Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,814,459	Δ1 bp	coding (275/516 nt)	luxS ←	S‑ribosylhomocysteine lyase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,814,459	0	A	.	93.1%	112.8 / 1.3	29	coding (275/516 nt)	luxS	S‑ribosylhomocysteine lyase
Reads supporting (aligned to +/- strand):  ref base A (2/0);  new base . (11/16);  total (13/16)
Fisher's exact test for biased strand distribution p-value = 1.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

ACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGTTGATGCGTACGTCACGTTCCAGAATGCTACGCGCAATATCCTGCGCTTCCTGCAACGAGTGCATCTGGTAAGTGCCACACTGGTAGACGTTCAGTTCCGGGATCTGATTCTGATCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCAATCAGACTCATATAAAAACC‑GGTGCGGCAGCCCATTGGCGAGATATCGATAATCTCTACACCATTACCGTTAAGATGGTTACGCATAAAACCAGCAAACAGGTGCTCCAGGGTATGGATCCCTCTTTCTGGCATCACTTCTTTGTTCGGCACGCAGAAGCGCAGATCGAACACGGTGATTGCGTCGCCATGCGGGGTGTTCATTGTTTTCGCCACCCGAACTGCAGGCGCTTCCATCCGGGT  >  NC_000913/2814217‑2814700                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                   aCTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGTTGATGCGTACGTCACGTTCCAGAATGCTACGCGCAATATCCTGCGCTTCCTGCAACGAGTGCATCTGGTAAGTGCCACACTGGTAGACGTTCAGTTCCGGGATCTGATTCTGATCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCa                                                                                                                                                                                                                                           <  1:6464/251‑1 (MQ=255)          gCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGTTGATGCGTACGTCACGTTCCAGAATGCTACGCGCAATATCCTGCGCTTCCTGCAACGAGTGCATCTGGTAAGTGCCACACTGGTAGACGTTCAGTTCCGGGATCTGATTCTGATCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAAc                                                                                                                                                                                                                                  <  1:254349/251‑1 (MQ=255)            aGTTCCTACAACTTCTCTTTCTGCAGTGCCAGTTCCTCGTTGCTGTTGATGCGTACTGCACGTTCCAGAATGTTACGCGCAATATCCTGCGCTTCCTGCAACGAGTGCATCTGGTAAGTGCCACACTGGTAGACGTTCAGTTCCGGGATCTGATTCTGATCCTGCTCTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAACC‑g                                                                                                                                                                                                                               <  1:267784/251‑1 (MQ=255)             gTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGTTGATGCGTACGTCACGTTCCAGAATGCTACGCGCAATATCCTGCGCTTCCTGCAACGAGTGCATCTGGTAAGTGCCACACTGGTAGACGTTCAGTTCCGGGATCTGATTCTGATCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCCTCAGCAACACGCTGCTCATCTGGCGT‑CCCATTAGACTCCTATAAACACC‑gg                                                                                                                                                                                                                              >  2:233872/1‑251 (MQ=255)                     aaCTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGTTGATGCGTACGTCACGTTCCAGAATGCTACGCGCAATATCCTGCGCTTCCTGCAACGAGTGCATCTGGTAAGTGCCACACTGGTAGACGTTCAGTTCCGGGATCTGATTCTGATCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAACC‑GGTGCGGCAg                                                                                                                                                                                                                      <  2:136543/251‑1 (MQ=255)                                                     gCTGTTGATGCGTACGGCACGTTCCAGAATGCTACTCGCAATATCCTGCGCTTCCTGCAACGAGTGCAACTGGTAAGTGCCACACTGGTAGACGTTCAGTTCCGGGATCTGATTCTGAGCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTCCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAACC‑GGTGCGTCAGCCCATTGGCGAGATATCGATAATCTCTacccc                                                                                                                                                                                      <  2:301528/251‑4 (MQ=255)                                                       tGTTGATGCGTACGTCACGTTCCAGAATGCTACGCGCAATATCCTGCGCTTCCTGCAACGAGTGCATCTGGTAAGTGCCACACTGGTAGACGTTCAGTTCCGGGATCTGATTCTGATCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAACC‑GGTGCGGCAGCCCATTGGCGAGATATCGATAATCTCTACACCAt                                                                                                                                                                                    >  2:80518/1‑251 (MQ=255)                                                                  aCGTCACGTTCCAGAATGCTACGCGCAATATCCTGCGCTTCCTGCAACGAGTGCATCTGGTAAGTGCCACACTGGTAGACGTTCAGTTCCGGGATCTGATTCTGATCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAACC‑GGTGCGGCAGCCCATTGGCGAGATATCGATAATCTCTACACCATTACCGTTAAGa                                                                                                                                                                         <  1:461290/251‑1 (MQ=255)                                                                               gAATGCTACGCGCAATATCCTGCGCTTCCTGCAACGAGTGCATCTGGTAAGTGCCACACTGGTAGACGTTCAGTTCCGGGATCTGATTCTGATCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAACC‑GGTGCGGCAGCCCATTGGCGAGATATCGATAATCTCTACACCATTACCGTTAAGATGATTACGCATa                                                                                                                                                             >  2:147821/1‑250 (MQ=255)                                                                                aaTGCTACGCGCAATATCCTGCGCTTCCTGCAACGAGTGCATCTGGTAAGTGCCACACTGGTAGACGTTCAGTTCCGGGATCTGATTCTGATCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAACC‑GGTGCGGCAGCCCATTGGCGAGATATCGATAATCTCTACACCATTACCGTTAAGATGGTTACGCATaaa                                                                                                                                                           <  1:153193/251‑1 (MQ=255)                                                                                   gCTACGCGTAATATCCTGCGCTTCCTGCAACGAGTGCATCTGGTAAGTGCCTCACTGGTAGTCGTTCAGTTCCGGGATCTGATTCTGATCCTGCACTTTCAGCTCGTCTTCTATTGACGCTTTCCAGGCATCAGCAACACGCGGCTTATCTGGCGTACCA‑TTAGTCTCTTATAAAACCC‑GGTTCGGCAGCCCATTGTCGATATATCGATACTCTCTACACCATTTCCGTTAAGATGGCTTCGCATAAAAcc                                                                                                                                                        <  1:313951/251‑1 (MQ=255)                                                                                      aCGCGCAATATCCTGCGCTTCCTGCAACGAGTGCATCTGGTAAGTGCCACACTGGTAGACGTTCAGTTCCGGGATCTGATTCTGATCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCAGCTGGCGTACCA‑TTAGACTCATATAAAAACC‑GGTGCGGCAGCCCATTGGCGAGATATCGATAATCTCTACACCATTACCGTTAAGATGGTTACGCATAAAACCa                                                                                                                                                       <  1:414474/249‑1 (MQ=255)                                                                                                    gcgcTTCCTGCAACGAGTGCATCTGGTAAGTGCCACACTGGTAGACGTTCAGTTCCGGGATCTGATTCTGATCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAACC‑GGTGCGGCAGCCCATTGGCGAGATATCGATAATCTCTACACCATTACCGTTAAGATGGTTACGCATAAAACCAGCAAACAGGTGCTCCa                                                                                                                                       <  1:22659/251‑1 (MQ=255)                                                                                                                   ggTGCATCTGGTACGTGCCACACTGGTAGACGTTCAGTTCCTGTATCTGATTCTGATCCTGCACTCTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCATCACGTTGCTCATCTTGCGTGCCA‑TTAGACTCATATAAAAACCCGGT‑CGGCAGCTCATTGTCGAGATACCGATAATCTCTACACCATTACCGTTAATATGGTTACGCATAAAACCATTAAACAGGTTCTCCAGGGTATGGATCCctc                                                                                                                        <  2:236963/250‑1 (MQ=255)                                                                                                                   aGTGCATCTGGTAAGTGCCACACTGGTAGACGTTCAGTTCCGGGATCTGATTCTGATCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAACC‑GGTGCGGCAGCCCATTGGCGAGATATCGATAATCTCTACACCATTACCGTTAAGATGGTTACGCATAAAACCAGCAAACAGGTGCTCCAGGGTATGGATCCctc                                                                                                                        <  2:29564/251‑1 (MQ=255)                                                                                                                     tGCATCTGGTAAGTGCCACACTGGTAGACGTTCAGTTCCGGGATCTGATTCTGATCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAACC‑GGTGCGGCAGCCCATTGGCGAGATATCGATAATCTCTACACCATTACCGTTAAGATGGTTACGCATAAAACCAGCAAACAGGTGCTCCAGGGTATGGATCCCTCtt                                                                                                                      >  1:41133/1‑251 (MQ=255)                                                                                                                        aTCTAGTAAATGCCCCACTGGTAGCCTTTCAGTTCCGAGATATGATTCTGATCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTCCTCATCTGGCGTAC‑AATAAGACTCATATAAAAACC‑GGTGCGGCAGCACATTGGCGAGATATCGATAATCACTACACCATTACCGTTAAGATCGTTACGCATAAAAAAAAAAAACAGGAGCTCCAGGGTATGGATCCCTCTTTCt                                                                                                                   >  2:481213/1‑251 (MQ=255)                                                                                                                           tGGTAAGTGCCACACTGGTAGACGTTCAGTTCCGGGATCTGATTCTGATCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAACC‑GGTGCGGCAGCCCATTGGCGAGATATCGATAATCTCTACACCATTACCGTTAAGATGGTTACGCATAAAACCAGCAAACAGGTGCTCCAGGGTATGGATCCCTCTTTCTGGc                                                                                                                >  1:6583/1‑251 (MQ=255)                                                                                                                                   gCCACACTGGTAGACGTTCAGTTCCGGGATCTGATTCTGATCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAACC‑GGTGCGGCAGCCCATTGGCGAGATATCGATAATCTCTACACCATTACCGTTAAGATGGTTACGCATAAAACCAGCAAACAGGTGCTCCAGGGTATGGATCCCTCTTTCTGGCATCActt                                                                                                         <  1:233872/250‑1 (MQ=255)                                                                                                                                                       gTTCCGGGATCTGATTCTGATCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAACC‑GGTGCGGCAGCCCATTGGCGAGATATCGATAATCTCTACACCATTACCGTTAAGATGGTTACGCATAAAACCAGCAAACAGGTGCTCCAGGGTATGGATCCCTCTTTCTGGCATCACTTCTTTGTTCGGCACGCAGAAgc                                                                                    >  2:105517/1‑251 (MQ=255)                                                                                                                                                           cGGGATCTGATTCTGATCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAACC‑GGTGCGGCAGCCCATTGGCGAGATATCGATAATCTCTACACCATTACCGTTAAGATGGTTACGCATAAAACCAGCAAACAGGTGCTCCAGGGTATGGATCCCTCTTTCTGGCATCACTTCTTTGTTCGGCACGCAGAAgcgc                                                                                  >  2:445621/1‑249 (MQ=255)                                                                                                                                                                      tctgatCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTGCCAGGCATCAGCAACACGCTGCTCATCTGGCGGACCA‑TTAGACTCATATAAAAACC‑GGTGCGGCAGCCCATTGGCGAGATATCGATAATCTCTACACCATTACCGTTAAGATGGTTACGCATAAAACCAGCAAACAGGTGCTCCAGGGTATGGATCCCTCTTTCTGGCATCACATCTTTGTTCGGCACGCAGAAGCGCAGATCGAACACg                                                                      <  2:6583/250‑1 (MQ=255)                                                                                                                                                                         gatCCTGCACTTTAAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAAAACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAACC‑GGTGCGGCAGCACATTGGCGAGATATCGATAATCTCTACACCATTACCGTTAAGATGGTTACGCATAAAACAAGAAAACAGGTGCTCCAGGGTTTGGATCCCTCTTTCTGGCATCCCTTATTTTTTCGGCACGCAGAAGAGCAGATCGAACAAGGTg                                                                   >  2:499757/1‑250 (MQ=255)                                                                                                                                                                                cACTTTCAGCACGTCTTCCATTGCCTCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAACC‑GGGGCGGCATCCCATTGGCGAGATATCGATAATCTCTACACCATTACCGTTAAGATGGTTACGCATAAAACCAGCAAACAGGTGCTCCAGGGTATGGATCCCGCTGTCTGTCATCACTTCTTTGTTCGGCACTCAGAAGCGCAGATCGAACACGGTGATTGCGTc                                                           <  2:401614/251‑1 (MQ=255)                                                                                                                                                                                 aCTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAACC‑GGTGCGGCAGCCCATTGGCGAGATATCGATAATCTCTACACCATTACCGTTAAGCTGGTTACGCATAAAACCAGCAAACAGGTGCTCCAGGGTATGGATCCCTCTTTCTGGCATCACTTCTTTGTTCGGCACGCAGAAGCGCAGATCGAACACGGTGATTGCGTCg                                                          >  1:276093/1‑251 (MQ=255)                                                                                                                                                                                         cACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAACC‑GGTGCGGCAGCCCATTGGCGAGATATCGATAATCTCTACACCATTACCGTTAAGATGGTTACGCATAAAACCAGCAAACAGGTGCTCCAGGGTATGGATCCCTCTTTCTGGCATCACTTCTTTGTTCGGCACGCAGAAGCGCAGATCGAACACGGTGATTGCGTCGCCATGCgg                                                  >  1:68421/1‑251 (MQ=255)                                                                                                                                                                                                        cgcgttCCAGGCCTCAGCAACACGCTGCTCATCTGGCGTACCA‑TTAGACTCATATAAAAACC‑GGTGCGGCAGCCCATTGGCGAGATATCGATAATCTCTACACCATTACCGTTAAGATGGTTACGCATAAAACCAGCAAACAGGTGCTCCAGGGTATGGATCCCTCTTTCTGGCATCACTTCTTTGTTCGGCACGCAGAAGCGCAGATCGAACACGGTGATTGCGTCGCCATGAGGGGTGTTAATTGtttt                                   >  2:399270/5‑251 (MQ=255)                                                                                                                                                                                                          ctgtCCAGGCATCAGCAACACTCTGCTCATCGTGCGGACCA‑TTAGTCTCATATAAAAACC‑GGTGCGGCAGCCCATTGGCGAGATATCTATAATCTCTACACCATTACCGTTAAGATGGTTACGCATAAAACCAGCAAACAGGTGCTCCAGGGTATGGATCCCTCTTTCTGGCATCACTTCTTTGTTCGGCACGCTGAAGCGCAGATCGTACACGGTGATTGCGTCTCCATGCGGGGTGTTCATTGtttt                                   <  2:363598/246‑1 (MQ=255)                                                                                                                                                                                                                                         tGGCGTACCA‑TTAGACTCATATAAAAACC‑GGTGCGGCAGCCCATTGACGAGATATCGATAATCTCTACACCATTACCGTGAAGATGGGTACGCATAAAACAAGCAAACAGGTGCTCAAGGGTATGGATCCCTCTTTCTGGCATCACTTCTTTGTTCGGCACGCAGAAGCGCAGATCGAACACGGTGATTGCGTCGCCATGCGGGGAGTTCATTGTTTTCGCCACCAGAACTGCAGGCGCTTCCATCCGGGt  >  1:185831/1‑251 (MQ=255)                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                   ACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGTTGATGCGTACGTCACGTTCCAGAATGCTACGCGCAATATCCTGCGCTTCCTGCAACGAGTGCATCTGGTAAGTGCCACACTGGTAGACGTTCAGTTCCGGGATCTGATTCTGATCCTGCACTTTCAGCACGTCTTCCATTGCCGCTTTCCAGGCATCAGCAACACGCTGCTCATCTGGCGTACCAATCAGACTCATATAAAAACC‑GGTGCGGCAGCCCATTGGCGAGATATCGATAATCTCTACACCATTACCGTTAAGATGGTTACGCATAAAACCAGCAAACAGGTGCTCCAGGGTATGGATCCCTCTTTCTGGCATCACTTCTTTGTTCGGCACGCAGAAGCGCAGATCGAACACGGTGATTGCGTCGCCATGCGGGGTGTTCATTGTTTTCGCCACCCGAACTGCAGGCGCTTCCATCCGGGT  >  NC_000913/2814217‑2814700

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑