Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,799,167	0	A	C	22.2%	85.9 / 25.5	45	intergenic (‑225/+59)	pheS/pheM	phenylalanine tRNA synthetase, alpha subunit/phenylalanyl‑tRNA synthetase operon leader peptide
Reads supporting (aligned to +/- strand):  ref base A (16/19);  new base C (4/6);  total (20/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.92e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TGCTCGAAATTCTCACGTACTTAAATACGCTCCGGTTTCTCCGCGCTGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATAGCAGCATTCATTGCTTGCGTTACCTTTTGGTACTCTTCAAAAGACCTTTATT  >  NC_000913/1799036‑1799311                                                                                                                                    |                                                                                                                                                 tgCTCGAAATTCTCACGTACTTAAATACGCTCCGGTTTCTCCGCGCTGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCCAGTGGAGGCtttttt                                                                                                                                   <  5:37607/147‑4 (MQ=38)   cTCGAAATTCTCACGTACTTAAATACGCTCCGGTGTATCCGCGCTGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCCAGTGGAGGCtttttttgta                                                                                                                               <  3:109071/149‑8 (MQ=255)    tCGAAATTCTCACGTACTTAAATACGCTCCGGTTTCTCCGCGCTGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCCAGTGGAGGCtttttttgt                                                                                                                                >  1:137758/1‑141 (MQ=38)    tCGAAATTCTCACGTACTTAAATACGCTCCGGTTTCTCCGCGCTGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCCAGTGGAGGCtttttttgt                                                                                                                                <  2:137758/147‑7 (MQ=38)          ttCTCACGTACTTAAATACGCTCCGGTTTCTCCGCGCTGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCCAGTGGAGGCtt                                                                                                                                       >  7:118977/1‑134 (MQ=255)          ttCTCACGTACTTAAATACGCTCCGGTTTCTCCGCGCTGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCCAGTGGAGGCtt                                                                                                                                       <  8:118977/134‑1 (MQ=255)           tctcACGTACTTAAATACGCTCCGGTTTCTCCGCGCTGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTcc                                                                                                                       >  3:22524/1‑149 (MQ=255)               aCGTACTTAAATACGCTCCGGTTTCTCCGCGCTGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGttt                                                                                                                   <  4:22524/149‑1 (MQ=255)                     ttAAATACGCTCCGGTTTCTCCGCGCTGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCCAGTGGAGGCttttt                                                                                                                                    <  2:70374/126‑3 (MQ=38)                     ttAAATACGCTCCGGTTTCTCCGCGCTGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCCAGTGGAGGCttttt                                                                                                                                    >  1:70374/1‑124 (MQ=38)                             gCTCCGGTTTCTCCGCGCTGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAg                                                                                                                                   <  7:156212/119‑1 (MQ=255)                             gCTCCGGTTTCTCCGCGCTGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAg                                                                                                                                   >  8:156212/1‑119 (MQ=255)                             gCTCCGGTTTCTCCGCGCTGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTGTTCCGTTTCTCTTCTCACgcgc                                                                                                     >  1:198981/1‑149 (MQ=255)                                       ctcCGCGCTGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGcctcct                                                                                            <  3:125484/148‑1 (MQ=255)                                       ctcCGCGCTGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGcctcct                                                                                            <  1:148837/148‑1 (MQ=255)                                       ctcCGCGCTGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTg                                                                                           >  4:125390/1‑149 (MQ=255)                                               tGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAgg                                                                                                                                  <  2:82960/102‑1 (MQ=255)                                               tGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAgg                                                                                                                                  >  1:82960/1‑102 (MQ=255)                                                 gCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCCAGTGGAGGCttttttt                                                                                                                                  <  2:192693/100‑5 (MQ=38)                                                 gCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCCAGTGGAGGCttttttt                                                                                                                                  >  1:192693/1‑96 (MQ=38)                                                 gCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGt                                                                                  <  7:130604/148‑1 (MQ=255)                                                   cGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTcc                                                                                                                       <  8:144090/109‑1 (MQ=255)                                                   cGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTcc                                                                                                                       >  7:144090/1‑109 (MQ=255)                                                    gtgtCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCt                                                                               >  2:159260/1‑148 (MQ=255)                                                    gtgtCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTa                                                                              <  3:125390/149‑1 (MQ=255)                                                         cAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGt                                                                          >  4:72618/1‑148 (MQ=255)                                                            tCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTaaa                                                                       >  1:119903/1‑148 (MQ=255)                                                                               ccTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATagca                                                   <  6:150570/149‑1 (MQ=255)                                                                                       gaCAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATAGCAGcattcat                                           <  1:159260/149‑1 (MQ=255)                                                                                            gCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGt                                                                                  >  5:35102/1‑105 (MQ=255)                                                                                            gCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGt                                                                                  <  6:35102/105‑1 (MQ=255)                                                                                            gCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATAGCAGCATTCAttgctt                                      >  2:125975/1‑149 (MQ=255)                                                                                            gCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATAGCAGCATTCAttgctt                                      >  5:186661/1‑149 (MQ=255)                                                                                            gCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATAGCAGCATTCAttgctt                                      >  6:133551/1‑149 (MQ=255)                                                                                             cTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATag                                                     <  8:32590/133‑1 (MQ=255)                                                                                             cTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATag                                                     >  7:32590/1‑133 (MQ=255)                                                                                              tttttATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATAGCAGCATTCAttgcttgc                                    >  8:13635/1‑149 (MQ=255)                                                                                                 ttATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATAGCAGCATTCATTGCTTGCGt                                  <  2:198981/148‑1 (MQ=255)                                                                                                       ttCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATAGCAGCATTCATTGCTTGCGTTACCtt                            <  2:119903/148‑1 (MQ=255)                                                                                                             aCGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATAGCAGCATTCATTGCTTGCGTTACCTTTTGGTAc                     <  1:125975/149‑1 (MQ=255)                                                                                                                 gcATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATAGCAGCATTCATTGCTTGCGTTACCTTTTGGTACTCtt                 <  3:72618/149‑1 (MQ=255)                                                                                                                         aaaaaGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCTTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATAGCAGCATTCATTGCTTGCGTTACCTTTTGGTACTCTTCAAAAGAc         <  5:133551/149‑1 (MQ=255)                                                                                                                         aaaaaGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATag                                                     >  2:62984/1‑105 (MQ=255)                                                                                                                         aaaaaGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATag                                                     <  1:62984/105‑1 (MQ=255)                                                                                                                                cTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATAGCAGCATTCATTGCTTGCGTTACCTTTTGGTACTCTTCAAAAGACCTTTAtt  <  3:7569/149‑1 (MQ=255)                                                                                                                                    |                                                                                                                                                 TGCTCGAAATTCTCACGTACTTAAATACGCTCCGGTTTCTCCGCGCTGGCCGTGTCCAGTCTGGCTGCGACAATTACACCTGATGAGACAGGCTTTTTATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATAGCAGCATTCATTGCTTGCGTTACCTTTTGGTACTCTTCAAAAGACCTTTATT  >  NC_000913/1799036‑1799311

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑