Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	196,898	T→A	intergenic (+51/‑71)	bamA → / → skp	outer membrane protein assembly factor BamA/molecular chaperone Skp

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	196,898	0	T	A	100.0%	153.0 / NA	37	intergenic (+51/‑71)	bamA/skp	outer membrane protein assembly factor BamA/molecular chaperone Skp
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (21/16);  total (21/16)

AGCCGTTCAAAAAGTACGATGGAGACAAGGCAGAACAGTTCCAGTTTAACATCGGTAAAACCTGGTAAGTGTTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGATCAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAGTGGTTATTAGCTGCAGGTCTCGGTTTAGCACTGGCAACTTCTGCTCAGGC  >  NZ_CP009273/196780‑197027                                                                                                                       |                                                                                                                                  aGCCGTTCAAAAAGTACGATGGAGACAAGGCAGAACAGTTCCAGTTTAACATCGGTAAAACCTGGTAAGTGTTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGc                                                                                                                >  1:691374/1‑138 (MQ=255)   ccGTTCAAAAAGTACGATGGAGACAAGGCAGAACAGTTCCAGTTTAACATCGGTAAAACCTGGTAAGTGTTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCAc                                                                                                             >  1:771134/1‑139 (MQ=255)      ttCAAAAAGTACGATGGAGACAAGGCAGAACAGTTCCAGTTTAACATCGGTAAAACCTGGTAAGTGTTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCa                                                                                                          <  2:477999/139‑1 (MQ=255)      ttCAAAAAGTACGATGGAGACAAGGCAGAACAGTTCCAGTTTAACATCGGTAAAACCTGGTAAGTGTTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCa                                                                                                          <  1:636368/139‑1 (MQ=255)                                       ttCCAGTTTAACATCGGTAAAACCTGGTAAGTGTTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATgg                                                                          >  1:162794/1‑138 (MQ=255)                                       ttCCAGTTTAACATCGGTAAAACCTGGTAAGTGTTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATgg                                                                          >  1:652452/1‑138 (MQ=255)                                       ttCCAGTTTAACATCGGTAAAACCTGGTAAGTGTTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGt                                                                         <  2:57415/139‑1 (MQ=255)                                          cAGTTTAACATCGGTAAAACCTGGTAAGTGTTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTaa                                                                       <  1:336232/138‑1 (MQ=255)                                            gTTTAACATCGGTAAAACCTGGTAAGTGTTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAg                                                                      >  1:103417/1‑137 (MQ=255)                                                 aCATCGGTAAAACCTGGTAAGTGTTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGa                                                                             >  2:581085/1‑125 (MQ=255)                                                 aCATCGGTAAAACCTGGTAAGTGTTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGa                                                                             <  1:581085/125‑1 (MQ=255)                                                            aCCTGGTAAGTGTTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAg                                                    <  2:491036/139‑1 (MQ=255)                                                                 gTAAGTGTTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCa                                                                                                <  1:443877/90‑1 (MQ=255)                                                                 gTAAGTGTTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCa                                                                                                >  2:443877/1‑90 (MQ=255)                                                                 gTAAGTGTTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAGTGGtt                                               <  2:103417/139‑1 (MQ=255)                                                                 gTAAGTGTTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAGTGGt                                                >  2:833658/1‑138 (MQ=255)                                                                      tgtTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCaaa                                                                                                        <  2:835856/77‑1 (MQ=255)                                                                      tgtTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCaaa                                                                                                        >  1:835856/1‑77 (MQ=255)                                                                       gtTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAGTGGTTATTAGc                                         >  2:57495/1‑139 (MQ=255)                                                                              acaAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAGTGGTTATTAGCTGCAGGt                                  <  1:135283/139‑1 (MQ=255)                                                                                aaaGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAGTGGTTATTAGCTGCAGGtct                                <  1:497361/139‑1 (MQ=255)                                                                                  aGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAGTGGTTATTAGCTGCAGGTCTCg                              >  2:695751/1‑139 (MQ=255)                                                                                    gAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAGTGGTTATTAGCTGCAGGTCTCGGt                            >  2:472990/1‑139 (MQ=255)                                                                                           gtggtagtgTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAGTGGTTATTAGCTGCAGGTCTCGGTTTAGCa                      <  1:57495/138‑1 (MQ=255)                                                                                              gtagtgTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATggg                                                                              <  1:67229/79‑1 (MQ=255)                                                                                              gtagtgTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATggg                                                                              >  2:67229/1‑79 (MQ=255)                                                                                              gtagtgTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAGCGGTTATTAGCTGCAGGTCTCGGTTTAGCACTgg                  >  2:816255/1‑139 (MQ=255)                                                                                               tagtgTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCt                                                                                            >  1:630793/1‑64 (MQ=255)                                                                                               tagtgTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCt                                                                                            <  2:630793/64‑1 (MQ=255)                                                                                               tagtgTAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAGTGGTTATTAGCTGCAGGTCTCGGTTTAGCACTGGc                 <  1:695751/139‑1 (MQ=255)                                                                                                 gtgtAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAGTGGTTATTAGCTGCAGGTCTCGGTTTAGCACTGGCaa               >  2:308053/1‑139 (MQ=255)                                                                                                  tgtAGCGATGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAGTGGTTATTAGCTGCAGGTCTCGGTTTAGCACTGGCAAc              <  2:652452/139‑1 (MQ=255)                                                                                                         aTGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAGTGGTTATTAGCTGCAGGTCTCGGTTTAGCACTGGCAACTTCTGCt       >  1:134259/1‑139 (MQ=255)                                                                                                         aTGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAGTGGTTATTAGCTGCAGGTCTCGGTTTAGCACTGGCAACTTCTGCt       >  1:283508/1‑139 (MQ=255)                                                                                                         aTGACTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAGTGGTTATTAGCTGCAGGTCTCGGTTTAGCACTGGCAACTTCTGCt       >  1:30742/1‑139 (MQ=255)                                                                                                            aCTTTAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAGTGGTTATTAGCTGCAGGTCTCGGTTTAGCACTGGCAACTTCTGCTCAg    >  2:352084/1‑139 (MQ=255)                                                                                                              tttAGGCGAACAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAGTGGTTATTAGCTGCAGGTCTCGGTTTAGCACTGGCAACTTCTGCTCAggc  >  1:518066/1‑139 (MQ=255)                                                                                                                       |                                                                                                                                  AGCCGTTCAAAAAGTACGATGGAGACAAGGCAGAACAGTTCCAGTTTAACATCGGTAAAACCTGGTAAGTGTTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGATGACTTTAGGCGATCAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGAGTTTATTGTGAAAAAGTGGTTATTAGCTGCAGGTCTCGGTTTAGCACTGGCAACTTCTGCTCAGGC  >  NZ_CP009273/196780‑197027

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: ‑