Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	214,743	A→C	Y174D (TAC→GAC)	proS ←	proline‑‑tRNA ligase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	214,743	0	A	C	94.1%	118.5 / ‑0.8	34	Y174D (TAC→GAC)	proS	proline‑‑tRNA ligase
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base C (12/20);  total (13/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.86e-01

TGTCGGCTTGTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTAGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATGACGCCGAAACG  >  NZ_CP009273/214668‑214827                                                                            |                                                                                     tgtCGGCTTGTACGGCGAGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAggg                                                                        <  1:1583828/90‑1 (MQ=255)   tCGGCTTGTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGAt                                                                      <  2:740264/90‑1 (MQ=255)      gCTTGTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTcc                                                                   <  2:530245/90‑1 (MQ=255)          gTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTgag                                                               <  2:1433057/90‑1 (MQ=255)          gTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTgag                                                               >  1:204634/1‑90 (MQ=255)          gTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTgag                                                               >  1:347551/1‑90 (MQ=255)            tcGGCGCTGAAATCCAGCCCCATGCGGCTGAAGATTTTGTTGTAGGCCGCATACATTGCACCGTCGGTTTCCTGCAGGGATCCCTGAGaa                                                             <  1:376217/89‑1 (MQ=255)            aCGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGaa                                                             <  1:707019/90‑1 (MQ=255)            aCGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGaa                                                             <  1:1452975/90‑1 (MQ=255)            aCGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGaa                                                             <  2:347551/90‑1 (MQ=255)              ggCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGt                                                           <  2:70003/90‑1 (MQ=255)                 gcgGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATg                                                        >  1:854523/1‑90 (MQ=255)                    gAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGaa                                                     <  2:455787/90‑1 (MQ=255)                    gAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGaa                                                     <  1:1315839/90‑1 (MQ=255)                    gAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGaa                                                     <  2:956480/90‑1 (MQ=255)                           aGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTgag                                                               >  2:1243728/1‑73 (MQ=255)                           aGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTgag                                                               <  1:1243728/73‑1 (MQ=255)                                 aTGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAggg                                                                        <  2:1187539/58‑1 (MQ=255)                                 aTGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAggg                                                                        >  1:1187539/1‑58 (MQ=255)                                 aTGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTgaga                                                              >  2:1292723/1‑68 (MQ=255)                                 aTGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTgaga                                                              <  1:1292723/68‑1 (MQ=255)                                      gCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTtcat                                   >  2:400897/1‑90 (MQ=255)                                                      tAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGaa                   <  2:440185/90‑1 (MQ=255)                                                           cGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCAt              <  1:400897/90‑1 (MQ=255)                                                            gCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTgag                                                               >  2:1413876/1‑40 (MQ=39)                                                            gCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTgag                                                               <  1:1413876/40‑1 (MQ=39)                                                            gCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATg             >  1:1566500/1‑90 (MQ=255)                                                            gCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATg             >  1:901814/1‑90 (MQ=255)                                                            gCATACATTGCATCGTAGGTTTCCTGCAGGGATTCCTGAGAAGTATGGaa                                                     <  1:53042/50‑1 (MQ=255)                                                            gCATACATTGCATCGTAGGTTTCCTGCAGGGATTCCTGAGAAGTATGGaa                                                     >  2:53042/1‑50 (MQ=255)                                                                   ttGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATg             <  1:678898/83‑1 (MQ=255)                                                                   ttGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATg             >  2:678898/1‑83 (MQ=255)                                                                      cATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATGACGCCGAAAc   <  1:295178/90‑1 (MQ=255)                                                                       aTCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATGACGCCGAAAcg  >  2:276132/1‑90 (MQ=255)                                                                            |                                                                                     TGTCGGCTTGTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTAGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATGACGCCGAAACG  >  NZ_CP009273/214668‑214827

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑