Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	ACB143	241,908	0	C	A	25.4%	120.0 / 14.0	59	Q148K (CAA→AAA)	rhtB_1	Homoserine/homoserine lactone efflux protein
Reads supporting (aligned to +/- strand):  ref base C (34/10);  new base A (0/15);  total (34/25)
Fisher's exact test for biased strand distribution p-value = 8.19e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GCCCGATCGGCAAGCCGCTGAGCCTGGTGTTCCGTGGTTTCCTGGTCAACATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCATGCTGCGCACGCCCAAACAGCAGAAGCGTTTGAACCGCACCTTT  >  ACB143/241780‑242039                                                                                                                                 |                                                                                                                                    ccccGATCGGCAAGCCGCTGAGCCTGGTGGTCCGTGGTTTCCTGGTCAACATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGAGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATAtgtg                                                                                                                             <  8:225812/136‑1 (MQ=255)   ccGATCGGCAAGCCGCTGAGCCTGGTGTTCCGTGGTTTCCTGGTCAACATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGc                                                                                                                           >  6:189726/1‑137 (MQ=255)   ccGATCGGCAAGCCGCTGAGCCTGGTGTTCCGTGGTTTCCTGGTCAACATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGc                                                                                                                           >  4:1523/1‑137 (MQ=255)   ccGATCGGCAAGCCGCTGAGCCTGGTGTTCCGTGGTTTCCTGGTCAACATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGc                                                                                                                           <  1:225781/137‑1 (MQ=255)       tCGGCAAGCCGCTGAGCCTGGTGTTCCGTGGTTTCCTGGTCAACATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATc                                                                                                                       <  3:1523/137‑1 (MQ=255)        cGGCAAGCCGCTGAGCCTGGTGTTCCGTGGTTTCCTGGTCAACATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCa                                                                                                                      >  7:138170/1‑137 (MQ=255)         ggCAAGCCGCTGAGCCTGGTGTTCCGTGGTTTCCTGGTCAACATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCAc                                                                                                                     <  3:200245/137‑1 (MQ=255)         ggCAAGCCGCTGAGCCTGGTGTTCCGTGGTTTCCTGGTCAACATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCAc                                                                                                                     >  3:203102/1‑137 (MQ=255)            aaGCCGCTGAGCCTGGTGTTCCGTGGTTTCCTGGTCAACATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGt                                                                                                                  <  2:155938/137‑1 (MQ=255)             aGCCGCTGAGCCTGGTGTTCCGTGGTTTCCTGGTCAACATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTg                                                                                                                 <  2:62295/137‑1 (MQ=255)             aGCCGCTGAGCCTGGTGTTCCGTGGTTTCCTGGTCAACATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTg                                                                                                                 <  8:113064/137‑1 (MQ=255)                      gCCTGGTGTTCCGTGGTTTCCTGGTCAACATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTc                                                                                                        >  4:168686/1‑137 (MQ=255)                        cTGGTGTTCCGTGGTTTCCTGGTCAACATAAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGGTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCAc                                                                                                      >  7:190456/1‑137 (MQ=255)                             gtTCCGTGGTTTCCTGGTCAACATCAGCACCCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCg                                                                                                 >  7:264114/1‑137 (MQ=255)                             gtTCCGTGGTTTCCTGGTCAACATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCg                                                                                                 >  2:120168/1‑137 (MQ=255)                              ttCCGTGGTTTCCTGGTCAACATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGa                                                                                                >  4:270006/1‑137 (MQ=255)                                      tttCCTGGTCAACATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTgg                                                                                        >  5:53563/1‑137 (MQ=255)                                           tGGTCAACATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATg                                                                                   >  3:8038/1‑137 (MQ=255)                                           tGGTCAACATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCACCATCCGCAGCTGCTGCCGCAATATGTGGAGATCACCGTGACCATGGTCACCGTCGACCTGCTGGTGATg                                                                                   >  4:71186/1‑137 (MQ=255)                                                aaCATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCggg                                                                              >  8:49584/1‑137 (MQ=255)                                                     cAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATaca                                                                         >  5:108142/1‑137 (MQ=255)                                                     cAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATaca                                                                         >  6:179443/1‑137 (MQ=255)                                                         ccccccACGGCGCTGGTGTTCATGGGGGCGGTGCTGCCGCAGTTCCTCAAACCCCATGCGCCGCTGCTGCCGAAATTTGGGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCgg                                                                     <  2:48163/135‑1 (MQ=255)                                                          cccccATGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCACAATCCCCATGCGCCGGTGCTGCCGAAATATGTGGCTATCACCGTGACCATGGTCAGGGTCGACCTGCTGGTGATGGCGGGATACACCggg                                                                    <  2:270085/136‑1 (MQ=255)                                                            cccAAGGGGCGGGTGTTCTTGCGGGGGGCGCTGCCCCTGTTCCAAAACCCCAAGGCGCCGCTGCTCCAGAAATTTGTGCCGCTCCCCGTCCCACTGGTCCGGGTCGACCTGCTGGTGATGGCGGGATACACCGGGtt                                                                  <  2:292072/137‑1 (MQ=255)                                                               aaGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGc                                                               >  4:281645/1‑137 (MQ=255)                                                                aGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCt                                                              >  6:223002/1‑137 (MQ=255)                                                                 ggggggggTGTTCTTGCTGGCGGGGCGGCCGCTTTCCCTCAACCCCCAGGCGCCGGTGCTGCCTAAATATGGGGCGATCCCCGTCACCTGGGCCAGGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCtt                                                             <  4:8038/131‑1 (MQ=255)                                                                   cgcTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCg                                                           >  6:271221/1‑137 (MQ=255)                                                                     gtGGTGTTCTGGCGGGCGGTGCTGCCGCCGTTCCACACCCCCCAGGCGCCGCGGCGGCCGAAATATGGGGCCACCACCGTCACCTTGGCCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCa                                                         <  2:191206/136‑1 (MQ=255)                                                                        gtgtTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCAtgc                                                      >  1:48163/1‑136 (MQ=255)                                                                         tgtTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCAtgtt                                                     >  5:117820/1‑136 (MQ=255)                                                                         tgtTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGGCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCAtgtg                                                     >  3:217954/1‑137 (MQ=255)                                                                          gtTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATgtgt                                                    >  2:18297/1‑137 (MQ=255)                                                                           ttCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGtt                                                   >  1:123037/1‑137 (MQ=255)                                                                              aTGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGAGCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCCTGTGTTgcg                                                >  8:122541/1‑137 (MQ=255)                                                                               ggCTGGCGGGGCTGCCGCAGTTCCTCAAACCCCATGCGCCGCGGCTGCCGAAATATGTGGCGAGCACCGGGCCCTGGGGCACGCTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTgcgc                                               <  1:199805/136‑1 (MQ=255)                                                                                gCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCa                                              >  8:8677/1‑137 (MQ=255)                                                                                    gCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCAtgct                                          >  1:153373/1‑137 (MQ=255)                                                                                    gCGGTGCCGCCGCTGTGCCTCAAGCCCCAGGCGCCGCTGCGGCCGCAATTTGTGCCGATCACCGTGACCTGGGCCCGGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCAtgct                                          <  7:86362/137‑1 (MQ=255)                                                                                    gCGGGGCTGCCGCTGTTCCTCAATCCCCATGCGCCGCTGCGGCCGAAATATGGGGCGATCACCGTCCCCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCAtgct                                          <  6:53563/137‑1 (MQ=255)                                                                                     cGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCAtgctg                                         >  1:278723/1‑137 (MQ=255)                                                                                            gcCGCAGTTCCTCAATCCCCTTGCGCGGCTGCGGCCGAAATAGGGGGCGAGCCCCGTCACCTTGGGCCCGCTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCATGCTGCGCACGc                                  <  1:195842/137‑1 (MQ=255)                                                                                            cccGCAGTTCCACAACCCCCAGGCGCCGCGGCCGCCTAAATATGGGCCGACCCCCGTGACCTTGGCCCCGCTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCATGCTGCGCACGc                                  <  7:15819/136‑1 (MQ=255)                                                                                              ccctgatCCTCACACCCCATGCGCCGCGGCCCCCCAATTTTGTGGCTACCCCGGTCACCTGGGCCCCGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCATGCTGCGCACGccc                                <  1:120168/131‑1 (MQ=255)                                                                                              cGCAGTACCACAACCCCCCGCCGCCGCTGCGGCCGAATTTTGGGGCTACCCCCGGCCCCCTGCCCCCGCTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCATGCTGCGCACGccc                                <  8:49461/137‑1 (MQ=255)                                                                                                     ccTCAAACCCCTTGCCCCGCTGCTGCCCAAATTTGGGGCTTTCACCGTGACCTTGGGCACGCTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCATGCTGCGCACGCCCAAAcagc                         <  5:223002/137‑1 (MQ=255)                                                                                                     ccTAAACCCCCAGCCGCGGATGCTCCCGAAATATGGGGCTATCCCCGTCACATTGGCCAGGCTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCATGCTGCGCACGCCCAAAcagc                         <  3:21943/137‑1 (MQ=255)                                                                                                          acccccAGGCGCCGCTGCTCCCGAAATTTGTGGCTAGCACCGTCACCAGGGGCACGCTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCATGCTGCGCACGCCCAAACAGCAGAAg                    <  5:272288/135‑1 (MQ=255)                                                                                                           tCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCATGATGAGCACGCCCAAACAGCAGAAGc                   >  8:240074/1‑137 (MQ=255)                                                                                                                  gcgcCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCATGCTGCGCACGCCCAAACAGCAGAAGCGTTTGaa            <  5:271221/137‑1 (MQ=255)                                                                                                                   cgccgcTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCATGCTGCGCACGCCCAAACAGCAGAAGCGTTTGAAc           >  7:297641/1‑137 (MQ=255)                                                                                                                     ccgcTGCCGCCTAAATCTGGCGCTAGCCCCGTCACCTTGCTCCCGCTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCATGCTGCGCACTCCCAAACAGCAGAAGCGTTTGAACCg         <  1:10351/137‑1 (MQ=255)                                                                                                                        ctgctgCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCATGCTGCTCACGCCCAAACAGCAGAAGCGTTTGAACCGCAc      >  1:240533/1‑137 (MQ=255)                                                                                                                        ctgctgCCGCAATATGTGGCGATCACCGTGACCATCGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTAGGCTTCGCATGTGTTGCGCATGCTGCGCACGCCCAAACAGCAGAAGCGTTTGAACCGCAc      >  8:7338/1‑137 (MQ=255)                                                                                                                          gctgcCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCATGCTGCGCACGCCCAAACAGCAGAAGCGTTTGAACCGCACCt    >  6:245747/1‑137 (MQ=255)                                                                                                                           ctgcCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCATGCTGCGCACGCCCAACCAGCAGAAGCGTTTGAACCGCACCtt   >  4:275299/1‑137 (MQ=255)                                                                                                                           ctgcCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCATGCTGCGCACGCCCAAACAGCAGAAGCGTTTGAACCGCACCtt   >  1:54421/1‑137 (MQ=255)                                                                                                                            ggcCTCAATTTGTGGCGATCACCGTCACCTTGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCATGCTGCGCACGCCCAAACAGCAGAAGCGTTTGAACCGCACCttt  <  7:273160/136‑1 (MQ=255)                                                                                                                                 |                                                                                                                                    GCCCGATCGGCAAGCCGCTGAGCCTGGTGTTCCGTGGTTTCCTGGTCAACATCAGCAACCCCAAGGCGCTGGTGTTCATGCTGGCGGTGCTGCCGCAGTTCCTCAATCCCCATGCGCCGCTGCTGCCGCAATATGTGGCGATCACCGTGACCATGGTCACGGTCGACCTGCTGGTGATGGCGGGATACACCGGGTTGGCTTCGCATGTGTTGCGCATGCTGCGCACGCCCAAACAGCAGAAGCGTTTGAACCGCACCTTT  >  ACB143/241780‑242039

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑