Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,734,543	(C)8→9	coding (492/732 nt)	yfiH ←	UPF0124 family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,734,535	1	.	C	90.6%	104.0 / 4.2	32	coding (500/732 nt)	yfiH	UPF0124 family protein
Reads supporting (aligned to +/- strand):  ref base . (2/1);  new base C (11/18);  total (13/19)
Fisher's exact test for biased strand distribution p-value = 5.52e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCT‑CC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCC  >  NC_000913/2734414‑2734655                                                                                                                           |                                                                                                                          aaCACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGTACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGaa                                                                                                          <  2:10018/139‑1 (MQ=255) aaCACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGaa                                                                                                          <  2:1104309/139‑1 (MQ=255)              gCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCa                                                                                             >  1:256593/1‑139 (MQ=255)                   aCGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc                                                                                        <  2:898534/139‑1 (MQ=255)                   aCGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc                                                                                        <  1:209986/139‑1 (MQ=255)                   aCGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc                                                                                        <  2:598154/139‑1 (MQ=255)                   aCGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc                                                                                        <  2:304241/139‑1 (MQ=255)                   aCGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc                                                                                        <  2:256593/139‑1 (MQ=255)                   aCGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATACTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc                                                                                        <  2:307803/139‑1 (MQ=255)                        gCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGcc                                                                                   <  2:393331/139‑1 (MQ=255)                                        aaTATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAat                                                                   <  2:859368/139‑1 (MQ=255)                                               gCCAGATACTTATCACCATGCTGAATGAAAGCTGCGCTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCCTGGACCAATTGCCGGCCCTAACACGGCGAGAATATTTTcc                                                            >  1:445903/1‑139 (MQ=255)                                               gCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCT‑CC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCg                                                           >  2:563412/1‑139 (MQ=255)                                                ccAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc                                                                                        <  1:190227/110‑1 (MQ=255)                                                ccAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc                                                                                        >  2:190227/1‑110 (MQ=255)                                                    aTACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGAtt                                                       >  2:158774/1‑139 (MQ=255)                                                      aCTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTAt                                                     <  2:437771/139‑1 (MQ=255)                                                                 tGCTGAATGGAAGCTGCACTTGCTTTAGCGTCTACTGTCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACC‑GGCGAGAATATTTTCCGGATTATCAGCAAAACAgg                                         >  2:124213/1‑139 (MQ=255)                                                                 tGCTGAATGAAAGCTGCGCTTGCTGTAGCGTCTACTGCTGTAGACGACTCGCGTACCT‑CCGCCCCCTACTTCGAACACCCGTGGGCCACTTGCCGTCCCTATCCAGGCCAGCATGCTTCACGGGTTCTCAGGAAAACac                                          >  1:156666/1‑138 (MQ=255)                                                                 tGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc                                                                                        >  1:489230/1‑93 (MQ=255)                                                                 tGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc                                                                                        <  2:489230/93‑1 (MQ=255)                                                                                    ttGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCa                       <  2:521614/139‑1 (MQ=255)                                                                                             cGTCTACTGCCATAAACGCCTCGCGAACCT‑CC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca             <  1:563412/139‑1 (MQ=255)                                                                                              gTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGcaca             <  1:158774/139‑1 (MQ=255)                                                                                              gTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca             <  1:863009/139‑1 (MQ=255)                                                                                                cTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGcaca           >  1:446943/1‑139 (MQ=255)                                                                                                       cATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGCGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACg    >  2:741600/1‑139 (MQ=255)                                                                                                        aTAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACgc   >  1:1078241/1‑139 (MQ=255)                                                                                                        aTAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACgc   <  2:793926/139‑1 (MQ=255)                                                                                                         tAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAAAAGGAAACCGTCCCTTCCAGCACGCCTGCGCACAGTCCACgcc  >  1:916539/1‑139 (MQ=255)                                                                                                                 tCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAgg                                                                          <  2:39095/59‑1 (MQ=255)                                                                                                                 tCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAgg                                                                          >  1:39095/1‑59 (MQ=255)                                                                                                                           |                                                                                                                          AACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCT‑CC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCC  >  NC_000913/2734414‑2734655

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑