Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,624,386	T→C	E522G (GAA→GGA)	yhiJ ←	YhiJ/YhiL family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,624,386	0	T	C	86.7%	105.2 / 11.4	45	E522G (GAA→GGA)	yhiJ	YhiJ/YhiL family protein
Reads supporting (aligned to +/- strand):  ref base T (3/3);  new base C (23/16);  total (26/19)
Fisher's exact test for biased strand distribution p-value = 6.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.15e-01

GTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCT  >  NZ_CP009273/3624299‑3624468                                                                                        |                                                                                   gTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCa                                                                                  >  1:86094/1‑90 (MQ=255)   aaCATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATg                                                                                <  1:161520/90‑1 (MQ=255)       ttAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTgg                                                                            >  2:422069/1‑90 (MQ=255)               cATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACtt                                                                    >  2:316134/1‑90 (MQ=255)               cATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACtt                                                                    >  1:534933/1‑90 (MQ=255)               cATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACtt                                                                    >  1:39695/1‑90 (MQ=255)                  gttgtCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCa                                                                 <  2:452927/90‑1 (MQ=255)                     gtCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAggg                                                              <  2:399100/90‑1 (MQ=255)                     gtCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAggg                                                              >  1:399100/1‑90 (MQ=255)                       cTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAg                                                            <  2:237200/90‑1 (MQ=255)                       cTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAg                                                            <  2:317612/90‑1 (MQ=255)                       cTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAg                                                            <  2:39695/90‑1 (MQ=255)                       cTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAg                                                            >  1:317612/1‑90 (MQ=255)                           ggTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGt                                                        <  2:32916/90‑1 (MQ=255)                                  agCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCa                                                 <  1:553073/90‑1 (MQ=255)                                  agCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCa                                                 <  1:217793/90‑1 (MQ=255)                                   gCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAg                                                >  2:384041/1‑90 (MQ=255)                                     tggaaCATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGc                                              <  1:130651/87‑1 (MQ=255)                                      gTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCa                                                                                  >  2:67540/1‑53 (MQ=255)                                      gTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCa                                                                                  <  1:67540/53‑1 (MQ=255)                                      gTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGcc                                             >  1:464420/1‑90 (MQ=255)                                      gTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGcc                                             >  2:186323/1‑90 (MQ=255)                                       tAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGccc                                            <  1:384041/90‑1 (MQ=255)                                             tgtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCAcc                                      >  1:360169/1‑90 (MQ=255)                                              gtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCa                                     <  2:416650/90‑1 (MQ=255)                                              gtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAggg                                                              <  2:533294/65‑1 (MQ=255)                                              gtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAggg                                                              >  1:533294/1‑65 (MQ=255)                                              gtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCa                                     >  2:532998/1‑90 (MQ=255)                                                gcgcCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAgg                                   >  2:351199/1‑90 (MQ=255)                                                gcgcCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAgg                                   >  1:448922/1‑90 (MQ=255)                                                   ccTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGATCGGTTATCTCAGGCCCTGCACCAGGGtt                                >  2:411290/1‑90 (MQ=255)                                                   ccTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGtt                                >  2:373206/1‑90 (MQ=255)                                                       cTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAAtt                            <  1:509673/90‑1 (MQ=255)                                                             aaaGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCaa                      >  1:538805/1‑90 (MQ=255)                                                             aaaGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCaa                      >  2:74748/1‑90 (MQ=255)                                                               aGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAAtt                    >  1:255494/1‑90 (MQ=255)                                                                   aTAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTatgc                >  2:491407/1‑90 (MQ=255)                                                                      aGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTatgcatg             <  2:322657/90‑1 (MQ=255)                                                                           aTTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGc                        <  1:358178/74‑1 (MQ=255)                                                                           aTTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGc                        >  2:358178/1‑74 (MQ=255)                                                                            tttCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTg                          >  1:222259/1‑71 (MQ=255)                                                                            tttCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTg                          <  2:222259/71‑1 (MQ=255)                                                                            tttCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGtt                                                       >  2:148509/1‑42 (MQ=255)                                                                            tttCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGtt                                                       <  1:148509/42‑1 (MQ=255)                                                                                 gTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACAttct  >  1:318580/1‑90 (MQ=255)                                                                                        |                                                                                   GTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCT  >  NZ_CP009273/3624299‑3624468

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑