Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,583,267	G→A	pseudogene (230/390 nt)	yrhA →	putative uncharacterized protein YrhA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,583,267	0	G	A	84.6%	19.9 / ‑2.0	13	pseudogene (230/390 nt)	yrhA	putative uncharacterized protein YrhA
Reads supporting (aligned to +/- strand):  ref base G (1/1);  new base A (4/7);  total (5/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.10e-01

ATTATGGACCACACAAAATGATGACTAAAACCCAAATAAATAAATTAATAAAAATGATGAATGATTTAGACTATCCATTTGAAGCACCGCTCAAGGAATCATTTATTGAAAGTATAATCCAAATAGAATTTAATTCTAATTCAACTAATTGCCTGGAGAAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATG  >  NC_000913/3583021‑3583434                                                                                                                                                                                                                                                       |                                                                                                                                                                        attatGGACCACACAAAATGATGACTAAAACCCAAATAAATAAATTAATAAAAATGATGAATGATTTAGACTATCCATTTGAAGCACAGCTCAAGGAATCATTTATTGAAAGTATAATCCAAATAGAATTTAATTCTAATTCAACTAATTGCCTGGAGAAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGAtt                                                                                                                                                                      >  1:5335/1‑250 (MQ=255)                  atgatgACTAAAACCCAAATAAATAAATTAATAAAAATGATGAATGATTTAGACTATCCATTTGAAGCACCGCTCAAGGAATCATTTATTGAAAGTATAATCCAAATAGAATTTAATTCTAAGTCAACTAAGTGCCTGGAGAAGTTATGTAATGAAGTTAGTATTCTGTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGAATTACGATTATTTAGCCtctc                                                                                                                                                    <  1:219550/251‑1 (MQ=255)                                                           gaatgaTTTAGACTATCCATTTGAAGCACCGCTCAAGGAATCATTTATTGAAAGTATAATCCAAATAGAATTTAATTC‑AATTCAACTAATTGCCTGGAGAAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAANg                                                                                                           <  1:255589/250‑1 (MQ=255)                                                                                          cTCAAGGAATCATTTATTGAAAGTATAATCCAAATAGAATTTAATTCTAATTCAACTAATTGCCTGGAGAAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGAATTACGat                                                                                                                                                                 >  1:124700/1‑166 (MQ=255)                                                                                                               aGTATAATCCAAATAGAATTTAATTCTAATTCAACTAATTGCCTGGAGAAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGAATTACGATTATTTAGCCGCTCGATTCCAGAACCTTCATTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGtt                                                       <  1:276258/251‑1 (MQ=255)                                                                                                                       ccAAATAGAATTTAATTCTAATTCAACTAATTGCCTGGAGAAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGAATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATc                                                <  1:7591/250‑1 (MQ=255)                                                                                                                                                          tggcgaAGTTATGTCATGAAGTTAGTATACTGTTTAAGAATAGACCTGATCCTAATACTTTTTTACGAGCCATGGATGGGTGCGCGGTTAATGAATTACGATTATATAGCATCTCGATTACCGAACCTTCAGTTCAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATACACCCTGATCTACAAGAACGGTTCGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACAtt            >  1:289161/5‑251 (MQ=255)                                                                                                                                                              gaAGTTATGGAATGAAGTTAGTATTCTTTTTAAGAAGCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGAATTACGATTATTTAGCCtctc                                                                                                                                                    <  1:156608/111‑1 (MQ=255)                                                                                                                                                                         aTGAAGTGAGTATTCTTTTTAAGAATCATCCTGAGTATCTTACTGTTTTAAGAGCAATGGATGGAGTCTAAGCTAATGAATTACGATTATTTAGCCTCTCGATTCCAGACCCTTCAGTTAAAAACCttttt                                                                                                                     <  1:41714/131‑1 (MQ=255)                                                                                                                                                                           gAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGAATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAACCCTTTTTGCCGTAAATGAAGTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCggn                                             <  1:79635/201‑2 (MQ=255)                                                                                                                                                                                               gAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGCTGGATTCGAAGTTAATGAATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTaaaac                                                                                                                            >  1:285332/1‑101 (MQ=255)                                                                                                                                                                                                                    ttttttAAGAGCAATGGATGGATTCGAAGTGAATGAAGTACGAGTATTTAGCCTCGCGAGTCCAGAAACGTCATTTAAAAACCTTTTAGCCGTAAATGAATTGTATAGAAATAATGATGATTTCAGAGACCCTGATCTACAAGAACGGTTAGTGATCGGGGAGTATAGCATTTCAATATTTACTTATGACATTAAAGGTGAtg  <  1:328328/203‑1 (MQ=255)                                                                                                                                                                                                                                            ngAAGTTAATGAATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAg                                     >  1:81198/2‑144 (MQ=255)                                                                                                                                                                                                                                                       |                                                                                                                                                                        ATTATGGACCACACAAAATGATGACTAAAACCCAAATAAATAAATTAATAAAAATGATGAATGATTTAGACTATCCATTTGAAGCACCGCTCAAGGAATCATTTATTGAAAGTATAATCCAAATAGAATTTAATTCTAATTCAACTAATTGCCTGGAGAAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATG  >  NC_000913/3583021‑3583434

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑