Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,592,082	G→A	L142L (CTG→CTA)	tsr →	methyl‑accepting chemotaxis protein Tsr

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,592,082	0	G	A	81.5%	45.4 / 6.0	29	L142L (CTG→CTA)	tsr	methyl‑accepting chemotaxis protein Tsr
Reads supporting (aligned to +/- strand):  ref base G (2/3);  new base A (13/9);  total (16/13)
Fisher's exact test for biased strand distribution p-value = 6.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.24e-01

TGTTGCAGACGCGTAACACCCTCAACCGCGCGGGTATCCGCTACATGATGGATCAGAATAATATTGGTAGCGGTTCAACCGTTGCTGAGCTGATGGAGAGTGCCAGTATTTCGCTGAAACAGGCGGAAAAAAACTGGGCGGATTACGAAGCGTTGCCGCGTGACCCGCGTCAGAGCACCGCCGCAGCGGCAGAGATCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTGTTAGGTGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GACCCAGGGATATCAGGACGGTTTCGAGAAGCAGTATGTGGCTTACATGGAGCAAAACGATCGGCTCCATGATATCGCCGTCAGCGATAACAATGCCTCCTACAGCCAGGCGATGTGGATTCTGGTGGGCGTGATGATCGTCGTACTGGCGGTCATCTTCGCCGTCTGGTTCGGTATTAAAGCCTCGCTGGTAGCGCCAATGAATCGC  >  NC_000913/4591835‑4592328                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                        ggttgcagctgagTAACCCCATCACCCGCGGGGGTCTCCGCTTTATGATGGATCAGAAAAAAATTGGTAGCGGTGCAACCGTTGCTGAGCGGATTCAGTGTGCCATAATTCCCCTGAAACAGGCGAAAAAAAATGGGGCAGATGACAAAGCGTTGCCGCGGGACCCGCGTCAGAGCCCCGCCGCAGCGGCAGAGATCAAACGTAATTACGATATTTAGCACAAGGCGCTGGCGGAGCTGATCCAACTATTa                                                                                                                                                                                                                                                      <  2:224919/239‑1 (MQ=255)               aaCACCCTCAACCGCGCGGGTATCCGCTACATGATGGATCAGAATAATATTGGTAGCGGTTCAACCGTTGCTGAGCTGATGCAGAGTGCCAGTATTTCGCTGAAACAGGCGGAAAAAAACTGGGCAGATTACGAAGCGTTGCCGCGTGACCCGCGTCAGAGCACCGCCGCAGCGGCAGAGATCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTATTAGGTGCAGGCAAAAt                                                                                                                                                                                                                                        >  1:10717/1‑251 (MQ=255)                 cacCCTCAACCGCGCGGGTATCCGCTAAATGATGGATCAGAATAATATTGGTAGCGGTTAAACCGTTGCTGAGCTGATGCAGAGTGCCAGTATTTCGCTGAAACAGGCGGAAAAAAACTGGGCAGATTACGAAGCGTTGCCGCGTGACCCGCGTCAGAGCACCGCCGCAGCGGCAGAGATCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTATTAGGTGCAGGCAAAATCa                                                                                                                                                                                                                                      <  1:1992/251‑1 (MQ=255)                   cccTCAACCGCGCGGGTATCCGCTACATGATGGATCAGAATAATATTGGTAGCGGTTCAACCGTTGCTGAGCTGATGCAGAGTGCCAGAATTTCGCTGAAACAGGCGGAAAAAAACTGGGCAGATTACGAAGCGTTGCCGCGTGACCCGCGTCAGAGCACCGCCGCAGAGGCAGAGATCAAACGTAATTACGATATTTATCACAATGCGCTGGAGGAGCTGATCCAACTATTAGGTGCAGGCAAAATCAAc                                                                                                                                                                                                                                    >  1:233252/1‑251 (MQ=255)                         aCCGCGCGGGTATCCGCTACATGATGGATCAGAATAATATTGGTAGCGGTTCAACCGTTGCTGAGCTGATGGAGAGTGCCGGTATTTCGCTGAAACAGGCGGAAAAAAACTGGGCGGATTACGAAGCGTTGCCGCGTGACCCGCGTCAGAGCACCGCCGCAGCGGCAGAGATCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTGTTAGGTGCAGGCAAAATCAACGAGTTc                                                                                                                                                                                                                              <  1:48817/251‑1 (MQ=255)                               cgGGTATCCGCTACATGATGGATCAGAATAATATGGGTAGCGGTTCAACCGTTGCTGAGCTGATGCAGAGTGCCAGTATTTCGCTGAAACAGGCGGAAAAAAACTGGGCAGATTACGAAGCGTTGCCGCGTGACCCGCGTCAGAGCACCGCCGCAGCGGCAGAGATCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTATTAGGTGCAGGCAAAATCAACGAGTTCTTTGAt                                                                                                                                                                                                                        <  1:65764/251‑1 (MQ=255)                                              tgatgGATCAGAATAATATTGGTAGCGGTTCAACCGTTGCTGAGCTGATGGAGAGTGCCAGTATTTCGCTGAAACAGGCGGACAAAAACTGGGCGAATTACGAAGCGTTGCAGCGTGACCCGCGTCAGAGCACCGCCGCAGCGGCAGCGATCAAACGTAATTACGATATTTCTCACACGGCGCTGGCGGAGATGATCCAACTGTTAGGTGCAGGCAAAATCACCGAGATCATTGATCAGCCAGACCCAgg                                                                                                                                                                                                          >  2:153345/1‑250 (MQ=255)                                                         cataataTTGGTAGCGGTTCAACCGTTGCTGAGCTGATGCAGCGTGCCAGTCTTTCGCTGAAACAGGCGGTAACCACCTGGGCAGATTCCGATGCGTTGCCGCGTGACCCGCGTCAGAGCACCGCCGCGGCGGCAGAGATCATCCGTCATTTCGATATTTATCACAATGAGCTGGCGGAGCTGATCCAACTTTTAAGTGCAGGCTAATTCTACGCGTTCTTTGTTATGCC‑GACCCATGGATATCGGGACgg                                                                                                                                                                                             >  2:37362/2‑251 (MQ=255)                                                          ataataTTGGTAGCGGTTCACCCGTTGCTGAGCTGATGGAGAGTGCCAGTATTTCGCTGAACCAGGCGGAAAAAAACTGGGCGGATTCCGAAGCGTTGCCGCGTGACCCGCGTCAGAGCACCGCCGCAGCGGCAGAGATCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTGTTAGGTGCAGGCAAAATCAACGAGTTCTTGGATCAGCC‑GACCCAGGGATATCAGGACGGt                                                                                                                                                                                            <  1:153345/251‑1 (MQ=255)                                                                             aaCCGTTGGTGAGCTGAGGGAGAGGGCCGGTATTTCGCTGAAACAGGCGGAAAAAAACTGGGCGGATTACGAAGCGTTGCCGTGTGACCCGCGTCAGAGCACCGCCGCAGCGGCAGAGATCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTGTTAGGTGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GATCCAGGGATATCAGGACGGTTTCGAGAAGCAGTATGTgg                                                                                                                                                                         <  1:147478/251‑1 (MQ=255)                                                                             aaCCGTTGCTGAGCTGATGCAGAGTGCCAGTATTTCGCTGAAACAGGCGGAAAAAAACTGGGCAGATTACGAAGCGTTGCCGCGTGACCCGCGTCAGAGCACCGCCGCAGCGGCAGAGATCAACCGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTATTAGGTGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GACCCAGGGATATCAGGACGGTTTCGAGAAGAAGTATGTgg                                                                                                                                                                         >  1:76699/1‑251 (MQ=255)                                                                                cGTTGCTGAGCTGATGCAGAGTGCCAGTATTTCGCTGAAACAGGCGGAAAAAAACTGGGCAGATTACGAAGCGTTGCCGCGTGACCCGCGTCAGAGCACCGCCGCAGCGGCAGAGATCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTATTAGGTGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GACCCAGGGATATCAGGACGGTTTCGAGAAGCAGTATGTGGCtt                                                                                                                                                                      >  1:165706/1‑251 (MQ=255)                                                                                 gTTGCTGAGCTGATGCAGAGTGCCAGTATTTCGATGAAACAGGCGGAAAAAAACTGGGCAGATTACGAAGCGTTGCCGCGTGACCCGCGTCAGAGCACCGCCGCAGCGGCAGAGATCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTATTAGGTGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GACCCAGGGATATCAGGACGGTTTCGAGAAGCAGTATGTGGCttc                                                                                                                                                                     >  1:296395/1‑250 (MQ=255)                                                                                        agctgaTGCAGAGTACCAGTATTTCGCTGAAACAGGCGGAAAAAAACTGGGCAGATTACGAAGCGTTGCCGCGTGACCCGCGTCAGAGCACCGCCGCAGCGGCAGAGATCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTATTAGGTGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GACCCAGGGATATCAGGCCGGTTTCGAGAAGCAGTATGTGGCTTACATgg                                                                                                                                                                >  1:282295/1‑249 (MQ=255)                                                                                                   agggCCAGTATTTGCCTGAACCAGGCGGAAAAAAACTGGGCAGATTACGAAGCGTTGCCGCTTGACCCGCGTCAGAGCACCGCCGCAGCGGCAGAGATCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTATTAGGTGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GACCCAGGGATATCAGGACGGTTTCGAGAAGCAGTATGTGGCTTACATGGAGCAAAACGATCg                                                                                                                                                   <  1:193823/248‑1 (MQ=255)                                                                                                      gCCAGTATTTCGCTGAAACAGGCGGCAAAAAACTGGGCAGATTACGAAGCGTTGCCGCGTGACCCGCGTCAGAGCACCGCCGCAGCGGCAGAGATCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTATTAGGTGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GACCCAGGGATATCAGTACGGTTTCGAGAAGCAGTATGTGGCTTACATGGAGCAAAACGATCGGCt                                                                                                                                                >  1:307004/1‑251 (MQ=255)                                                                                                                      accAGGCGGAAAAAAACGGGGCAGATTACGAAGCGTTGCCGCGGGACCCGCGTCAGAGCACCGCCGCAGCGGCAGAGATCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTATTAGGTGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GACCCAGGGATATCAGGACGGTTTCGAGAAGCAGTATGTGGCTTACATGGAGCAAAACGATCGGCTCTATGATATCGCCGTc                                                                                                                                <  1:147019/249‑1 (MQ=255)                                                                                                                                   aaaCTGGGCAGATTACGAAGCGTTGCCGCGTGACCCGCGTCAGAGCACCGCCGCAGCGGCAGAGATCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTATTAGGTGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GACCCAGGGATATCAGGACGGTTTCGAGAAGCAGTATGTGGCTTACATGGAGCAAAACGATCGGCTCTATGATATCGCCGTCAGCGATAACAATg                                                                                                                   >  1:102649/1‑251 (MQ=255)                                                                                                                                   aaaCTGGGCAGATTACGAAGCGTTGCCGCGTAACCCGCGACAGAGCACCGCCGCAAAGGCAGAGATCAACCGAAATTACGATATTTATCACAATTCGCTGGCGGAGCTGATCCAACTATTTGGTGCAGGCAAAATCAACGCGTTATTTGATAAGCC‑GACCCAGGGATATCCGGACGGTTTCGAGAAGCAGTATGTGGCTTACATGGAGCAAAACGGACGGATCTATAATATCGCCGTCAGCGATAACAATg                                                                                                                   >  2:328884/1‑251 (MQ=255)                                                                                                                                            agATTACGAAGGTTTCCCGCGTGTCCCGTGTCAGAGATCCGCCGCAGCGGCAGAGATCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTATTAGGTGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GACCCAGTGATATCAGGACGGTTTCGAGAAGCAGTATGTGGCTTACATGGAGCAAAACTATCGGCTCTATGATATCGCCGTCAGCGAGAACAATGCCTCCTACa                                                                                                          <  1:341447/250‑1 (MQ=255)                                                                                                                                                                                                gagaTCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTGTTAGGTGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GACCCAGGGATATCAGGACGGTTTCGAGAAGCAGTATGTGGCTTACATGGAGCAAAACGATCGGCTCCATGATATCGCCGTCAGCGATAACAATGCCTCCTACAGCCAGGCGATGTGGATTCTGGTGGGCGTGATGATCGGCGTACTGGCGGTCAt                                                      >  2:75180/1‑251 (MQ=255)                                                                                                                                                                                                 agaTCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTTTTAGGTGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GACCCAGGGATATTAGGACTGTTTCGAGAAGCAGTATGTTGCTTACATGGAGCAAAACGATCGGCTCCATGATATCGCCGTCAGCGATAACAATGCCTCCTACATCCAGGCGATTTGGAGTCTGGTGGGCGTGATGATCGTCGTACTGGCGGTCATc                                                     <  1:113573/251‑1 (MQ=255)                                                                                                                                                                                                  gaTCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTATTAGGTGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GACCCAGGGATATCAGGACGGTTTCGAGAAGCAGTATGTGGCTTACATGGAGCAAAACGATCGGCTCTATGATATCGCCGTCAGCGATAACAATGCCTCCTACAGCCAGGCGATGTGGATTCTGGTGGGCGTGATGATCGTCGTACTGGCGGTCctct                                                    >  1:173040/1‑251 (MQ=255)                                                                                                                                                                                                    tCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTATTAGGTGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GACCCAGGGATATCAGGACGGTTTCGAGAAGCAGTATGTGGCTTACATGGAGCAAAACGATCGGCTCTATGATATCGCCGTCAGCAATAACAATGCCTCCTACAGCCAGGCGATGTGGATTCTGGTGGGCGTGATGATCGTCGTACTGGCGGTAATCttt                                                  >  1:11613/1‑250 (MQ=255)                                                                                                                                                                                                                        tATCACAATTCGCGGGCGGATCTGATCCAACTATTAGGAGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GACCCAGGGATATCAGGACGGTTTCTAGAAGCAGTATGTGGCTTACATGGAGCAAAACGATCGGCTCTATGATATCGCCGTCAGCGATAACAATGCCTCCTACAGCCAGGCGATGTGGATTCTGGTGGGCGTGATGATCGTCGTACTGGCGGTCATCTTCGCCGTCTGGTTCGGTATTa                               <  2:173040/250‑1 (MQ=255)                                                                                                                                                                                                                         agcacaATGCGCTGGCGGAGCTGATCCAACTATTAGGTGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GACCCAGGGATATCAGGACGGTTTCGAGAAGCAGTATGTGGCTTACATGGAGCAAAACGATCGGCTCTATGATATCGCCGTCAGCGATAACAATGCCTCCTACAGCCAGGCGATGTGGATTCTGGTGGGCGTGATGATCGTCGTACTGGCGGTCATCTTCGCCGTCTGGTTCGGTATTaaa                             <  1:174174/249‑1 (MQ=255)                                                                                                                                                                                                                                  cgcTGGCGGAGCTGATCCAACTATTAGGTGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GACCCAGGGATATCAGGACGGTTTCGAGAAGCAGTATGTGGCTTACATGGAGCAAAACGATCGGCTCTATGATATCGCCGTCAGCGATAACAATGCCTCCTACAGCCAGGCGATGTGGATTCTGGTGGGCGTGATGATCGTCGTACTGGCGGTCATATTCCCCGTTTGGGTTGGTGTTAAAGACTCGcct                    >  1:357417/1‑249 (MQ=255)                                                                                                                                                                                                                                                 gccAACTATTAGGGGCTGGTAAAATCAACGAGTTCTTTGAGCCGCC‑GACCCAGGGATATCAGGACGGTTTCGATAAGCAGTATTTCGCTTACAGGGAGCAAAACGATCGGCTCTATGATATCGCCGTCAGCGATAACAATGCCTCCTACAGCCAGGCGATGTGGATTCTTGTGGTCGTGATGATCGTCGTACTGGCGGTCATCTTCGCCGTCTGGTTCGGTATTAAAGCCTCGCTGGTAGCGCCAATGAAt     <  1:217961/250‑1 (MQ=255)                                                                                                                                                                                                                                                    aaCTATTAGGTGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GACCCAGGGATATCAGGACGGTTTCGAGAAGCAGTATGTGGCTTACATGGAGCAAAACGCTCGGCTCTATGATATCGCCGTCAGCGATAACAATGCCTCCTACAGCCAGGCGATGTGGATTCTGGTGGGCGTGATGATCGTCGTACTGGCGGTCATCTTGTCCGTCTGGTTCGGGCTTTAAGCCTAGCTGGGAGCGCCAATGAATCGc  >  1:33635/1‑251 (MQ=255)                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                        TGTTGCAGACGCGTAACACCCTCAACCGCGCGGGTATCCGCTACATGATGGATCAGAATAATATTGGTAGCGGTTCAACCGTTGCTGAGCTGATGGAGAGTGCCAGTATTTCGCTGAAACAGGCGGAAAAAAACTGGGCGGATTACGAAGCGTTGCCGCGTGACCCGCGTCAGAGCACCGCCGCAGCGGCAGAGATCAAACGTAATTACGATATTTATCACAATGCGCTGGCGGAGCTGATCCAACTGTTAGGTGCAGGCAAAATCAACGAGTTCTTTGATCAGCC‑GACCCAGGGATATCAGGACGGTTTCGAGAAGCAGTATGTGGCTTACATGGAGCAAAACGATCGGCTCCATGATATCGCCGTCAGCGATAACAATGCCTCCTACAGCCAGGCGATGTGGATTCTGGTGGGCGTGATGATCGTCGTACTGGCGGTCATCTTCGCCGTCTGGTTCGGTATTAAAGCCTCGCTGGTAGCGCCAATGAATCGC  >  NC_000913/4591835‑4592328

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑