Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,956,875	G→A	*515* (TAG→TAA)	ilvA →	l‑threonine dehydratase, biosynthetic, also known as threonine deaminase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,956,875	0	G	A	97.7%	135.8 / NA	43	*515* (TAG→TAA)	ilvA	l‑threonine dehydratase, biosynthetic, also known as threonine deaminase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (19/23);  minor base C (1/0);  total (20/23)
Fisher's exact test for biased strand distribution p-value = 4.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GACTACGGGCGCGTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAGGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGCCGCTTTTTCTGCGCACACACGCCCAGCTC  >  NC_000913/3956741‑3957010                                                                                                                                       |                                                                                                                                        gACTACGGGCGCGTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGaa                                                                                                                                     <  1:1275361/139‑1 (MQ=255)              tACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAg                                                                                                                        >  2:348996/1‑139 (MQ=255)                   gcggcgTTCGAACTTGGCGACCATGAACCGGATTTCTAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGcgctt                                                                                                                   <  2:1012363/139‑1 (MQ=255)                   gcggcgTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGcgctt                                                                                                                   >  2:672715/1‑139 (MQ=255)                       cgTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGaa                                                                                                                                     >  2:445763/1‑117 (MQ=255)                       cgTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGaa                                                                                                                                     <  1:445763/117‑1 (MQ=255)                        gTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAgcg                                                                                                                      >  2:290907/1‑131 (MQ=255)                        gTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAgcg                                                                                                                      <  1:290907/131‑1 (MQ=255)                         ttCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTa                                                                                                             >  1:1301594/1‑139 (MQ=255)                                            aaCCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGAc                                                                                          <  1:1535809/139‑1 (MQ=255)                                               cGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAAc                                                                                       <  1:883975/139‑1 (MQ=255)                                                 gATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGAc                                                                                          >  2:220431/1‑134 (MQ=255)                                                 gATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGAc                                                                                          <  1:220431/134‑1 (MQ=255)                                                  aTTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATg                                                                                                                                <  2:440849/95‑1 (MQ=255)                                                  aTTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATg                                                                                                                                >  1:440849/1‑95 (MQ=255)                                                           cccGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGt                                                                           <  2:1301594/139‑1 (MQ=255)                                                               gCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTACGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCgg                                                                       >  1:207641/1‑139 (MQ=255)                                                                             gCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTAt                                                                                                            >  2:282452/1‑88 (MQ=255)                                                                             gCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTAt                                                                                                            <  1:282452/88‑1 (MQ=255)                                                                             gCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGa                                                         >  1:846945/1‑139 (MQ=255)                                                                                aCGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATg                                                      <  1:348996/139‑1 (MQ=255)                                                                                aCGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATg                                                      <  2:705359/139‑1 (MQ=255)                                                                                      gCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCa                                                                     <  1:1111913/118‑1 (MQ=255)                                                                                      gCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCa                                                                     >  2:1111913/1‑118 (MQ=255)                                                                                      gCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCa                                                                     >  2:163986/1‑118 (MQ=255)                                                                                      gCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCa                                                                     <  1:163986/118‑1 (MQ=255)                                                                                      gCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCa                                                           >  2:924895/1‑128 (MQ=255)                                                                                      gCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCa                                                           <  1:924895/128‑1 (MQ=255)                                                                                         acgacgAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTa                                             <  2:846945/139‑1 (MQ=255)                                                                                          cgacgaAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAAATAg                                            <  1:195438/139‑1 (MQ=255)                                                                                                     aTAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTa                                 <  1:672715/139‑1 (MQ=255)                                                                                                     aTAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTa                                 >  1:166630/1‑139 (MQ=255)                                                                                                       aaCCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGcgcttcg                                                                                                                 >  2:321805/1‑57 (MQ=255)                                                                                                       aaCCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGcgcttcg                                                                                                                 <  1:321805/57‑1 (MQ=255)                                                                                                            ggCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGCCGCtt                          >  2:96840/1‑139 (MQ=255)                                                                                                             gCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAg                                            <  2:433547/120‑1 (MQ=255)                                                                                                             gCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAg                                            >  1:433547/1‑120 (MQ=255)                                                                                                             gCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGCCGCttt                         >  2:179251/1‑139 (MQ=255)                                                                                                               gTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGCCGCttttt                       <  2:166630/139‑1 (MQ=255)                                                                                                                  cAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGCCGCTTTTTCTg                    <  1:179251/139‑1 (MQ=255)                                                                                                                          ttttGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCAt                                    >  2:557443/1‑115 (MQ=255)                                                                                                                          ttttGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCAt                                    <  1:557443/115‑1 (MQ=255)                                                                                                                                    ttAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGCCGCTTTTTCTGCGCACACACGCCCAGCTc  >  1:512073/1‑139 (MQ=255)                                                                                                                                       |                                                                                                                                        GACTACGGGCGCGTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAGGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGCCGCTTTTTCTGCGCACACACGCCCAGCTC  >  NC_000913/3956741‑3957010

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑