Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,026,655	C→T	12.9%	E87K (GAA→AAA)	vraR ←	response regulator VraR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,026,655	0	C	T	12.9%	82.9 / 5.7	31	E87K (GAA→AAA)	vraR	response regulator VraR
Reads supporting (aligned to +/- strand):  ref base C (14/13);  new base T (2/2);  total (16/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.42e-01

CACTAAAACTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCTTTGGCAA  >  CP000730/2026518‑2026792                                                                                                                                          |                                                                                                                                          cACTAAAACTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAAt                                                                                                                                        <  1:39918/141‑1 (MQ=255)   cTAAAACTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTtaataa                                                                                                                                      <  1:179026/141‑1 (MQ=255)   cTAAAACTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATaa                                                                                                                                      >  1:297337/1‑141 (MQ=255)      aaaCTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAAc                                                                                                                                   <  1:356846/141‑1 (MQ=255)         cTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAg                                                                                                                                >  2:64759/1‑141 (MQ=255)             cGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTaa                                                                                                                            >  2:78474/1‑141 (MQ=255)             cGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTaa                                                                                                                            >  1:195643/1‑141 (MQ=255)                   aaaaaCAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTaa                                                                                                                      >  2:343912/1‑141 (MQ=255)                      aaCAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTTTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATAc                                                                                                                   <  2:171041/141‑1 (MQ=255)                      aaCAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATAc                                                                                                                   <  2:239013/141‑1 (MQ=255)                                  tatAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCgg                                                                                                       <  1:362087/139‑1 (MQ=255)                                     aGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTaa                                                                                                    >  2:257737/1‑141 (MQ=255)                                         gTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCt                                                                                                <  2:267219/141‑1 (MQ=255)                                         gTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCt                                                                                                >  2:301520/1‑141 (MQ=255)                                             tACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCttttt                                                                                            >  1:156112/1‑141 (MQ=255)                                             tACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATACCCGATATACCTCTTTATCTTCAATAAAACTATTTAACATAAATACCTTAATTTGCGGTAAATCttttt                                                                                            >  1:354710/1‑141 (MQ=255)                                                       aTCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAgt                                                                                  >  2:192548/1‑141 (MQ=255)                                                             gATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGc                                                                            >  1:84944/1‑141 (MQ=255)                                                                          cTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACAccatcc                                                               <  2:69528/141‑1 (MQ=255)                                                                           ttgttgTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACAccatcca                                                              <  1:178538/141‑1 (MQ=255)                                                                            tgttgtTTTTAAAATGTAACTATCGACACCTGGATCTATTGCACGATATCCCTCTTTATCTTCAATAACACTAGTTAACAGTCATACTTTCTGTTGCTGTTATTCTTTGTTAAGCTGACTCCCCGCTTCTACAccatccat                                                             <  2:99125/141‑1 (MQ=255)                                                                                  ttttAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATc                                                       >  1:280420/1‑141 (MQ=255)                                                                                       aaaTGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGCCGTCGCTTCTACACCATCCATGTCATCCATaa                                                  >  1:290012/1‑141 (MQ=255)                                                                                        aaTGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCTCTTCTACACCATCCATGTCATCCATAAg                                                 <  2:297337/141‑1 (MQ=255)                                                                                          tGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTa                                               >  2:266236/1‑141 (MQ=255)                                                                                            tAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTaaa                                             <  1:38451/141‑1 (MQ=255)                                                                                                                    gCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTc                     <  1:279823/141‑1 (MQ=255)                                                                                                                     cACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCa                    <  1:277837/141‑1 (MQ=255)                                                                                                                      aCGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCaa                   <  1:257737/141‑1 (MQ=255)                                                                                                                         atatACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTc                <  2:271669/141‑1 (MQ=255)                                                                                                                                      tCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCTTTGGCa   >  2:8108/1‑141 (MQ=255)                                                                                                                                       cTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCTTTGGCaa  >  1:62928/1‑141 (MQ=255)                                                                                                                                          |                                                                                                                                          CACTAAAACTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCTTTGGCAA  >  CP000730/2026518‑2026792

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑