Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,765,827	Δ1 bp	coding (3645/4134 nt)	rhsA →	rhs element protein RhsA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,765,824	0	G	.	75.9%	30.3 / 38.0	29	coding (3642/4134 nt)	rhsA	rhs element protein RhsA
Reads supporting (aligned to +/- strand):  ref base G (5/2);  new base . (7/15);  total (12/17)
Fisher's exact test for biased strand distribution p-value = 9.20e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.21e-01

CTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTT  >  NC_000913/3765753‑3765899                                                                        |                                                                            cTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCA‑GGGCGGtata                                                                   <  1:678886/81‑1 (MQ=12) cTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCA‑GGGCGGtata                                                                   >  1:678923/1‑81 (MQ=12)  tGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGAACCGCTGCAGGGGCGGtata                                                                   >  1:678920/1‑81 (MQ=18)    ccGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGGtata                                                                   <  1:678887/79‑1 (MQ=34)    ccGGGGCAGCAGTATGATGAGGAGTCCAGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCA‑GGGCGGTatat                                                                  <  1:678888/79‑1 (MQ=11)      ggggCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCA‑GGGCGGTATATCACt                                                              >  2:678924/1‑81 (MQ=16)          cagcagTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCA‑GGGCGGTATATCACTCAgg                                                          <  2:678889/81‑1 (MQ=16)           agcagTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCA‑GGGCGGTATATCACTCAGGa                                                         >  1:678921/1‑81 (MQ=16)            gcagTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCA‑GGGCGGTATATCACTCAGGAt                                                        <  1:678890/81‑1 (MQ=16)                   gatgaGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCA‑GGGCGGTATATCACTCAGGATCCGATTg                                                 >  2:678919/1‑81 (MQ=16)                        ggagTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCA‑GGGCGGTATATCACTCAGGATCCGATTGGGCt                                             >  2:678933/1‑80 (MQ=255)                                  cTGTATTACAACCGCCACCGCTATTATGACCCGCTGCA‑GGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGAt                                  <  2:678891/81‑1 (MQ=16)                                     tATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGATg                                 >  2:678929/1‑80 (MQ=34)                                     tATTACAACCGCCACCGCTATTATGACCCGCTGCA‑GGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGATg                                 <  2:678894/79‑1 (MQ=255)                                     tATTACAACCGCCACCGCTATTATGACCCGCTGCA‑GGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGATGGa                               <  1:678893/81‑1 (MQ=16)                                     tATTACAACCGCCACCGCTATTATGACCCGCTGCA‑GGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGATGGa                               <  2:678892/81‑1 (MQ=16)                                      aTTACAACCGCCACCGCTATTATGACCCGCTGCA‑GGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGATGGaa                              >  1:678928/1‑81 (MQ=16)                                         aaaaCCGCCACCGCTATTATGACCCGCTGGA‑GGGCGGTATATCACTAAGGATCCGATTGGGCTGAAGGGGGGATGGAAtt                            <  1:678895/78‑1 (MQ=11)                                              cGCCACCGCTATTATGACCCGCTGCAGGGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGATGGAATTTTTAt                       >  2:678930/1‑81 (MQ=33)                                              cGCCACCGCTATTATGACCCGCTGCA‑GGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGATGGAATTTTTATc                      <  1:678897/81‑1 (MQ=16)                                              cGCCACCGCTATTATGACCCGCTGCA‑GGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGATGGAATTTTTATc                      <  1:678896/81‑1 (MQ=16)                                                ccACCGCTATTATGACCCGCTGCA‑GGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGATGGAATTTTTATCAg                    <  1:678898/81‑1 (MQ=16)                                                 cACCGCTATTATGACCCGCTGCAGGGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGATGGAATTTTTATCAg                    >  1:678932/1‑81 (MQ=33)                                                  aCCGCTATTATGACCCGCTGCA‑GGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGATGGAATTTTTATCAGTa                  >  1:678931/1‑81 (MQ=16)                                                      cTATTATGACCCGCTGCAGGGGCGGTATATCGCTCAGGATCCGATTGGGCTGAAGGGGGGATGGAATTTTTATCAGTATcc               <  2:678899/81‑1 (MQ=18)                                                        attatGATCCGCTGCAGGGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGATGGAATTTTTATCAGTATCCGt             >  2:678927/1‑81 (MQ=25)                                                         ttatGACCCGCTGCA‑GGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGATGGAATTTTTATCAGTATCCGtt            <  2:678900/80‑1 (MQ=255)                                                            tGACCCGCTGCA‑GGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGaa         <  2:678901/80‑1 (MQ=255)                                                                  gCTGCA‑GGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGtt  <  2:678902/81‑1 (MQ=255)                                                                        |                                                                            CTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTT  >  NC_000913/3765753‑3765899

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑