Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,044,642	T→C	intergenic (+18/‑296)	asnT → / → yeeJ	tRNA‑Asn/inverse autotransporter adhesin

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,044,642	0	T	C	96.4%	92.0 / ‑3.3	29	intergenic (+18/‑296)	asnT/yeeJ	tRNA‑Asn/inverse autotransporter adhesin
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (15/12);  total (15/14)
Fisher's exact test for biased strand distribution p-value = 4.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.39e-01

CTGCATCACGCTAATGATACAGACTCGTTTTCGGCGACGAATGTTCATTAATTAACAACTTTGCAGATTAATTAACCAATTGAAATGACTTATGAAATTTAGTGTTGACAGACAAGGTACCGCTAAGTAATATTCGCCCCGTTCACACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTTTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATAGCGGGTTTTTAACATCTTAAGCGCCCTCGACCTTTATGGTTGAGGGCGTTTTGCTATGAACGCCATCACCATTTTCCCCTCGATTATAAAACTTGAGTTATTCAGTAGTCTCCCCTCTTGCAACTCACACCCAAAACTGCCTAACGAAAAGTTATTAATTTTCAATCATATTGCTATCAGTATTTACAT  >  NC_000913/2044398‑2044881                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                cTGCATCACGCTAATGATACAGACTCGTTTTCGGCGACGAATGTTCATTAATTAACAACTTTGCAGATTAATTCACCAATTGAAATGACTTATGAAATTTAGTGTTGACAGACAAGGTACCGCTAAGTAATATTCGCCCCGTTCACACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCtctttt                                                                                                                                                                                                                                             >  2:23118/1‑249 (MQ=255)             aaTGATACAGACTCGTTTTCGGCGACGAATGTTCATTAAGTAACAACGTTGCAGATTAATTAACCAATTGAAATGACTTATGAAATTTAGTGTTGACAGACAAGGTACCGCTAAGTAATATTCGCCCCGTTCACACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCTTATGTCACTGGTTCGAGGCCAGTTAGAGGAGCCAAATTCTAAAAATTCGCTCTTATAGCGCAATGTCa                                                                                                                                                                                                                                 <  2:92143/249‑1 (MQ=37)                gATACAGACTCGTTTTCGGCGACGAATGTTCATTAATTAACAACTTTGCAGATTAATTAACCAATTGAAATGACTTATGAAATTTAGTGTTGACAGACAAGGTACCGCTAAGTAATATTCGCCCCGTTCACACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGAc                                                                                                                                                                                                                            <  1:119650/251‑1 (MQ=255)                      gACTTGTTTTCGGCGACGAATGTTGATTAATTAACAACTGTGCAGATTAATTAACCAATTGAAATGACTTATGAAATTTAGTGTTGACAGACAATGTACCGCTAAGTAAGATTCGCTCCTTTCACACGATTTCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAAGTCGGATGTCACTGGGTCTATTCCAGTTAGATGAGGCAAATTCTAAAAATTCGCTGTTTTTGCGCAATGTCACTGCCCTTAGt                                                                                                                                                                                                                      <  2:63180/251‑1 (MQ=255)                                            ttCATTAATTAACAACTTTGCAGATTAATTAACCAATTGAAATGACTTATGAAATTTAGTGTTGACAGACAAGGTACCGCTAAGTAATATTCGCCCCGTTCACACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGAt                                                                                                                                                                                                >  1:136553/1‑251 (MQ=255)                                             tCATTAATTAACAACTTTGGAGATTAATTAACCAATTGAAATGACTTATGAAATTTAGTGTTGACAGACAAGGTACCGCTAAGTAATATTCGCCACGTTCACACGATTCCTCTGTAGATCAGTAGGTAGAACGGCGGACTGTTAATCCGTATGACACTGGTTCGAGTCAAGTCAGAGGTGCCAATTTCTAAAAATTCGATCTTTTAGCGCCATGTCACTGACATACGTTGAACATTGTTTTTTCACGGAt                                                                                                                                                                                                >  2:316182/1‑250 (MQ=25)                                                   attaaCAACTTTGCAGATTAATTAACCAATTGAAATGACTTATGAAATTTAGTGTTGACAGACAAGGTACCGCTAAGTAATATTCGCCCCGTTCACACGATTCCTCTGTAGTCCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATAGCGGGt                                                                                                                                                                                         <  2:434127/251‑1 (MQ=255)                                                          acTTTGCAGATTAATTAACCAATTGAAATGACTTATGAAATTTAGTGTTGACAGACAAGGTACCGCTAAGTAATATTCGCCCCGTTCACACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATAGCGGGTTTTTAAc                                                                                                                                                                                  <  1:44609/251‑1 (MQ=255)                                                               gCAGATTAATTAACCAATTGAAATGACTTATGAAATTTAGTGTTGACAGACAAGGTACCGCTAAGTAATATTCGCCCCGTTCACACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATAGCGGGTTTTTAACATCtt                                                                                                                                                                             <  2:114339/251‑1 (MQ=255)                                                                                        aCTTATGAAATTTAGTGTTGACAGACAAGGTACCGCTAAGTCATATTCGCCCCGTTCACACGATTCCTCTGTCGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGCGTCCAGTCAGAGGAGCCAACTTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCTTAGtt                                                                                                                                                                                                                     >  2:262694/1‑186 (MQ=25)                                                                                        aCTTATGAAATTTAGTGTTGACAGACAAGGTACCGCTAAGTAATATTCGCCCCGTTCACACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCTTAGtt                                                                                                                                                                                                                     <  1:262694/186‑1 (MQ=255)                                                                                            aTGAAATTTAGTGTTGACAGACAAGGTACCGCTAAGTAATATTCGCCCCGTTCACACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATAGCGGGTTTTTAACATCTTAAGCGCCCTCGACCTTTATGGTTGAGGGc                                                                                                                                                <  2:248224/251‑1 (MQ=255)                                                                                              gAAATTCAGTGTTGACAGACAAGGTACCGCTAAGTAATATTCGCCCCGTTCACACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTCCTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATAGCGGGTTTTTAACATCTTAAGCGCCCTCGACCTTTATGGTTGAGGGCGt                                                                                                                                              >  1:128535/1‑251 (MQ=255)                                                                                                              agacaAGGTACCGCTACGTAATATTCGCCCCGTTCACACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATAGCGGGTTTTTAACATCTTAAGCGCCCTCGACCTTTATGGTTGAGGGCGTTTTGCTATGAACGcc                                                                                                                               >  2:42149/1‑250 (MQ=255)                                                                                                                  aaGGTACCGCTAAGTAATATTCGCCCCGTTCACACGATTCCTCTGTAGTTCAGACGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATAGCGGGTTTTTAACCTCTTAAGCGCCCTCGACCTTTATGGTTGAGGGCGTTTTGCTATGAACGCCATCAc                                                                                                                          >  1:61385/1‑251 (MQ=255)                                                                                                                                                 acacGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATAGCGGGTTTTTAACATCTTAAGCGCCCTCGACCTTTATGGTTGAGGGCGtttt                                                                                                                                           >  1:354771/1‑203 (MQ=255)                                                                                                                                                 acacGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATAGCGGGTTTTTAACATCTTAAGCGCCCTCGACCTTTATGGTTGAGGGCGtttt                                                                                                                                           <  2:354771/203‑1 (MQ=255)                                                                                                                                                                aGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTTTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATAGCGGGTTTTTAACATCTTAAGCGCCCTCGACCTTTATGGTTGAGGGCGTTTTGCTATGAACGCCATCACCATTTTCCCCTCGACTATAAAACTTGAGTTATTCAGTAGTCTccc                                                                             <  1:194566/250‑1 (MQ=255)                                                                                                                                                                   tCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGCGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATa                                                                                                                                                                                               >  2:408077/1‑133 (MQ=255)                                                                                                                                                                   tCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATa                                                                                                                                                                                               <  1:408077/133‑1 (MQ=255)                                                                                                                                                                      gTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATAGCGGGTTTTTAACATCTTAAGCGCCCTCGACCTTTATGGTTGAGGGCGTTTTGCTATGAACGCCATCACCATTTTCCCCTCGATTATAAAACTTGAGTTATTCAGTAGTCTCCCCTCTTGc                                                                      >  2:308000/1‑251 (MQ=255)                                                                                                                                                                        cGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCtt                                                                                                                                                                                                                         <  1:454487/102‑1 (MQ=255)                                                                                                                                                                        cGGTAGAACGGCGGACTGTTAATCAGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCtt                                                                                                                                                                                                                         >  2:454487/1‑102 (MQ=255)                                                                                                                                                                                                           ggTTCGAGTCCAGTCCGAGGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATAGCGGGTTTTTAACATCTTAAGCGCCCTCGACCTTTATGGTTGAGGGCGTTTTGCTATGAACGCCATCACCATTTTCCCCTCGATTATAAAACTTGAGTTATTCAGTAGTCTCCCCTCTTGCAACTCACACCCAAAACTGCCTAACGAAAAGatatta                                  >  1:388809/1‑250 (MQ=255)                                                                                                                                                                                                           ggTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATAGCGGGTTTTTAACATCTTAAGCGCCCTCGACCTTTATGGTTGAGGGCGTTTTGCTATGAACGCCATCACCATTTTCCCCTCGATTATAAAACTTGAGTTATTCAGTAGTCTCCCCTCTTGCAACTCACACCCAAAACTGCCTAACGCAAAGttatta                                  >  2:3197/1‑250 (MQ=255)                                                                                                                                                                                                                      aGTCAGAGGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATAGCGGGTTTTTAACATCTTAAGCGCCCTCGACCTTTATGGTTGAGGGCGTTTTGCTATGAACGCCATCACCATTTTCCCCTCGATTATAAAACTTGAGTTATTCAGTAGTCTCCCCTCTTGCAACTCACACCCAAAACTGCCTAACGAAAAGTTATTAATTTTCAATCat                      >  1:185941/1‑251 (MQ=255)                                                                                                                                                                                                                          agagGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATAGCGGGTTTTTAACATCTTAAGCGCCCTCGACCTTTATGGTTGAGGGCGTTTTGCTATGAACGCCATCACCATTTTCCCCTc                                                                                                              >  2:245830/1‑159 (MQ=255)                                                                                                                                                                                                                          agagGAGCCAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATAGCGGGTTTTTAACATCTTAAGCGCCCTCGACCTTTATGGTTGAGGGCGTTTTGCTATGAACGCCATCACCATTTTCCCCTc                                                                                                              <  1:245830/159‑1 (MQ=255)                                                                                                                                                                                                                                  cAAATTCTAAAAATTCGCTCTTTTAGCGCAATGTAACTGACCTTAGCTGCACATTGTTTTTTAACGGATAACGGGTTTTTACCATCTCAAGCGCCCTCGACATTTATGGTTGAGGGCGTTTTGCTATGCACGCCATCACCATTTTCCCCTCGATTATAATACTTGAGTTATTCAGTAGCCTCCCCTCTTGCAACTCACACCCAAAACTGCCTAACGAAAAGTTATTAATTTTCAATCATATTGCTATCAGt          >  1:286172/1‑251 (MQ=255)                                                                                                                                                                                                                                          aaaaaTTCGCTCTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATATCGGGTTTTTAACATCTTAAGCGCCCTCGACCTTTATGGTTGAGGGCGTTTTGCTATGAACGCCATCACCATTTTCCCCACGATTATAAAACTTGAGTTATTCAGTAGTCTCCCCTCTTTCAACTCACACCCAAAACTGGTTAACGAAAAGTTATGAATTTTCAATCATATGGCTATCATTGTTTACAt  <  2:29065/251‑1 (MQ=255)                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                CTGCATCACGCTAATGATACAGACTCGTTTTCGGCGACGAATGTTCATTAATTAACAACTTTGCAGATTAATTAACCAATTGAAATGACTTATGAAATTTAGTGTTGACAGACAAGGTACCGCTAAGTAATATTCGCCCCGTTCACACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCTAAAAATTCGCTTTTTTAGCGCAATGTCACTGACCTTAGTTGAACATTGTTTTTTAACGGATAGCGGGTTTTTAACATCTTAAGCGCCCTCGACCTTTATGGTTGAGGGCGTTTTGCTATGAACGCCATCACCATTTTCCCCTCGATTATAAAACTTGAGTTATTCAGTAGTCTCCCCTCTTGCAACTCACACCCAAAACTGCCTAACGAAAAGTTATTAATTTTCAATCATATTGCTATCAGTATTTACAT  >  NC_000913/2044398‑2044881

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑