Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,850,001	0	C	A	44.4%	30.5 / 10.2	27	G46C (GGT→TGT)	uhpB	sensory histidine kinase in two‑component regulatory sytem with UhpA
Reads supporting (aligned to +/- strand):  ref base C (11/4);  new base A (0/12);  total (11/16)
Fisher's exact test for biased strand distribution p-value = 1.82e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTAACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCCATC  >  NC_000913/3849854‑3850147                                                                                                                                                    |                                                                                                                                                    gTAACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCaa                                                                                                                                                   >  2:575186/1‑150 (MQ=255)         attAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATa                                                                                                                                         <  2:214236/149‑1 (MQ=255)              aCTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCGGACCAAACGG‑AAATAACAGc                                                                                                                                    >  2:657455/1‑151 (MQ=255)                        atcaATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAACAGCACCGcc                                                                                                                              <  1:128769/147‑1 (MQ=255)                                                  gaccgCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTg                                                                                                >  2:296151/1‑151 (MQ=255)                                                   cccccgtGCTTTACCCAAAAAATCAGCACCCCCCCCGCCCCCAGCAATGGGGGCAAGTACCCGCGGGGGCTTTGAAGCATGAGCCCCAGACGAAGACAAAAGGA‑AAAGACCAGCACCGCCATATCAGGGCGCTCAACCAGATGCAgg                                                                                                   <  1:200278/141‑1 (MQ=255)                                                     cgCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGAt                                                                                              >  2:634409/1‑150 (MQ=255)                                                             ttAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCcac                                                                                       >  1:344269/1‑149 (MQ=255)                                                                                cccccccGCGCCCAACAATCCGGCCCAGTCCCCGCGGGGACTTCTCGTCATAACCCCCAAACGCAAACCAACGGA‑AAAAAACAGCCCCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCagag                                                                  <  1:367785/146‑1 (MQ=255)                                                                                ccACCCCGCCCCCAAAAAGACGGGCCAGTACCCGGGCGGACTTTGCAGAATTCGCCCCAGACGCA‑AAAAAACGGAAAATAACACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCag                                                                    <  2:307316/149‑1 (MQ=255)                                                                                 cccccccccccccaaaaTCCGGGCCAGTACCCGCGGGGCCTGCCCAGCATTCCCCCCAGACCAAGAAAAAACGA‑AAAAAACGCCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAgaga                                                                 <  2:557017/136‑1 (MQ=255)                                                                                          ccaaGCAATGCGGGCCAGTATCCGCGCGGGCATTGCAGCATTACCCCCAGACGCAAACAAAACGA‑AAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATaa                                                           <  1:338563/145‑1 (MQ=255)                                                                                           ccAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATaaaaa                                                        >  2:288819/1‑150 (MQ=255)                                                                                           acAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATaaaaa                                                        >  2:62332/2‑150 (MQ=255)                                                                                               cAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGc                                                     >  2:506635/1‑149 (MQ=255)                                                                                                aacccGGCCCAGTACCCGCGCGGCCATTCCACCATTCCCCCCAGCCCCACCCAAAACAA‑AAAAAACACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCa                                                    <  2:325091/145‑1 (MQ=255)                                                                                                aaagggggCCAGTCCCCGGGGGGGCATGCCAGCATAGGCCCCAGACGCAAACAAAGGGG‑AAAAACCAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATaaaa                                                         <  2:483466/139‑1 (MQ=255)                                                                                                        ccactccccGCGGGGGCATTGCAGCATCACCCCCAGACGAAGACAAAAGAA‑AAAAAACACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGc                                                 <  2:330845/137‑1 (MQ=255)                                                                                                        cagctacccGCGGGGCCTTTGCACCATCACCCCAAGCCGAAGACAAAAGGA‑AAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAAc                                           <  2:110505/143‑1 (MQ=255)                                                                                                                     gggCATTCCACCATTGCCCCAAGACCCAGACAAAGCGA‑AAAAAACACGGCCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAg                                 <  2:443368/147‑1 (MQ=255)                                                                                                                     ggactttGCAACATCAGCCCAAGACGCAAACAAAGGGA‑AAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTaa                                      <  1:330899/137‑1 (MQ=255)                                                                                                                             cagcaTAACCCCCAGACGAAGACAAAAGGA‑AAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGaaca                       <  2:320967/149‑1 (MQ=255)                                                                                                                                       cccAGACGCAGACCAAACGG‑AAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTtcatc            >  2:390981/1‑150 (MQ=255)                                                                                                                                        ccAGACGCAGACAAAACGA‑AAAAAACAGCCCCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTtca              <  1:383984/147‑1 (MQ=255)                                                                                                                                          aGACGCAGACCAAACGG‑AAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCAcc         >  2:118847/1‑150 (MQ=255)                                                                                                                                                aGACCAAACGG‑AAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCCATc  >  2:236142/1‑151 (MQ=255)                                                                                                                                                  aCCAAACAA‑AAAAAACACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAg       <  2:334195/144‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                    GTAACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCCATC  >  NC_000913/3849854‑3850147

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑