)

AAAAATTCACCTTTGGATAAGCTTGCTCCATAATTTCTTGTTTTTCCATGCCCAAATTCATAAGGTTTAATTTGATATAATCTAACATTATCATGGTTTTTTATAATATTATTTAAATATTCAACAGAACCATCTTTAGAACCAGAATCAATTACAATAACCTCAAATGGAGCGTCTAATTTTTGTAATAAAACACTAGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATAATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGCTTTTTGGCAAAGCTCTTTTACCTGATCGACAGAGTGAGATACAAATAATAAAGTTGTCCCACTTTCTAACATTTCGGTCATTCTCTTTTTACATTTTTCCTGAAATGCCGCATCACCAACAGCTAGCACCTCGTCAATGATAAGGA  >  1/1844216‑1844701                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                    aaaaaTTCACCTTTGGATAAGCTTGCTCCATAATTTCTTGTTTTTCCATGCCCAAATTCATAAGGTTTAATTTGATATAATCTAACATTATCATGGTTTTTTATAATATTATTTAAATATTCAACAGAACCATCTTTAGAACCAGAATCAATTACAATAACCTCAAATGGAGCGTCTAATTTTTGTAATAAAACACTAGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGa                                                                                                                                                                                                                                             <  1:830912/251‑1 (MQ=255)               ggATAAGCTTGCTCCATAATTTCTTGTTTTTCCATGCCCAAATTCATAAGGTTTAATTTGATATAATCTAACATTATCATGGTTTTTTATAATATTATTTAAATATTCAACAGAACCATCTTTAGAACCAGAATCAATTACAATAACCTCAAATGGAGCGTCTAATTTTTGTAATAAAACACTAGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCAtt                                                                                                                                                                                                                               >  1:677069/1‑251 (MQ=255)                               tAATTTCTTGTTTTTCCATGCCCAAATTCATAAGGTTTAATTTGATATAATCTAACATTATCATGGTTTTTTATAATATTATTTAAATATTCAACAGAACCATCTTTAGAACCAGAATCAATTACAATAACCTCAAATGGAGCGTCTAATTTTTGTAATAAAACACTAGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATaaa                                                                                                                                                                                                               <  1:552327/251‑1 (MQ=255)                                                                                                     ttATAATATTATTTAAATATTCAACAGAACCATCTTTAGAACCAGAATCAATTACAATAACCTCAAATGGAGCGTCTAATTTTTGTAATAAAACACTAGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGCTTTTTGGCaaa                                                                                                                                         >  1:246452/1‑251 (MQ=255)                                                                                                               attTAAATATTCAACAGAACCATCTTTAGAACCAGAATCAATTACAATAACCTCAAATGGAGCGTCTAATTTTTGTAATAAAACACTAGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTcc                                                                                                                                                                      >  1:532067/1‑212 (MQ=255)                                                                                                                        ttCAACAGAACCATCTTTAGAACCAGAATCAATTACAATAACCTCAAATGGAGCGTCTAATTTTTGTAATAAAACACTAGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGCTTTTTGGCAAAGCTCTTTTACCTGATCGAc                                                                                                                      <  1:173516/251‑1 (MQ=255)                                                                                                                                    aTCTTTAGAACCAGAATCAATTACAATAACCTCAAATGGAGCGTCTAATTTTTGTAATAAAACACTAGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCaa                                                                                                                                                                                      <  1:292963/175‑1 (MQ=255)                                                                                                                                      cTTTAGAACCAGAATCAATTACAATAACCTCAAATGGAGCGTCTAATTTTTGTAATAAAACACTAGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGCTTTTTGGCAAAGCTCTTTTACCTGATCGACAGAGTga                                                                                                               <  1:774687/244‑1 (MQ=255)                                                                                                                                                                aCCTCAAATGGAGCGTCTAATTTTTGTAATAAAACACTAGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACa                                                                                                                                                                                             <  1:179558/140‑1 (MQ=255)                                                                                                                                                                 ccTCAAATGGAGCGTCTAATTTTTGTAATAAAACACTAGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGCTTTTTGGCAAAGCTCTTTTACCTGATCGACAGAGTGAGATACAAATAATAAAGTTGTCCCACTTTCTAACa                                                                             >  1:289973/1‑251 (MQ=255)                                                                                                                                                                  cTCAAATGGAGCGTCTAATTTTTGTAATAAAACACTAGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGAc                                                                                                                                                                            <  1:204501/155‑1 (MQ=255)                                                                                                                                                                    cAAATGGAGCGTCTAATTTTTGTAATAAAACACTAGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGCTTTTTGGCAAAGCTCTTTTACCTGATCGACAGAGTGAGATACAAATAATAAAg                                                                                               <  1:143955/230‑1 (MQ=255)                                                                                                                                                                    cAAATGGAGCGTCTAATTTTTGTAATAAAACACTAGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGCTTTTTGGCAAAGCTCTTTTACCTGATCGACAGAGTGAGATACAAATAATAAAGTTGTCCCACTTTCTAACAttt                                                                          >  1:861235/1‑251 (MQ=255)                                                                                                                                                                              gTCTAATTTTTGTAATAAAACACTAGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGCTTTTTGGCAAAGCTCTTTTACCTGATCGACAGAGTGAGATACAAATAATAAAg                                                                                               <  1:358797/220‑1 (MQ=255)                                                                                                                                                                                         gTAATAAAACACTAGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGCTTTTTGGCAAAGCTCTTTTACCTGATCGACAGAGTGAGATACAAATAATAAAGTTGTCCCACTTTCTAACATTTCGGTCATTCTCTTTTTACAtt                                                     >  1:829832/1‑251 (MQ=255)                                                                                                                                                                                            ataaAACACTAGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGCTTTTTGGCAAAGCTCTTTTACCTGATCGACAGAGTGAGATACAAATAATAAAGTTGTCCCACTTTCTAACATTTCGGTCATTCTCTTTTTACAttttt                                                  >  1:186007/1‑251 (MQ=255)                                                                                                                                                                                                 acacTAGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTg                                                                                                                                                                                                                                              <  1:150672/58‑1 (MQ=255)                                                                                                                                                                                                      aGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTcc                                                                                                                                                                                                                         >  1:202288/1‑74 (MQ=255)                                                                                                                                                                                                      aGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATaaa                                                                                                                                                                                                               >  1:695713/1‑84 (MQ=255)                                                                                                                                                                                                      aGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGCTTTTTGGCAAAGCTCTTTTACCTGATCGAc                                                                                                                      <  1:768823/173‑1 (MQ=255)                                                                                                                                                                                                      aGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGCTTTTTGGCAAAGCTCTTTTACCTGATCGACAGAGTGAGATACAAATAATAAAGt                                                                                              >  1:215587/1‑197 (MQ=255)                                                                                                                                                                                                       gATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTcc                                                                                                                                                                      <  1:93545/124‑1 (MQ=255)                                                                                                                                                                                                            aaCTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGCTTTTTGGCAAAGCTCTTTTACCTGATCGACAGAGTGAGATACAAATAATAAAGTTGTCCCACTTTCTAACATTTCGGTCATTCTCTTTTTACATTTTTCCTGAAATGCCGCATc                                  <  1:251133/251‑1 (MQ=255)                                                                                                                                                                                                                 gCTTAAAAATATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGCTTTTTGGCAAAGCTCTTTTACCTGATCGACAGAGTGAGATACAAATAATAAAGTTGTCCCACTTTCTAACATTTCGGTCATTCTCTTTTTACa                                                       >  1:616261/1‑225 (MQ=255)                                                                                                                                                                                                                     aaaaaTATCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGCTTTTTGGCAAAGCTCTTTTACCTGATCGACAGAGTGAGATACAAATAATAAAGTTGTCCCACTTTCTAACATTTCGGTCATTCTCTTTTTACATTTTTCCTGAAATGCCGCATCACCAACAg                          >  1:127920/1‑250 (MQ=255)                                                                                                                                                                                                                           atCTCCACCATTTTTGAGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGCTTTTTGGCAAAGCTCTTTTACCTGATCGACAGAGTGAGATACAAATAATAAAGTTGTCCCACTTTCTAACATTTCGGTCATTCTCTTTTTACATTTTTCCTGAAATGCCGCATCACCAACAGCTAGCAc                   <  1:400133/251‑1 (MQ=255)                                                                                                                                                                                                                                caccaTTTTTGTGTGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCt                                                                                                                                                               >  1:453617/1‑106 (MQ=255)                                                                                                                                                                                                                                             tGGAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGCTTTTTGGCAAAGCTCTTTTACCTGATCGACAGAGTGAGATACAAATAATAAAGTTGTCCCACTTTCTAACATTTCGGTCATTCTCTTTTTACATTTTTCCTGAAATGCCGCATCACCAACAGCTAGCAACTCGTCAATGATAAGGa  <  1:471266/250‑1 (MQ=255)                                                                                                                                                                                                                                               gAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACAt                                                                                                                                                                                            <  1:560713/62‑1 (MQ=255)                                                                                                                                                                                                                                               gAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAg                                                                                                                                                                                   <  1:151854/71‑1 (MQ=255)                                                                                                                                                                                                                                               gAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGc                                                                                                                                                    >  1:833785/1‑102 (MQ=255)                                                                                                                                                                                                                                               gAATGATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGCTTTTTGGCAAAGCTCTTTTACCTGATCGACAGAGTGAGATACAAATAATAAAGTTGTCCCACTTTCTAACATTTCGGTCATTCTCTTTTTACATTTTTCCTGAAATGCCGCATCACCAACAGCt                        >  1:35205/1‑226 (MQ=255)                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                    AAAAATTCACCTTTGGATAAGCTTGCTCCATAATTTCTTGTTTTTCCATGCCCAAATTCATAAGGTTTAATTTGATATAATCTAACATTATCATGGTTTTTTATAATATTATTTAAATATTCAACAGAACCATCTTTAGAACCAGAATCAATTACAATAACCTCAAATGGAGCGTCTAATTTTTGTAATAAAACACTAGATAAAACTTGCTTAAAAATATCTCCACCATTTTTGAGTGGAATAATTATTGAGGCTTTCATGCATTTTTTCCCATGTATAAATTTGTAATTTCTTCAACATCACCAATAGCTTTGACATTTCCTTTATCTAACCATATAGCTTTTTGGCAAAGCTCTTTTACCTGATCGACAGAGTGAGATACAAATAATAAAGTTGTCCCACTTTCTAACATTTCGGTCATTCTCTTTTTACATTTTTCCTGAAATGCCGCATCACCAACAGCTAGCACCTCGTCAATGATAAGGA  >  1/1844216‑1844701

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: ‑