Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_vch_tpiA	4,159,190	0	T	A	68.8%	42.7 / 17.9	32	L224Q (CTG→CAG)	oxyR	oxidative and nitrosative stress transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (5/5);  new base A (14/8);  total (19/13)
Fisher's exact test for biased strand distribution p-value = 6.99e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GAACCGCGAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATCTGCCGTGCATTAAGCCGGAACCACGCCGCACTATTGGCC  >  NC_000913_3_vch_tpiA/4159047‑4159327                                                                                                                                                |                                                                                                                                          gAACCGCGAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGaaa                                                                                                                                      >  1:306881/1‑149 (MQ=255)       cgAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCAGCGCGACCAGCCTGGAAACTCTgc                                                                                                                                <  1:496824/149‑1 (MQ=255)               tACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGAGCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCAGGAAACTCTGCGCAACAtg                                                                                                                        >  1:500101/1‑149 (MQ=255)                  cGATGGCCGATCTGGCAGGGGCAAAACTGCTGATGCTGGAAAAAGGACACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCAGGAAACTCTGCGCAACatgatg                                                                                                                     >  1:36348/1‑149 (MQ=255)                  cGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGGAGATACACACTTACGCGCGACCAGCCTGGAAACTCTGCGCAACAtggtg                                                                                                                     >  2:397172/1‑149 (MQ=255)                  cGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCAGGAAACTCTGCGCAACAtggtg                                                                                                                     <  2:137773/149‑1 (MQ=255)                    aggccccaTCTGGCAGGGGACAATCTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCCGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCAGGAAACTCTGCGCAACATGGTggc                                                                                                                   <  1:403126/142‑1 (MQ=255)                         cGATCTGGCAGGGGAAAAACTTCTGATGCTGGAAGATAGTCACAGTTTGCGCGATCAGGGAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCAGGAAACTCTGCGCAACATGGTGGCGGCAg                                                                                                              >  1:291829/1‑149 (MQ=255)                                 cAGGGGAAAAACGGTGTATTGTGGGAGATTGTCACTGTGTGCGTGATCAGGCAATGGGTTTCTGTTTGGAAGCCGGGGGGGATGAAGATACACACTTCCGGTCGACCAGCCAGGAAACTCTGCGCAACAGGGTGGCGTCAGGTAGCggg                                                                                                      <  2:391761/149‑1 (MQ=255)                                      gAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTAAAGCCGGGGCGCATGAAGATACACACTTCCGCGCGACCAGCCAGGAAACCCTACGCAACATGCTCGAGGCACGTAGACCGATCAc                                                                                                 >  2:349239/1‑149 (MQ=255)                                       aaaaaCTGCTGATGCTGGAAGATGGTCACTGTTTGCGCTATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCAGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACt                                                                                                <  2:25626/149‑1 (MQ=255)                                         aaaCTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAAGCAATGAGATTCTGTATTGAAGCCAGGGCGAATGAAGATACACACTTCCGCGCGACCAACCAGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACttt                                                                                              >  1:41162/1‑149 (MQ=255)                                          aaCTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCAGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTa                                                                                             >  2:396422/1‑149 (MQ=255)                                                 gATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTTGAATTTTTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAg                                                                                      <  1:473646/149‑1 (MQ=255)                                                    gCTGGAAGATGGTCACTGTTTGCGCGATCAGGCATTGGGTTTCTGTTTTGAAGGCGGGGATTATGAAGATACACACTTCCGCGCGACCAGCCAGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAgcgc                                                                                   >  1:420659/1‑149 (MQ=255)                                                        gAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTAAAGCCGAAGCGGATGAAAATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCgctggc                                                                               >  1:145046/1‑149 (MQ=255)                                                          aGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCAGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCa                                                                                                  >  1:301732/1‑128 (MQ=255)                                                          aGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCAGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCa                                                                                                  <  2:301732/128‑1 (MQ=255)                                                              ggTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCAGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTgcc                                                                         <  1:396422/149‑1 (MQ=255)                                                                tCACTGTTTGCGCGATCAGGCAAAGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACAATTCCGAGCGAGCAGCCTGGAAAGTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCAGTTTACCGCCGACCCCGGCtgtgacac                                                                       >  2:130140/1‑145 (MQ=255)                                                                    tGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCAGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGa                                                                   >  1:518590/1‑149 (MQ=255)                                                                      tttGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCAGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCCGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGGgc                                                                 >  2:468625/1‑149 (MQ=255)                                                                                             tCTGTTTTGAAGCCGGGGCGGATGAAGATACCAAGTTCCGCGCGACCAGCCAGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTAt                                          <  2:518590/149‑1 (MQ=255)                                                                                              cTGTTTCGAAGCCGGGGAGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCTGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATc                                         <  1:130140/149‑1 (MQ=255)                                                                                                 ttttGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCAGGAAAATCTGCACAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATCTGc                                      >  1:196536/1‑149 (MQ=255)                                                                                                    tGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGAAAACGCGATGGGGTTGTTTATCTGCCGt                                   <  1:193118/149‑1 (MQ=255)                                                                                                                            acacTTCCGCGCGACCAGCCAGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCAATTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATCTGCCGTGCATTAAACCGGAACCACGCCGCa           >  1:23030/1‑149 (MQ=255)                                                                                                                              acTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGAGCGCTTTACTGCCAGCGCTGGCGTTGCCGCCGGAGCGCAAATGCGAACGGGGGGGTTATCTGCCGTGAATCAAGCCGAAACCAGGACGCaaa         >  2:385155/1‑147 (MQ=255)                                                                                                                              acTTCCGCGCGACCAGCCAGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATCTGCCGTGCATTAAGCCGCAACCACGTCGCACt         >  2:320838/1‑149 (MQ=255)                                                                                                                                     cgcgACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATCTGCCGTGCATTAAGCCGGAACCACGCCGCACTATTGGcc  <  2:145046/149‑1 (MQ=255)                                                                                                                                           cAGCCAGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGa                                                                   <  1:416459/78‑1 (MQ=255)                                                                                                                                           cAGCCAGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGa                                                                   >  2:416459/1‑78 (MQ=255)                                                                                                                                                |                                                                                                                                          GAACCGCGAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATCTGCCGTGCATTAAGCCGGAACCACGCCGCACTATTGGCC  >  NC_000913_3_vch_tpiA/4159047‑4159327

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑