Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,487,041	C→T	T275I (ACC→ATC)	lptF →	lipopolysaccharide export ABC permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,487,041	0	C	T	100.0%	124.1 / NA	36	T275I (ACC→ATC)	lptF	lipopolysaccharide export ABC permease
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (16/20);  total (16/20)

ATCAGGCGATCATTGGTCACCAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCACCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCTGAAATCGAAC  >  NC_000913/4486906‑4487174                                                                                                                                        |                                                                                                                                      aTCAGGCGATCATTGGTCACCAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCgt                                                                                                                                    >  2:399669/1‑139 (MQ=255)         aTCATTGGTCACCAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTatga                                                                                                                            >  2:54503/1‑139 (MQ=255)           cATTGGTCACCAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTatgatg                                                                                                                          <  1:399669/139‑1 (MQ=255)                    ccAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATg                                                                                                                 >  2:252703/1‑139 (MQ=255)                                        cGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGt                                                                                             <  1:204751/139‑1 (MQ=255)                                                    aCCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCa                                                                                 >  2:204533/1‑139 (MQ=255)                                                                      caTTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAAcc                                                                                        >  1:165743/1‑114 (MQ=255)                                                                      caTTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAAcc                                                                                        <  2:165743/114‑1 (MQ=255)                                                                                   tGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtg                                                  >  2:74547/1‑139 (MQ=255)                                                                                   tGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtg                                                  >  2:257478/1‑139 (MQ=255)                                                                                   tGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtg                                                  <  2:256528/139‑1 (MQ=255)                                                                                     acacCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGAcgcg                                                                         <  2:256753/114‑1 (MQ=255)                                                                                     acacCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGAcgcg                                                                         >  1:256753/1‑114 (MQ=255)                                                                                      cacCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgctg                                               <  1:252703/139‑1 (MQ=255)                                                                                      cacCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgctg                                               <  2:43292/139‑1 (MQ=255)                                                                                       acCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgctgc                                              <  2:459872/139‑1 (MQ=255)                                                                                       acCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgctgc                                              <  1:257478/139‑1 (MQ=255)                                                                                           aTCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTa                                          >  2:199253/1‑139 (MQ=255)                                                                                            tCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATgctgct                                             <  2:426145/135‑1 (MQ=255)                                                                                            tCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATgctgct                                             >  1:426145/1‑135 (MQ=255)                                                                                              gTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCt                                       <  1:504702/139‑1 (MQ=255)                                                                                               tGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgctg                                               <  2:167357/130‑1 (MQ=255)                                                                                               tGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgctg                                               >  1:167357/1‑130 (MQ=255)                                                                                               tGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTa                                      >  1:457525/1‑139 (MQ=255)                                                                                                gCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGt                                                                                             >  1:315864/1‑83 (MQ=255)                                                                                                gCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGt                                                                                             <  2:315864/83‑1 (MQ=255)                                                                                                    gcgcAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACtttt                                 <  1:204533/139‑1 (MQ=255)                                                                                                        aGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTttcttc                             <  2:425396/139‑1 (MQ=255)                                                                                                         gaactgaactGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTcc                            <  1:199253/139‑1 (MQ=255)                                                                                                                    gCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAAcc                                                                                        <  1:224677/68‑1 (MQ=255)                                                                                                                    gCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAAcc                                                                                        >  2:224677/1‑68 (MQ=255)                                                                                                                    gCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACtttt                                 <  2:156737/123‑1 (MQ=255)                                                                                                                    gCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACtttt                                 >  1:156737/1‑123 (MQ=255)                                                                                                                            cGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAgg                                                                               <  2:460974/69‑1 (MQ=255)                                                                                                                            cGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAgg                                                                               >  1:460974/1‑69 (MQ=255)                                                                                                                                   aTTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCTGAAATCGAAc  <  2:457525/139‑1 (MQ=255)                                                                                                                                        |                                                                                                                                      ATCAGGCGATCATTGGTCACCAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCACCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCTGAAATCGAAC  >  NC_000913/4486906‑4487174

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑