Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_017635	3,127,767	0	T	G	52.6%	10.7 / 22.2	20	pseudogene (1083/1425 nt)	tssA	type VI secretion system protein TssA
Reads supporting (aligned to +/- strand):  ref base T (5/4);  new base G (2/8);  total (8/12)
Fisher's exact test for biased strand distribution p-value = 1.70e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CGGAAGCACTGGAGATGGCAGACAGTCAGGGCGTGGAAGCGGCTCTGGGCTGGATACAGACCCGTCCGGGCATCACCACGGCAC  >  NC_017635/3127724‑3127807                                            |                                         cGGAAGCACTGGAGATGGCAGACAGTCAGGGCGTGGAAGCGGCGCTGGGc                                    <  1:1690517/50‑1 (MQ=255)  ggAAGCACTGGAGATGGCAGACAGTCAGGGCGTGGAAGCGGCGCTGGGCt                                   <  1:1998812/50‑1 (MQ=255)  ggAAGCACTGGAGATGGCAGACAGTCAGGGCGTGGAAGCGGCGCTGGGCt                                   <  2:1952796/50‑1 (MQ=255)   gAAGCACTGGAGATGGCAGACAGTCAGGGCGTGGAAGCGGCTCTGGGCTg                                  >  1:1315579/1‑50 (MQ=255)      gCACTGGAGATGGCAGACAGTCAGGGCGTGGAAGCGGCTCTGGGCTGGAt                               <  2:1980091/50‑1 (MQ=255)      gCACTGGAGATGGCAGACAGTCAGGGCGTGGAAGCGGCCCTGGGCTggg                                >  2:1563738/1‑48 (MQ=255)           ggAGATGGCAGACAGTCAGGGCGTGGAAGCGGCTCTGGGCTGGATACAGa                          >  2:219925/1‑50 (MQ=255)             agaTGGCAGACAGTCAGGGCGTGGAAGCGGCGCTGGGCTGGATACAGAcc                        <  2:673317/50‑1 (MQ=255)             agaTGGCAGACAGTCAGGGCGTGGAAGCGGCGCTGGGCTGGATACAGAcc                        <  1:1819372/50‑1 (MQ=255)              gaTGGCAGACAGTCAGGGCGTGGAAGCGGCTCTGGGCTGGATACAGAccc                       <  2:457301/50‑1 (MQ=255)               aTGGCAGACAGTCAGGGCGTGGAAGCGGCGCTGGGCTGGATACAGACCCg                      >  1:1199588/1‑50 (MQ=255)                        aGTCAGGGCGTGGAAGCGGCTCTGGGCTGGATACAGACCCGTCCGGGCAt             <  1:1662292/50‑1 (MQ=255)                            aGGGCGTGGAAGCGGCTCTGGGCTGGATACAGACCCGTCCGGGCATcac          >  1:1730983/1‑49 (MQ=255)                            aGGGCGTGGAAGCGGCTCTGGGCTGGATACAGACCCGTCCGGGCATcac          >  1:1380474/1‑49 (MQ=255)                             gggCGTGGAAGCGGCTCTGGGCTGGATACAGACCCGTCCGGGCATcacca        <  2:1795406/50‑1 (MQ=255)                             gggCGTGGAAGCGGCGCTGGGCTGGATACAGACCCGTCCGGGCATcacca        <  2:442971/50‑1 (MQ=255)                             gggCGTGGAAGCGGCGCTGGGCTGGATACAGACCCGTCCGGGCATcacca        >  1:1102127/1‑50 (MQ=255)                               gCGTGGAAGCGGCGCTGGGCTGGATACAGACCCGTCCGGGCATcaccact      <  2:1836342/50‑2 (MQ=255)                               gCGTGGAAGCGGCGCTGGGCTGGATACAGACCCGTCCGGGCATcaccact      <  1:831988/50‑2 (MQ=255)                                   ggAAGCGGCTCTGGGCTGGATACAGACCCGTCCGGGCATCACCACGGCAc  >  2:1527946/1‑50 (MQ=255)                                            |                                         CGGAAGCACTGGAGATGGCAGACAGTCAGGGCGTGGAAGCGGCTCTGGGCTGGATACAGACCCGTCCGGGCATCACCACGGCAC  >  NC_017635/3127724‑3127807

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑