Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,554,342	C→T	Q420* (CAA→TAA)	malT →	mal regulon transcriptional activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,554,342	0	C	T	97.6%	144.9 / ‑3.8	41	Q420* (CAA→TAA)	malT	mal regulon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (16/24);  total (17/24)
Fisher's exact test for biased strand distribution p-value = 4.15e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.14e-01

ATGCTGCGCGATATTCTGCTTAATCACGCCTGGAGTCTGTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGCAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTCTGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGG  >  NC_000913/3554198‑3554489                                                                                                                                                 |                                                                                                                                                    aTGCTGCGCGATATTCTGCTTAATCACGCCTGGAGTCTGTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGc                                                                                                                                                <  2:529387/150‑1 (MQ=255)    ctgcGCGATATTCTGCTTAATCACGCCTGGAGTCTGTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCaa                                                                                                                                             >  2:614315/1‑150 (MQ=255)       cgcgATATTCTGCTTAATCACGCCTGGAGTCTGTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACAt                                                                                                                                          <  2:453190/150‑1 (MQ=255)       cgcgATATTCTGCTTAATCACGCCTGGAGTCTGTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATc                                                                                                                                         <  2:168214/151‑1 (MQ=255)           atatTCTGCTTAATCACGCCTGGAGTCTGTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTa                                                                                                                                     >  1:557059/1‑151 (MQ=255)                          aCGCCTGGAGTCTGTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAacac                                                                                                                      <  2:506020/151‑1 (MQ=255)                          aCGCCTGGAGTCTGTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAacac                                                                                                                      <  1:609693/151‑1 (MQ=255)                           cGCCTGGAGTCTGTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAacac                                                                                                                      >  1:376688/1‑150 (MQ=255)                             ccTGGAGTCTGTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACAccc                                                                                                                    <  2:384291/150‑1 (MQ=255)                             ccTGGAGTCTGTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACAccc                                                                                                                    <  1:583029/150‑1 (MQ=255)                                 gAGTCTGTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGCAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTa                                                                                                               >  2:600818/1‑151 (MQ=255)                                    tCTGTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAg                                                                                                              <  2:479590/149‑1 (MQ=255)                                    tCTGTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGcc                                                                                                            <  2:142873/151‑1 (MQ=255)                                    tCTGTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGcc                                                                                                            <  1:353763/151‑1 (MQ=255)                                    tCTGTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACAGCGCTACGGCGAAGTTAACACCCTGCTAGcc                                                                                                            <  1:418369/151‑1 (MQ=255)                                    tCTGTTCAACCATAGCGAACTGCCGCTGCTGCAAGAGTCGCTGATGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGCCGGTGTTACTGCAGGCGTCGCTGATGTAAAGCGAATATCGGTACGGGGAAATTAACCCTATGCTAGcc                                                                                                            <  2:235794/151‑1 (MQ=255)                                     cTGTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACAccc                                                                                                                    >  1:440812/1‑142 (MQ=255)                                     cTGTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACAccc                                                                                                                    <  2:440803/142‑1 (MQ=255)                                       gTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGt                                                                                                         >  2:368253/1‑151 (MQ=255)                                         tCATCCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAACTCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAACCCCACATCGGTACGGCGAAGTTAACACCCTGCTTGCCCGTGc                                                                                                       <  2:158325/151‑1 (MQ=255)                                            aCCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGa                                                                                                    >  1:195921/1‑151 (MQ=255)                                            aCCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGa                                                                                                    >  1:92805/1‑151 (MQ=255)                                             ccATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGaa                                                                                                   >  1:474276/1‑151 (MQ=255)                                              cATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAAc                                                                                                  <  1:257925/151‑1 (MQ=255)                                               aTAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACa                                                                                                 >  1:249889/1‑151 (MQ=255)                                                      aCTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATc                                                                                          <  1:489381/151‑1 (MQ=255)                                                             ctgctgGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACa                                                                                   >  2:220673/1‑151 (MQ=255)                                                              cgctgGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACCCCCTGCTAGCCCGCGCTGAACATGAAATCAAGGACAt                                                                                  >  2:18766/2‑151 (MQ=255)                                                                 tgGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCag                                                                               <  1:432112/151‑1 (MQ=255)                                                                          cGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGacac                                                                      <  2:247455/151‑1 (MQ=255)                                                                              tAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATg                                                                  <  2:376683/151‑1 (MQ=255)                                                                                       gCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGaa                                                         >  2:344608/1‑151 (MQ=255)                                                                                              gACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAAc                                                   <  1:569190/150‑1 (MQ=255)                                                                                                   cTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGc                                                 <  2:154588/147‑1 (MQ=255)                                                                                                   cTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAACCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGctc                                               <  1:208524/149‑1 (MQ=255)                                                                                                              aTCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTCTGCGCGCCCAGGt                                  <  2:71593/151‑1 (MQ=255)                                                                                                                ccGCAGTTGGTGTTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTCTGCGCGCCCAGGTgg                                <  1:238923/151‑1 (MQ=255)                                                                                                                         gtgtTATTGCAGGCGTGGCTGATGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTCTGCGCGCCCAGGTGGCGATTAACg                       >  2:549282/1‑151 (MQ=255)                                                                                                                                              aTGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTCTGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCgg  >  2:156732/1‑151 (MQ=255)                                                                                                                                              aTGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTCTGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCgg  >  1:637502/1‑151 (MQ=255)                                                                                                                                              aTGTAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTCTGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCgg  >  2:619409/1‑151 (MQ=255)                                                                                                                                                 |                                                                                                                                                    ATGCTGCGCGATATTCTGCTTAATCACGCCTGGAGTCTGTTCAACCATAGCGAACTGTCGCTGCTGGAAGAGTCGCTTAAGGCCCTGCCGTGGGACAGCTTGCTGGAAAATCCGCAGTTGGTGTTATTGCAGGCGTGGCTGATGCAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTCTGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGG  >  NC_000913/3554198‑3554489

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑