Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,332,009	A→G	V200A (GTC→GCC)	mlaE ←	lipid asymmetry maintenance ABC transporter permease subunit MlaE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,332,009	0	A	G	100.0%	172.9 / NA	45	V200A (GTC→GCC)	mlaE	lipid asymmetry maintenance ABC transporter permease subunit MlaE
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (26/19);  total (26/19)

GCCAGAGACGAGTGGACAACGGTGCGAGTGGTTGCCCGGCTAATCCCGGCAGACGTCGGGATGGCGTCGTAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGACCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCAGAGATCCGCCCCAGATCCCCACGGCGACGAAAATAACCGTCAACAGTGGT  >  NZ_CP009273/3331874‑3332143                                                                                                                                        |                                                                                                                                       gCCAGAGACGAGTGGACAACGGTGCGAGTGGTTGCCCGGCTAATCCCGGCAGACGTCGGGATGGCGTCGTAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCa                                                                                                                                     <  1:100498/139‑1 (MQ=255) gCCAGAGACGAGTGGACAACGGTGCGAGTGGTTGCCCGGCTAATCCCGGCAGACGTCGGGATGGCGTCGTAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCa                                                                                                                                     <  1:478664/139‑1 (MQ=255)  ccAGAGACGAGTGGACAACGGTGCGAGTGGTTGCCCGGCTAATCCCGGCAGACGTCGGGATGGCGTCGTAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAg                                                                                                                                    <  2:25820/139‑1 (MQ=255)  ccAGAGACGAGTGGACAACGGTGCGAGTGGTTGCCCGGCTAATCCCGGCAGACGTCGGGATGGCGTCGTAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAg                                                                                                                                    <  1:710332/139‑1 (MQ=255)            gTGGACAACGGTGCGAGTGGTTGCCCGGCTAATCCCGGCAGACGTCGGGATGGCGTCGTAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGc                                                                                                                          >  1:196381/1‑139 (MQ=255)             tGGACAACGGTGCGAGTGGTTGCCCGGCTAATCCCGGCAGACGTCGGGATGGCGTCGTAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGc                                                                                                                          >  1:335138/1‑138 (MQ=255)                   aCGGTGCGAGTGGTTGCCCGGCTAATCCCGGCAGACGTCGGGATGGCGTCGTAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGa                                                                                                                   <  2:297345/139‑1 (MQ=255)                       tGCGAGTGGTTGCCCGGCTAATCCCGGCAGACGTCGGGATGGCGTCGTAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACgg                                                                                                                >  1:626280/1‑138 (MQ=255)                          gAGTGGTTGCCCGGCTAATCCCGGCAGACGTCGGGATGGCGTCGTAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCAtt                                                                                                            >  2:166450/1‑139 (MQ=255)                               gTTGCCCGGCTAATCCCGGCAGACGTCGGGATGGCGTCGTAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCa                                                                                                       >  2:708519/1‑139 (MQ=255)                               gTTGCCCGGCTAATCCCGGCAGACGTCGGGATGGCGTCGTAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCa                                                                                                       >  1:40329/1‑139 (MQ=255)                                 tGCCCGGCTAATCCCGGCAGACGTCGGGATGGCGTCGTAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCAtt                                                                                                     >  2:564047/1‑139 (MQ=255)                                 tGCCCGGCTAATCCCGGCAGACGTCGGGATGGCGTCGTAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCAtt                                                                                                     >  1:271332/1‑139 (MQ=255)                                 tGCCCGGCTAATCCCGGCAGACGTCGGGATGGCGTCGTAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCAtt                                                                                                     >  1:671937/1‑139 (MQ=255)                                              ccGGCAGACGTCGGGATGGCGTCGTAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCagaag                                                                                         <  2:743762/138‑1 (MQ=255)                                                   aGACGTCGGGATGGCGTCGTAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCg                                                                                   <  2:271332/139‑1 (MQ=255)                                                                 cgtcgtAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAg                                                                                                                                    >  2:415546/1‑76 (MQ=255)                                                                 cgtcgtAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAg                                                                                                                                    <  1:415546/76‑1 (MQ=255)                                                                 cgtcgtAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCttt                                                                     >  2:126491/1‑139 (MQ=255)                                                                 cgtcgtAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCttt                                                                     >  2:384569/1‑139 (MQ=255)                                                                      tAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCagaag                                                                                         <  1:677659/114‑1 (MQ=255)                                                                      tAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCagaag                                                                                         >  2:677659/1‑114 (MQ=255)                                                                      tAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAAc                                                                >  2:573347/1‑139 (MQ=255)                                                                           gTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACg                                                           <  2:660642/139‑1 (MQ=255)                                                                                acaacGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGAc                                                      <  2:473864/139‑1 (MQ=255)                                                                                  aacGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCa                                                    <  2:335138/139‑1 (MQ=255)                                                                                        aTCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCAGAGATc                                              <  2:215461/139‑1 (MQ=255)                                                                                           cACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCAGAGATCCg                                            <  2:223510/138‑1 (MQ=255)                                                                                                   cGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCAGAGATCCGCCCCAGATc                                   >  2:608130/1‑139 (MQ=255)                                                                                                             aaCACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGcc                                                         >  2:609684/1‑107 (MQ=255)                                                                                                             aaCACCACGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGcc                                                         <  1:609684/107‑1 (MQ=255)                                                                                                                 ccacGCTCTTAATCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCAGAGATCCGCCCCAGATCCCCACGGcgacga                      >  1:431827/1‑138 (MQ=255)                                                                                                                            aTCAGACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCAGAGATCCGCCCCAGATCCCCACGGCGACGAAAATAACCGTc           >  1:299059/1‑138 (MQ=255)                                                                                                                                gACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCAGAGATCCGCCCCAGATCCCCACGGCGACGAAAATAACCGTCAACAg      <  1:564047/139‑1 (MQ=255)                                                                                                                                gACAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCAGAGATCCGCCCCAGATCCCCACGGCGACGAAAATAACCGTCAACAg      <  2:340272/139‑1 (MQ=255)                                                                                                                                 aCAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCAGAGATCCg                                            <  1:31809/100‑1 (MQ=255)                                                                                                                                 aCAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCAGAGATCCg                                            >  2:31809/1‑100 (MQ=255)                                                                                                                                 aCAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCAGAGATCCGCCCCAGATCCCCACGGCGACGACAATAACCGTCAACAGt     >  2:558637/1‑139 (MQ=255)                                                                                                                                 aCAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCAGAGATCCGCCCCAGATCCCCACGGCGACGAAAATAACCGTCaa         >  1:733218/1‑135 (MQ=255)                                                                                                                                 aCAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCAGAGATCCGCCCCAGATCCCCACGGCGACGAAAATAACCGTCaa         <  2:733218/135‑1 (MQ=255)                                                                                                                                 aCAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCAGAGATCCGCCCCAGATCCCCACGGCGACGAAAATAACCGTCAACAGt     >  2:221015/1‑139 (MQ=255)                                                                                                                                 aCAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCAGAGATCCGCCCCAGATCCCCACGGCGACGAAAATAACCGTCAACAGt     >  2:161910/1‑139 (MQ=255)                                                                                                                                 aCAGTTGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCAGAGATCCGCCCCAGATCCCCACGGCGACGAAAATAACCGTCAACAGt     >  1:678125/1‑139 (MQ=255)                                                                                                                                     ttGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCAGAGATCCGCCCCAGATCCCCACGGCGACGAAAATAACCGTCAACAGTGGt  >  2:161295/1‑138 (MQ=255)                                                                                                                                     ttGGCCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCAGAGATCCGCCCCAGATCCCCACGGCGACGAAAATAACCGTCAACAGTGGt  >  1:573214/1‑138 (MQ=255)                                                                                                                                        |                                                                                                                                       GCCAGAGACGAGTGGACAACGGTGCGAGTGGTTGCCCGGCTAATCCCGGCAGACGTCGGGATGGCGTCGTAGCCGTTAAACAACGAAATCCACGTCACCGTGATGGCGAACACCACGCTCTTAATCAGACAGTTGACCAGATCCATACGCCAGTCGACGGCATTTTGCATTGCCGACCAGAAGAACCCGCTATCAATGCCTTTCCAACTGACGCCGACCAGAGATCCGCCCCAGATCCCCACGGCGACGAAAATAACCGTCAACAGTGGT  >  NZ_CP009273/3331874‑3332143

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑