Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,377,189	C→T	H105H (CAC→CAT)  *178* (TAG→TAA)	sugE → blc ←	multidrug efflux system protein outer membrane lipoprotein cell division and growth lipocalin

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,377,189	0	C	T	100.0%	147.3 / NA	46	H105H (CAC→CAT)  *178* (TAG→TAA)	sugE blc	multidrug efflux system protein outer membrane lipoprotein cell division and growth lipocalin
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (17/29);  total (17/29)

GTGTGGACGGGTATTGGCGCAGTCGGCGCGGCCATAACCGGCATTGTGCTGCTCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCACTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTCGCGACTGCCAGCATCTCCTGTTTCACTTCGTCAGAAATGGTTGGCGTGCGGGAGAGTATCCACAGGTAGTCGCGGTC  >  NC_000913/4377055‑4377323                                                                                                                                       |                                                                                                                                       gtgtGGACGGGTATTGGCGCAGTCGGCGCGGCCATAACCGGCATTGTGCTGCTCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCattaac                                                                                                                                    >  2:531076/1‑139 (MQ=255)        cGGGTATTGGCGCAGTCGGCGCGGCCATAACCGGCATTGTGCTGCTCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAgg                                                                                                                             <  2:809430/139‑1 (MQ=255)        cGGGTATTGGCGCAGTCGGCGCGGCCATAACCGGCATTGTGCTGCTCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAgg                                                                                                                             <  1:790346/139‑1 (MQ=255)        cGGGTATTGGCGCAGTCGGCGCGGCCATAACCGGCATTGTGCTGCTCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAgg                                                                                                                             <  1:649977/139‑1 (MQ=255)        cGGGTATTGGCGCAGTCGGCGCGGCCATAACCGGCATTGTGCTGCTCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAgg                                                                                                                             <  1:777756/139‑1 (MQ=255)           gTATTGGCGCAGTCGGCGCGGCCATAACCGGCATTGTGCTGCTCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGgctg                                                                                                                          <  1:230294/139‑1 (MQ=255)             aTTGGCGCAGTCGGCGCGGCCATAACCGGCATTGTGCTGCTCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGgctgct                                                                                                                        <  2:864583/139‑1 (MQ=255)              ttGGCGCAGTCGGCGCGGCCATAACCGGCATTGTGCTGCTCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGctgctg                                                                                                                       <  2:1071938/139‑1 (MQ=255)                ggCGCAGTCGGCGCGGCCATAACCGGCATTGTGCTGCTCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTa                                                                                                                     <  2:959727/139‑1 (MQ=255)                   gcAGTCGGCGCGGCCATAACCGGCATTGTGCTGCTCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGgctg                                                                                                                          >  2:820490/1‑131 (MQ=255)                   gcAGTCGGCGCGGCCATAACCGGCATTGTGCTGCTCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGgctg                                                                                                                          <  1:820490/131‑1 (MQ=255)                      gTCGGCGCGGCCATAACCGGCATTGTGCTGCTCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCaaa                                                                                                               >  1:1041751/1‑139 (MQ=255)                                ccATAACCGGCATTGTGCTGCTCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACt                                                                                                     <  1:729686/139‑1 (MQ=255)                                 cATAACCGGCATTGTGCTGCTCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTAc                                                                                                                                 <  1:529064/110‑1 (MQ=255)                                 cATAACCGGCATTGTGCTGCTCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTg                                                                                                    >  1:876727/1‑139 (MQ=255)                                 cATAACCGGCATTGTGCTGCTCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACACATTAACTAc                                                                                                                                 >  2:529064/1‑110 (MQ=255)                                 cATAACCGGCATTGTGCCGCTCGGTGAGCCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGTATTATTGGTCTGAAACTCAGCACCCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTg                                                                                                    <  1:761887/139‑1 (MQ=255)                                          cATTGTGCTGCTCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAAc                                                                                           <  2:876727/139‑1 (MQ=255)                                                    ctCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCggg                                                                                 >  2:135574/1‑139 (MQ=255)                                                       ggggAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGCGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTcg                                                                              >  2:643707/4‑139 (MQ=255)                                                        gTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTcgc                                                                             <  1:905124/139‑1 (MQ=255)                                                           aGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTCGCGAc                                                                          <  1:1065052/139‑1 (MQ=255)                                                              ccGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTCGCGACTGc                                                                       >  2:614843/1‑139 (MQ=255)                                                                 cTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTCGCGACTGCCAg                                                                    >  1:346352/1‑139 (MQ=255)                                                                  tAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTCGCGACTGCCAGc                                                                   <  2:1041751/139‑1 (MQ=255)                                                                                 ggCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTCGCGTCTGCCAGCATCTCCTGTTTCACt                                                    <  1:548324/139‑1 (MQ=255)                                                                                         tGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCa                                                                                                                               >  2:803148/1‑56 (MQ=255)                                                                                         tGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCa                                                                                                                               <  1:803148/56‑1 (MQ=255)                                                                                                   cGTATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTCGCGACTGCCAGCATCTCCTGTTTCACTTCGTCAGAAATGGTTGGc                                  <  1:768955/139‑1 (MQ=255)                                                                                                     tATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACt                                                                                                     >  2:43827/1‑70 (MQ=255)                                                                                                     tATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACt                                                                                                     <  1:43827/70‑1 (MQ=255)                                                                                                     tATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTCGCGa                                                                           >  2:416163/1‑96 (MQ=255)                                                                                                     tATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTCGCGa                                                                           <  1:416163/96‑1 (MQ=255)                                                                                                     tATTGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTCGCGACTGCCAGCATCTCCTGTTTCACTTCGTCAGAAATGGTTGGCGt                                >  1:702852/1‑139 (MQ=255)                                                                                                        tGGGGATTATTGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTCGCGACTGCCAGCATCTCCTGTTTCACTTCGTCAGAAATGGTTGGCGTGCg                             <  1:531076/139‑1 (MQ=255)                                                                                                             attattGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTCGCGACTGCCAGCATCTCCTGTTTCACTTCGTCAGAAATGGTTGGCGTGCGGgaga                        <  2:169402/139‑1 (MQ=255)                                                                                                              ttattGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTCGCGACTGCCAGCATCTCCTGTTTCACTTCGTCAGAAATGGTTGGCGTGCGGGagag                       <  2:911271/139‑1 (MQ=255)                                                                                                               tattGGTCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTCGCGACTGCCAGCATCTCCTGTTTCACTTCGTCAGAAATGGTTGGCGTGCGGGAGAGt                      <  1:80148/139‑1 (MQ=255)                                                                                                                     tCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTCGCGACTGCCAGCATCTCCTGTTTCACTTCGTCAGAAATGGTTGGCGTGCGGgaga                        >  2:829062/1‑131 (MQ=255)                                                                                                                     tCTGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTCGCGACTGCCAGCATCTCCTGTTTCACTTCGTCAGAAATGGTTGGCGTGCGGgaga                        <  1:829062/131‑1 (MQ=255)                                                                                                                       tGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACt                                                                                                     >  1:263749/1‑52 (MQ=255)                                                                                                                       tGAAACTCAGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACt                                                                                                     <  2:263749/52‑1 (MQ=255)                                                                                                                         aaaCTCAGCACTCATTAACTACCAGGCTACTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTCGCGACTGCCAGCATCTCCTGTTTCACTTCGTCAGAAATGGTTGGCGTGCGGGAGAGTATCCACAGGt            >  2:935207/1‑139 (MQ=255)                                                                                                                               aGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTcgcg                                                                            >  2:496168/1‑69 (MQ=255)                                                                                                                               aGCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTcgcg                                                                            <  1:496168/69‑1 (MQ=255)                                                                                                                                gCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTcc                                                                                     >  2:729835/1‑59 (MQ=255)                                                                                                                                gCACTCATTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTcc                                                                                     <  1:729835/59‑1 (MQ=255)                                                                                                                                   ctcattAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTCGCGACTGCCAGCATCTCCTGTTTCACTTCGTCAGAAATGGTTGGCGTGCGGGAGAGTATCCACAGGTAGTCGCGGTc  <  1:643707/139‑1 (MQ=255)                                                                                                                                       |                                                                                                                                       GTGTGGACGGGTATTGGCGCAGTCGGCGCGGCCATAACCGGCATTGTGCTGCTCGGTGAGTCCGCTAACCCGATGCGCCTGGCGAGTCTGGCGTTAATCGTATTGGGGATTATTGGTCTGAAACTCAGCACTCACTAACTACCAGGCTGCTGTACCCAAATAAATTTACTGACATCAAACCCTTCCCGGGTCGCGACTGCCAGCATCTCCTGTTTCACTTCGTCAGAAATGGTTGGCGTGCGGGAGAGTATCCACAGGTAGTCGCGGTC  >  NC_000913/4377055‑4377323

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑