Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,535,690	0	T	G	52.0%	‑0.9 / 35.7	25	F542C (TTC→TGC)	ptsI	PTS enzyme I
Reads supporting (aligned to +/- strand):  ref base T (5/7);  new base G (7/6);  total (12/13)
Fisher's exact test for biased strand distribution p-value = 6.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.38e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TTGACCGTGGTAATGATATGATTTCACACCTTTACCAGCCAATGTCACCGTCCGTGCTGAACTTGATCAAGCAAGTTATTGATGCTTCTCATGCTGAAGGCAAATGGACTGGCATGTGTGGTGAGCTTGCTGGCGATGAACGTGCTACACTTCTGTTGCTGGGGATGGGTCTGGACGAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTTCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGACGAGTTAATGACGCTGGTTAACAAGTTCATTGAAGAAAAAACAATCTGCTAATCCACGAGATGCGGCCCAATTTACTGCTTAGGAGAAGATCATGGGTTTGTTCGATAAACTGAAATCTCTGGTTTCCGACGACAAGAAGGATACCGGAACTATTGAGATCATTGCTCCGCTCTCTGGCGAGATCGTCAATAT  >  NC_000913/2535453‑2535934                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                     ttGACCGTGGTAATGATATGATTACACACCTTTACCAGCCAATGTCACCGTCCGTGCTGAACTTGATCAAGCAAGTTATTGATGCTTCTCATGCTGAAGGCAAATGGACTGGCATGTGTGGTGAGCTTGCTGGCGATGAACGTGCTACACTTCTGTTGCTGGGGATGGGTCTGGACGAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTTCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCt                                                                                                                                                                                                                 >  1:419653/1‑275 (MQ=255)              taatatggtTACAAACCTTAACCAGCCAACTTAACCGGCCGTGCTGAACTTGATCAAGCAAGTTATTGATGCTTCTCATGCTGAAGGCAAATGGACTGGCATGTGTGGTGAGCTTGCTGGCGATGAACGTGCTACACTTCTGTTGCTGGGGATGGGTCTGGACGAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTTCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGa                                                                                                                                                                                                   <  2:419649/274‑1 (MQ=255)                                                                                              cTGAAGGCAAATGGACTGGCATGTGTGGTGAGCTTGCTGGCGATGAACGTGCTACACTTCTGTTGCTGGGGATGGGTCTGGACGAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTTCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGACGAGTTAATGACTCTGGTTAACAAGTTCATTGAAGAAAAAACAATCTGCTAATCCACGAGATGCGGCCCAATTTACTGCt                                                                                                                   <  1:409498/276‑1 (MQ=255)                                                                                                gAAGGCAAATGGACTGGCATGTGTGGTGAGCTTGCTGGCGATGAACGTGCTACACTTCTGTTGCTGGGGATGGGTCTGGACGAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTGCGAAGAt                                                                                                                                                                                                                                               >  1:185250/1‑150 (MQ=255)                                                                                                   ggCAAATGGACTGGCATGTGTGGTGAGCTTGCTGGCGATGAACGTGCTACACTTCTGTTGCTGGGGATGGGTCTGGACGAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTGCGAAGATGCg                                                                                                                                                                                                                                            <  2:185249/150‑1 (MQ=255)                                                                                                     cAAATGGACTGGCATTTGTGGTGAGCTTGCGGGCGATGAACGTACTACACTTCTGTTGCTGGGGACGGGTCTGGACGAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTGGGGAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGACGAGTTAATGTCGCGGGTTAACAAGTTCATTGAAGAAAAAACAATCTGCTAATCCACGGGAGGTGGCCCAATTTACTGCTTAGgaga                                                                                                            <  1:239760/276‑1 (MQ=255)                                                                                                                gCATGTGTGGTGAGCTTGCTGGCGATGAACGTGCTACACTTCTGTTGCTGGGGATGGGTCTGGACGAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTTCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGACGAGTTAATGACGCTGGTTAACAAGTTCATTGAAGAAAAAACAATCTGCTAATCCACgag                                                                                                                                       >  1:108161/1‑238 (MQ=255)                                                                                                                   tgtgtgGTGAGCTTGCTGGCGATGAACGTGCTACACTTCTGTTGCTGGGGATGGGTCTGGACGAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTTCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGACGAGTTAATGACGCTGGTTAACAAGTTCATTGAAGAAAAAACAATCTGCTAATCCACGAGATg                                                                                                                                    <  2:108161/238‑1 (MQ=255)                                                                                                                            aGCTTGCTGGCGATGAACGTGCTACACTTCTGTTGCTGGGGATGGGTCTGGACGAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTTCGAAGATGCGaa                                                                                                                                                                                                                                          >  1:102598/1‑127 (MQ=255)                                                                                                                               ttGCTGGCGATGAACGTGCTACACTTCTGTTGCTGGGGATGGGTCTGGACGAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTTCGAAGATGCGAAGgt                                                                                                                                                                                                                                       <  2:102598/127‑1 (MQ=255)                                                                                                                                               tGCTACACTTCTGTTGCTGGGGATGGGTCTGGACGAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTGCGAAGAt                                                                                                                                                                                                                                               >  1:142514/1‑103 (MQ=255)                                                                                                                                                  tACACTTCTGTTGCTGGGGATGGGTCTGGACGAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTGCGAAGATGCg                                                                                                                                                                                                                                            <  2:142514/103‑1 (MQ=255)                                                                                                                                                         cTGTTGCTGGGGATGGGTCTGGACGAATTCTCTATTAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTGCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGACGAGTTAATGACGCTGGTTAACAAGCTCATTGAAGAAAAAACAATCTGCTAATCCACGAGATGCGGCCCAATTTACTGCTTAg                                                                                                                >  1:196307/1‑220 (MQ=255)                                                                                                                                                                 ggggATGGGTCTGGACGAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTGCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCg                                                                                                                                                                                                           >  2:124621/1‑121 (MQ=255)                                                                                                                                                                 ggggATGGGTCTGGACGAATTCTCTATGAGCGCCATTTCTATCCCGCGAATTAAGAAGATTATCCGTAACACGAACTTCGAAAATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGACGAGTTAATGACGCt                                                                                                                                                                                    <  1:129433/144‑1 (MQ=255)                                                                                                                                                                    gATGGGTCTGGACGAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTGCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACa                                                                                                                                                                                                        <  1:124621/121‑1 (MQ=255)                                                                                                                                                                              gACGAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTGCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGACGAGTTAATGACGCTGGTTAACAAGTTCATTg                                                                                                                                                                   >  1:409696/1‑148 (MQ=255)                                                                                                                                                                                 gAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTGCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGACGAGTTAATGACGCTGGTTAACAAGTTCATTgaag                                                                                                                                                                <  2:409692/148‑1 (MQ=255)                                                                                                                                                                                   aTTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTTCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGACGAGTTAATGACGCTGGTTAACAAGTTCATTGAAGAAAAAACAATCTGCTAATCCACGAGATGCGGCCCAAt                                                                                                                           >  2:190138/1‑183 (MQ=255)                                                                                                                                                                                      ctctATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTTCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGACGAGTTAATGACGCTGGTTAACAAGTTCATTGAAGAAAAAACAATCTGCTAATCCACGAGATGCGGCCCAATTTa                                                                                                                        <  1:190139/183‑1 (MQ=255)                                                                                                                                                                                         tATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTTCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGACGAGTTAATGACGCTGGTTAACAAGTTCATTGAAGAAAAAACAATCTGCTAATCCACGAGATGCGGCCCAAt                                                                                                                           >  1:49974/1‑177 (MQ=255)                                                                                                                                                                                            gAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTTCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGACGAGTTAATGACGCTGGTTAACAAGTTCATTGAAGAAAAAACAATCTGCTAATCCACGAGATGCGGCCCAATTTa                                                                                                                        <  2:49974/177‑1 (MQ=255)                                                                                                                                                                                                       cTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTGCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGACGAGTTAATGACGCTGGTTAACAAGTTCATTGAAGAAAAAACAATCTGCTAATCCACGAGATGCg                                                                                                                                  >  2:426552/1‑156 (MQ=255)                                                                                                                                                                                                          tCCCGCGCATTAAGAAGATTATCCGTAACACGAACTGCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGACGAGTTAATGACGCTGGTTAACAAGTTCATTGAAGAAAAAACAATCTGCTAATCCACGAGATGCGGcc                                                                                                                               <  1:426556/156‑1 (MQ=255)                                                                                                                                                                                                               cgcATTAAGAAGATTATCCGTAACACGAACTGCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGACGAGTTAATGACGCTGGTTAACAAGTTCATTGAAGAAAAAACAATCTGCTAATCCACGAGATGCGGCCCAATTTACTGCTTAGGAGAAGATCATGGGTTTGTTAGATAAACTGAAATCTCTGGTTTCCGACGACAAGACGGATACCGGAACTATTGAGATCATTGCTCCGCTCTCTGGCGAGATCGTCAatat  >  1:410288/1‑276 (MQ=255)                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                     TTGACCGTGGTAATGATATGATTTCACACCTTTACCAGCCAATGTCACCGTCCGTGCTGAACTTGATCAAGCAAGTTATTGATGCTTCTCATGCTGAAGGCAAATGGACTGGCATGTGTGGTGAGCTTGCTGGCGATGAACGTGCTACACTTCTGTTGCTGGGGATGGGTCTGGACGAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTTCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGACGAGTTAATGACGCTGGTTAACAAGTTCATTGAAGAAAAAACAATCTGCTAATCCACGAGATGCGGCCCAATTTACTGCTTAGGAGAAGATCATGGGTTTGTTCGATAAACTGAAATCTCTGGTTTCCGACGACAAGAAGGATACCGGAACTATTGAGATCATTGCTCCGCTCTCTGGCGAGATCGTCAATAT  >  NC_000913/2535453‑2535934

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑