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	93.3%	221.7 / 5.3	60	Y174D (TAC→GAC)	proS	proline‑‑tRNA ligase
Reads supporting (aligned to +/- strand):  ref base A (1/3);  new base C (28/28);  total (29/31)
Fisher's exact test for biased strand distribution p-value = 6.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.50e-01

ATAGAACCGGTGTCGGCTTGTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTAGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATGACGCCGAAACGC  >  NZ_CP009273/214658‑214828                                                                                      |                                                                                      aTAGAACCGGTGT‑GGCTTGTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGttt                                                                                  <  2:677950/90‑1 (MQ=255)       ccGGTGTCGGCTTGTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGc                                                                             <  2:385593/90‑1 (MQ=255)         ggTGTCGGCTTGTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAg                                                                           >  2:242361/1‑90 (MQ=255)         ggTGTCGGCTTGTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAg                                                                           <  2:462087/90‑1 (MQ=255)           tgtCGGCTTGTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAggg                                                                         <  2:546080/90‑1 (MQ=255)           tgtCGGCTTGTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAggg                                                                         <  2:1561292/90‑1 (MQ=255)              cGGCTTGTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGAtt                                                                      >  1:230288/1‑90 (MQ=255)               ggCTTGTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTc                                                                     <  1:1331459/90‑1 (MQ=255)                  ttGTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTg                                                                  <  1:242361/90‑1 (MQ=255)                    gTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTgag                                                                >  2:827297/1‑90 (MQ=255)                    gTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTgag                                                                >  2:166925/1‑90 (MQ=255)                    gTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTgag                                                                <  1:827297/90‑1 (MQ=255)                     tACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTgaga                                                               <  1:1141830/90‑1 (MQ=255)                      aCGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGaa                                                              <  1:700980/90‑1 (MQ=255)                      aCGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGaa                                                              <  1:1588083/90‑1 (MQ=255)                         gcgcGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTa                                                           >  2:689955/1‑90 (MQ=255)                         gcgcGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTa                                                           >  2:250278/1‑90 (MQ=255)                         gcgcGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTa                                                           >  1:1188966/1‑90 (MQ=255)                         gcgcGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTa                                                           >  1:235038/1‑90 (MQ=255)                           gcgGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTAGGTTTCCTGCAGGGATTCCTGAGAAGt                                                            >  1:757198/1‑87 (MQ=255)                           gcgGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTAGGTTTCCTGCAGGGATTCCTGAGAAGt                                                            <  2:757198/87‑1 (MQ=255)                             ggAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTAGGTTTCCTGCAGGGATTCCTGAGAAGTATGGa                                                       <  1:328557/90‑1 (MQ=255)                              gAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGaa                                                      >  2:1560452/1‑90 (MQ=255)                              gAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGaa                                                      <  1:1366655/90‑1 (MQ=255)                              gAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGaa                                                      <  1:734881/90‑1 (MQ=255)                              gAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGaa                                                      <  2:27740/90‑1 (MQ=255)                              gAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTAGGTTTCCTGCAGGGATTCCTGAGAAGTATGGaa                                                      <  2:1639662/90‑1 (MQ=255)                               aaaTCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGaaa                                                     <  2:637431/90‑1 (MQ=255)                                aaTCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAag                                                    <  2:1188966/90‑1 (MQ=255)                                       ccccATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGc                                             <  1:474734/90‑1 (MQ=255)                                       ccccATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGc                                             <  2:1083678/90‑1 (MQ=255)                                         ccATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCAt                                           <  1:1390423/90‑1 (MQ=255)                                          cATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATc                                          >  2:110918/1‑90 (MQ=255)                                           aTGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGTTTCCTGGGAAGAATGGAAAGGGAAACCAttt                                         >  1:1462767/1‑88 (MQ=255)                                           aTGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGt                                                            >  2:1543977/1‑71 (MQ=255)                                           aTGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGt                                                            <  1:1543977/71‑1 (MQ=255)                                           aTGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGc                                             <  2:1580040/86‑1 (MQ=255)                                           aTGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGc                                             >  1:1580040/1‑86 (MQ=255)                                           aTGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCt                                         >  2:1574252/1‑90 (MQ=255)                                           aTGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCt                                         >  1:144529/1‑90 (MQ=255)                                                          ttGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTcg                          >  2:1389680/1‑90 (MQ=255)                                                          ttGCTGTAGGCCGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTcg                          >  2:903856/1‑90 (MQ=255)                                                                    ccGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCa                >  2:1505339/1‑90 (MQ=255)                                                                     cGCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCAt               <  2:230288/90‑1 (MQ=255)                                                                      gCATACATTGCATCGTCGGTTTCCTGCAGGGATTc                                                                     >  2:134153/1‑35 (MQ=38)                                                                      gCATACATTGCATCGTCGGTTTCCTGCAGGGATTc                                                                     <  1:134153/35‑1 (MQ=38)                                                                      gCATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATg              >  2:1580348/1‑90 (MQ=255)                                                                       cATACATTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATGa             <  1:1130345/90‑1 (MQ=255)                                                                            aTTGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATGACGCCg        <  1:186662/90‑1 (MQ=255)                                                                             ttGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGc                                             <  1:1505550/52‑1 (MQ=255)                                                                             ttGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGc                                             >  2:1505550/1‑52 (MQ=255)                                                                             ttGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATGACGCCGa       >  2:262966/1‑90 (MQ=255)                                                                              tGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATGACGCCGaa      >  2:927309/1‑90 (MQ=255)                                                                              tGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATGACGCCGaa      <  1:110918/90‑1 (MQ=255)                                                                              tGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATGACGCCGaa      >  2:1296743/1‑90 (MQ=255)                                                                              tGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATGACGCCGaa      >  2:1207267/1‑90 (MQ=255)                                                                              tGCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATGACGCCGaa      >  1:1237631/1‑90 (MQ=255)                                                                               gCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATGACGCCGaaa     >  2:459569/1‑90 (MQ=255)                                                                               gCATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATGACGCCGaaa     >  2:1326099/1‑90 (MQ=255)                                                                                cATCGTCGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATGACGCCGAAAc    <  1:262966/90‑1 (MQ=255)                                                                                  tcgtcgGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATGACGCCGAAAcgc  >  2:1114096/1‑90 (MQ=255)                                                                                      |                                                                                      ATAGAACCGGTGTCGGCTTGTACGGCGCGGAAATCCAGCCCCATGCGGCTGAAGATTTTGCTGTAGGCCGCATACATTGCATCGTAGGTTTCCTGCAGGGATTCCTGAGAAGTATGGAAAGAGTAAGCATCTTTCATCAGGAATTCGCGGGAACGCATGACGCCGAAACGC  >  NZ_CP009273/214658‑214828

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑