Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,357,755	0	A	T	54.2%	7.7 / 30.2	24	P530P (CCA→CCT)	yhcD	fimbrial biogenesis outer membrane usher protein
Reads supporting (aligned to +/- strand):  ref base A (7/4);  new base T (0/13);  total (7/17)
Fisher's exact test for biased strand distribution p-value = 9.53e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.43e-04
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ACTGGCAGCATCAACTTAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGA  >  NZ_CP009273/3357679‑3357844                                                                             |                                                                                          aCTGGCAGCATCAACTTAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCaa                                                                              <  1:323579/90‑1 (MQ=255)   tGGCAGCATCAATTTAGTGCTTAAAAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCTTTTTGGCAGAACAAac                                                                            <  1:343428/90‑1 (MQ=255)   tGGCACCATCAACTTAGTGTTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCTTTTGGCAGATCAAac                                                                            <  2:589341/90‑1 (MQ=255)        gcaTCAACTTAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGc                                                                       <  1:283432/90‑1 (MQ=255)           caaaCTTAGTCCTTCAGAAAATAATGAAGAGGAGGGTGATCTCTTCTCCGTCACCATCAGTATTCCTTTTGGCAGACCAAACACCGCcac                                                                    <  2:61821/88‑1 (MQ=255)            cAACTTAGTGCTTCAAAAAATAATGAAGACGATGGTGATCTGTTCTACGACAACATCAGTATTCCTTTTGGCAGATCAAACACCGCcaca                                                                   <  1:176055/90‑1 (MQ=255)             aatttAGTGCTTAAAAAAATAATGAAGCGGATGGTGATCTGTTCTACGCCAACATCAGTTTTCCTTTTGGCAGATCAAACCCCGCCacac                                                                  <  1:331576/87‑1 (MQ=255)             aaCTTAGTGCTTAAAAAAATAATAAAGACGATGGTGATCTGTTCTACGTAAACATCATTATTCCTTTTGGAAGATCAAACCCCGCCacac                                                                  <  1:505443/90‑1 (MQ=255)                    tGCTTCAAAAAAAAATGAAGACGATGGTGATCTTTTCTACGTCAACATCAGTATCCCTTTTGGCAGATCAAACACCGCCACACTGTATAc                                                           <  2:468571/90‑1 (MQ=255)                        tCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGc                                                       >  2:599946/1‑90 (MQ=255)                                  atGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATc                                             >  1:493783/1‑90 (MQ=255)                                       gACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATaaa                                        >  2:6035/1‑90 (MQ=255)                                           aTGGTTATCTGTTCTACGTCAACAACAGTATTCCTTTTGGAAAATAAACCCCCGCCACACTGTATACTCGCCATGACGATCATAAAAccc                                    <  1:337116/90‑1 (MQ=255)                                           aTGGTGATTTGTTCTACGTCAACATCAGTATTCCTTTTGGCAGATAAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAAccc                                    <  2:605634/90‑1 (MQ=255)                                           aTGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAAccc                                    <  2:95779/90‑1 (MQ=255)                                                     gTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTAc                          >  1:165839/1‑90 (MQ=255)                                                          aCGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGgtg                     >  1:556044/1‑90 (MQ=255)                                                                     atttttCCTTTTGGAAGAAAAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAgtc          <  1:339108/86‑1 (MQ=255)                                                                     attATTCCTTTTGGCAAAAAAAACCCCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAgtc          <  2:401492/88‑1 (MQ=255)                                                                     aGTATTCCTTTGGGAAGAAAAAACCCCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAgtc          <  1:34457/90‑1 (MQ=255)                                                                     aGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAgtc          >  2:103679/1‑90 (MQ=255)                                                                        aTTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACt                                 >  2:214176/1‑64 (MQ=255)                                                                        aTTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACt                                 <  1:214176/64‑1 (MQ=255)                                                                          tCCTTTTGGCAGATCAAACCCCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGtctc     <  2:211400/90‑1 (MQ=255)                                                                             aTTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCaga  >  1:605375/1‑90 (MQ=255)                                                                             |                                                                                          ACTGGCAGCATCAACTTAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGA  >  NZ_CP009273/3357679‑3357844

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑