Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,801,078	(T)7→6	coding (922/1017 nt)	waaJ ←	UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,801,072	0	T	.	100.0%	122.1 / NA	27	coding (928/1017 nt)	waaJ	UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (15/12);  total (15/12)

CTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATC  >  NC_000913/3801024‑3801117                                                 |                                              cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt                                              >  1:2402027/1‑50 (MQ=255)    taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt                                           >  1:21422/1‑50 (MQ=255)    taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttt                                            <  1:964505/49‑1 (MQ=255)    taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttt                                            <  1:2027572/49‑1 (MQ=255)      aTTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttttt                                          <  1:2482347/49‑1 (MQ=255)      aTTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttttt                                          <  1:829648/49‑1 (MQ=255)       ttCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttttaa                                        <  1:1892412/50‑3 (MQ=255)          cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt                                    <  1:2629290/50‑1 (MQ=255)             agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTc                                   <  1:1870472/48‑1 (MQ=39)             agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTc                                   <  1:355341/48‑1 (MQ=39)             agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTc                                   <  1:1524157/48‑1 (MQ=39)             agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaa                                 <  1:825088/50‑1 (MQ=255)             agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCa                                  <  1:1839959/49‑1 (MQ=39)              gaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaat                                <  1:269257/50‑1 (MQ=255)               atatAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaata                               <  1:1002104/50‑1 (MQ=255)               atatAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaat                                >  1:73633/1‑49 (MQ=39)                tataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa                              >  1:1658417/1‑50 (MQ=255)                  taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt                            <  1:58653/50‑1 (MQ=255)                    atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTg                           <  1:1384129/49‑1 (MQ=39)                     tgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAt                         <  1:932413/50‑1 (MQ=255)                        tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc                      >  1:2664404/1‑50 (MQ=255)                            gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAt                  >  1:2469780/1‑50 (MQ=255)                            gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAt                  >  1:1082642/1‑50 (MQ=255)                              aCTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtct                >  1:480877/1‑50 (MQ=255)                                 aaaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt             >  1:282324/1‑50 (MQ=255)                                  aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCg              <  1:1706875/48‑1 (MQ=39)                                    aGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg            >  1:1722994/1‑48 (MQ=39)                                      aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGga          >  1:1813441/1‑48 (MQ=39)                                         tttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt      >  1:563522/1‑49 (MQ=39)                                          ttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCa    >  1:1875125/1‑50 (MQ=255)                                          ttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCa    >  1:94466/1‑50 (MQ=255)                                           tataTC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAt   >  1:1572361/1‑50 (MQ=255)                                            atatC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATc  >  1:2521794/1‑50 (MQ=255)                                            atatC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATc  >  1:1396733/1‑50 (MQ=255)                                                 |                                              CTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATC  >  NC_000913/3801024‑3801117

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑