Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,291,943	0	T	C	70.6%	49.6 / 23.3	34	F196F (TTT→TTC)	nrfA	nitrite reductase, formate‑dependent, cytochrome
Reads supporting (aligned to +/- strand):  ref base T (7/3);  new base C (24/0);  total (31/3)
Fisher's exact test for biased strand distribution p-value = 2.01e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.07e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TCCCGTCCGTATGCGGCTCGCGCGATGGAAGCCATTGGTAAACCTTTTGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGTCAGTGCCATGTGGAGTATT  >  W3110S.gb/4291896‑4292004                                                |                                                              tCCCGTCCGTATGCGGCTCGCGCGATGGAAGCCATTGGTAAACCTTTTGAGAAAGCCGGACg                                                 >  1:4645071/1‑62 (MQ=255) tCCCGTCCGTATGCGGCTCGCGCGATGGAAGCCATTGGTAAACCTTTTGAGAAAGCCGGACg                                                 >  1:4020513/1‑62 (MQ=255) tCCCGTCCGTATGCGGCTCGCGCGATGGAAGCCATTGGTAAACCTTTTGAGAAAGCCGGACg                                                 >  1:222990/1‑62 (MQ=255)      tccgtATGCGGCTCGCGCGATGGAAGCCATTGGTAAACCTTTTGAGAAAGCCGGACGTTTCg                                            <  1:3926301/62‑1 (MQ=255)                   cgcgcgATGGAAGCCATTGGTAAACCTTTTAAGAAAGc                                                       >  1:266014/1‑38 (MQ=255)                       cgATGGAAGCCATTGGTAAACCTTTTGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGtt                           <  1:2194451/62‑1 (MQ=255)                                   ttGGTAAACCTTTTGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGTCAGTGc               >  1:1703800/1‑62 (MQ=255)                                   ttGGTAAACCTTTTGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGTCAGTGc               >  1:4446348/1‑62 (MQ=255)                                   ttGGTAAACCTTTTGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGTCAGTGc               >  1:2507521/1‑62 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:3468606/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:127659/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:3530028/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:353228/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:4278495/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:42895/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:4423340/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:4543315/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:4586051/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:4692665/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:487756/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:622095/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:713037/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:3182183/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:1355585/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:1739757/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:1891930/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:2100950/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:2266361/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:2552281/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:2642522/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:304907/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:3050758/1‑56 (MQ=255)                                   ttGGTAAACCTTTCGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGt                     >  1:3418283/1‑56 (MQ=255)                                        aaaCCTTTTGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGTCAGTGCCAtgt          <  1:1190229/62‑1 (MQ=255)                                              tttGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGTCAGTGCCATGTGGAGTa    <  1:795805/62‑1 (MQ=255)                                                tGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGTCAGTGc               >  1:2078252/1‑49 (MQ=255)                                                tGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGTCAGTGCCATGTGGAg      >  1:2510820/1‑58 (MQ=255)                                                tGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGTCAGTGCCATGTGGAg      >  1:2902036/1‑58 (MQ=255)                                                tGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGTCAGTGCCATGTGGAg      >  1:1880194/1‑58 (MQ=255)                                                tGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGTCAGTGCCATGTGGAg      >  1:734836/1‑58 (MQ=255)                                                tGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGTCAGTGCCATGTGGAGTAtt  >  1:4105694/1‑62 (MQ=255)                                                |                                                              TCCCGTCCGTATGCGGCTCGCGCGATGGAAGCCATTGGTAAACCTTTTGAGAAAGCCGGACGTTTCGACCAGCAATCGATGGTTTGCGGTCAGTGCCATGTGGAGTATT  >  W3110S.gb/4291896‑4292004

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑