Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,027,423	0	T	C	40.0%	‑2.5 / 20.1	20	intergenic (+195/+186)	fre/fadA	NAD(P)H‑flavin reductase/3‑ketoacyl‑CoA thiolase
Reads supporting (aligned to +/- strand):  ref base T (10/2);  new base C (6/2);  total (16/4)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.42e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

AATGCGCGGGAAGATCGCCTGTTTGGCGATGCGTTTGCATTTATCTGAGATATAAAAAAACCCGCCCCTGACAGGCGGGAAGAACGGCAACTAAACTGTTATTCAGTGGCATTTAGATCTATGACGTATCTGGCAAACCATGCCCGATGCGACGCTGTCGCGTCTTATCGTGCCTACAAATAGTCCGAACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGACGCTGTCGCGTCTTATCGTGCCTACAAATAGT‑CCG‑AACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACATTGGTGCCGGATCGGTAGACCGGATAAGGCGTTCACGCCGCATCCGGCAAGTGGTTAAACCCGCTCAAACACCGTCGCAATACCCTGACCCAGACCGATACACATCGTCGCC  >  NC_000913/4027181‑4027666                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                      aaTGCGGGGGAAGACCCCCTGTTGGGCGATGTGTTTGCATTTATTGGAAATATAAAAAACCCCGCCCCTGACAGGCGGGAAGAACGGCAACTAAACTGTTATTCAGTGGCATTTAGATCTATGACGTATCTGGCAAACCATGCCCGATGCGACGCTGTCGCGTCTTATCGTGCCTACAAATAGTCCGAACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGAc                                                                                                                                                                                                                                               <  1:448577/251‑1 (MQ=25)   ggcgggggaagccggctggttgggCGGTGCGTTTGCATTTACCGGATATAGAAAAATCCCCGCCCCTGACAGGCGGGAAGAACGGCACCTAAACTGTTATTCAGTGGCATTGAGATCTATGACGTATCTGGCAAACCATGCCCGATGCGACGCTGTCGCGTCTTATCTTGCCTACAAATAGTCCGAACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGTCAATTGGTGCATGATGCCTGATGCGACGc                                                                                                                                                                                                                                             <  2:53965/229‑1 (MQ=21)        gggAAGATCGCCTGTTTGGCGATGCGTTTGCATTTATCTGAGATATAAAAAAACCCGCCCCTGACAGGCGGGAAGAACGGCAACTAAACTGTTATTCAGTGGCATTTAGATCTATGACGTATCTGGCAAACCATGCCCGATGCGACGCTGTCGCGTCTTATCGTGCCTACAAATAGTCCGAACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGACGCTggcg                                                                                                                                                                                                                                        >  1:116834/1‑248 (MQ=255)             gATCGCCTGTTTGGCGATGCGTTTGCATTTATCTGAGATATAAAAAAACCCGCCCCTGACAGGCGGGAAGAACGGCAACTAAACTGTTATTCAGTGGCATTTAGATCTATGACGTATCTGGCAAACCATGCCCGATTCGACGCTGTCGCGTCTTATCGTGCCTACAAATAGGACGAACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGAGGCCTGATGCGACGCTGGCGCGTCt                                                                                                                                                                                                                                   >  1:201438/1‑251 (MQ=255)                     gTTTGGCGATGCGTTTGCATTTATCTGAGATATAAAAAAACCCGCCCCTGACAGGCGGGAAGAACGGCAACTAAACTGTTATTCAGTGGCATTTAGATCTATGACGTATCTGGCAAACCATGCCCGATGCGACGCTGTCGTGTCTTATCGTGCCTACAAATAGTCCGAACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGACGCTGGCGCGTCTTATcaggc                                                                                                                                                                                                                           >  1:106558/1‑247 (MQ=255)                                 gTTTGCATTTATCTGAGATATAAAAAAACCCGCCCCTGACAGGCGGGAAGAACGGCAACTCAACTGTTAATCAGTGGCATTTAGCTCTATGACGTATCTTGCAAACCATGCCCGAGGCGACGCTGTCGCGTCTTATCGTGCCTACCAATAGTCCGAACCGGAGGCCGGATAAGGCGTTTACGCCGCCTCCGGCAATTGGTGCATGATGCCTGATGCGACGCTGGCGCGTCTTATcaggccttcattggtgc                                                                                                                                                                                                               >  1:319633/1‑235 (MQ=21)                                                agaTATAAAAAAACCCGCCCCTGACAGGCGGGAAGAACGGCAACTAAACTGTTATTCAGTGGCATTTAGATCTATGACGTATCTGGCAAACCATGCCCGATGCGACGCTGTCGCGTCTTATCGTGCCTACAAATAGTCCGAACCGTAGGCCGGATAAGGCGTTTACCCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACattggtgccggatcggtagaccg                                                                                                                                                                                                >  1:71816/1‑229 (MQ=18)                                                                                aagaaCGGCAACTAAACTGTTATTCAGTGGCATTTAGATCTATGACGTATCTGGCAAACCATGCCCGATGCGACGCTGTCGCGTCTTATCGTGCCTACAAATAGTCCGAACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACAT‑TGGTGCCGGATCGGTAGACCGGATAAGGCGTTCACGCCTCATCCGGCaagagg                                                                                                                                                               >  2:55047/1‑247 (MQ=11)                                                                                aagaaCGGCAACTAAACTGTTATTCAGTGGCATTTAGATCTATGACGTATCTGGCAAACCATGCCCGATGCGACGCTGTCGCGTCTTATCGTGCCTACAAATAGTCCGAACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACAT‑TGGTGCCGGATCGGTAGACCGGATAAGGCGTTCACGCCGCATCCGGCAAGTgg                                                                                                                                                               >  1:305515/1‑251 (MQ=11)                                                                                aagaaCGGCAACTAAACTGTTATTCAGTGGCATTTAGATCTATGACGTATCTGGCAAACCATGCCCGATGCGACGCTGTCGCGTCTTATCGTGCCTACAAATAGTCCGAACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACAT‑TGGTGCCGGATCGGTAGACCGGATAAGGCGTTCACGCCGCATCCGGCAAGTgg                                                                                                                                                               >  2:455701/1‑251 (MQ=11)                                                                                 agaaCGGCAACTAAACTGTTATTCAGTGGCATTTAGATCTATGACGTATCTGGCAAACCATGCCCGATGCGACGCTGTCGCGTCTTATCGTGCCTACAAATAGTCCGAACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACAT‑TGGTGCCGGATCGGTAGACCGGATAAGGCGTTCACGCCGCATCCGGCAAGTggg                                                                                                                                                              >  1:176919/1‑250 (MQ=11)                                                                                   aaCGGCAACTAAACTGTTATTCAGTGGCATTTAGATCTATGACGTATCTGGCAAACCATGCCCGATGCGACGCTGTCGCGTCTTATCGTGCCTACAAATAGTCCGAACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACAT‑TGGTGCCGGATCGGTAGACCGGATAAGGCGATCACGCCGCATCCGGCAAGTGGtt                                                                                                                                                             >  1:397517/1‑249 (MQ=11)                                                                                                                                                                                                                     agatctatgacgtatctggcaaaccatgCCCGATGCGACGCTGTCGCGTCTTATCGTGCCTACAAATAGT‑CCG‑AACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACATTGGTGCCGGATCGGTAGACCGGATAAGGCGTTCACGCCGCATCCGGCAAGTGGTTAAACCCGCTCAAACACCGTCGCAATACCCTGAc                         >  1:58029/26‑251 (MQ=18)                                                                                                                                                                                                                      gatctatgacgtatctggcaaaccatgCCCGATGCGACGCTGTCGCGTCTTATCGTGCCTACAAATAGT‑CCG‑AACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACATTGGTGCCGGATCGGTAGACCGGATAAGGCGTTCACGCCGCATCCGGCAAGTGGTTAAACCCGCTCAAACACCGTCGCAATACCCTGAcc                        >  1:475718/25‑251 (MQ=18)                                                                                                                                                                                                                         ctatgacgtatctggcaaaccatgCCCGATGCGACGCTGTCGCGTCTTATCGTGCCTACAAATAGT‑CCG‑AACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACATTGGTGCCGGATCGGTAGACCGGATAAGGCGTTCACGCCGCATCCGGCAAGTGGTTAAACCCGCTCAAACACCGTCGCAATACCCTGAccc                       >  2:206459/22‑249 (MQ=18)                                                                                                                                                                                                                          tatgacgtatctggcaaaccatgCCCGATGCGACGCTGTCGCGTCTTATCGTGCCTACAAATAGT‑CCG‑AACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACATTGGTGCCGGATCGGTAGACCGGATAAGGCGTTCACGCCGCATCCGGCAAGTGGTTAAACCCGCTCAAACACCGTCGCAATACCCTGaacc                       >  1:202749/21‑245 (MQ=18)                                                                                                                                                                                                                               cgtatctggcagaccctgCCCGATGCGACGCTGTCGCGTCTTAGCGTGCCTACAAATAGT‑CCG‑AACCGTAGGCTGGATAAGGCGTTTACGCCGCTTCCGGCAATTGGTGCATGATGCCTTATGCGTCGCTGGCGCGTCTTATCAGGCGTCCATTGGTGCCGGATCGGTAGACCGGGTAAGGCGGTCACGCCGCATCCGGCAAGTGGTTAAACCCGCTGAAACACCGTCGCAATACCCTGACCCAGACCGAt               <  1:131843/235‑1 (MQ=255)                                                                                                                                                                                                                                gtatctggcaaaccatgCCCGATGCGACGCTGTCGCGTCTTATCGTGCCTACAAATAGT‑CCG‑AACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACATTGGTGCCGGATCGGTAGACCGGATAAGGCGTTCACGCCGCATCCGGCAAGTGGTTAAACCCGCTCAAACACCGTCGCAATACCCTGACCCAGACCGATa              <  1:310256/237‑1 (MQ=255)                                                                                                                                                                                                                                         aaaccatgCCCGATGCGGCGCTGTCGCGTCTTATCGTGCCTACAAATAGT‑CCG‑AACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACATTGGTGCCGGATCGGTAGACCGGATAAGGCGTTCACGCCGCATCCGGCAAGTGGTTAAACCCGCTCAAACACCGTCGCAATACCCTGACCCAGACCGATACACAtcgtc     >  1:106010/6‑251 (MQ=255)                                                                                                                                                                                                                                              atgCCCGATGCGACGCTGTCGCGTCTTATCGTGCCTACAAATAGT‑CCG‑AACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACATTGGTGCCGGATCGGTAGACCGGATAAGGCGTTCACGCCGCATCCGGCAAGTGGTTAAACCCGCTCAAACACCGTCGCAATACCCTGACCCAGACCGATACACATCGTCGcc  >  1:412508/1‑249 (MQ=255)                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                      AATGCGCGGGAAGATCGCCTGTTTGGCGATGCGTTTGCATTTATCTGAGATATAAAAAAACCCGCCCCTGACAGGCGGGAAGAACGGCAACTAAACTGTTATTCAGTGGCATTTAGATCTATGACGTATCTGGCAAACCATGCCCGATGCGACGCTGTCGCGTCTTATCGTGCCTACAAATAGTCCGAACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGACGCTGTCGCGTCTTATCGTGCCTACAAATAGT‑CCG‑AACCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATTGGTGCATGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACATTGGTGCCGGATCGGTAGACCGGATAAGGCGTTCACGCCGCATCCGGCAAGTGGTTAAACCCGCTCAAACACCGTCGCAATACCCTGACCCAGACCGATACACATCGTCGCC  >  NC_000913/4027181‑4027666

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑