Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,941,874	C→T	noncoding (67/1542 nt)	rrsC →	16S ribosomal RNA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,941,874	0	C	T	92.0%	44.4 / ‑3.3	25	noncoding (67/1542 nt)	rrsC	16S ribosomal RNA
Reads supporting (aligned to +/- strand):  ref base C (2/0);  new base T (13/10);  total (15/10)
Fisher's exact test for biased strand distribution p-value = 5.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAGACGAAAAATGAATACCAAGTCTCAAGAGTGAACACGTAATTCATTACGAAGTTTAATTCTTTGAGCATCAAACTTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGA‑AACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCC‑TGATGGAGGGGGATAACTACTGGAAACG‑GTAGCTAATACCGCATAACGTCGCAAGACCAAA‑GAGGGGGACCTTCGGGCCTCTTGCCATCAG‑ATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACC  >  NC_000913/3941641‑3942115                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                                       gcTGAGAAAAAGCAACGCGGCACGCCTCTTTAACACTTTATCAACCACTCTGTGTGGGCACTAGAAGATACGGATTCTTAACGTCGCAAGACGAAAATTGAATACCAAGGCTCGAGAGTGAACACGTAGTTCATTACACAGTTAAATTCTTTAAACATCAAACTCTTAAATTGAAGAGTTTGATCTTGGATCAGATTGACCGCTGGCGGAAGGCCTACCACATGCAAGTCGCACGGTAACAGGa‑agacgat                                                                                                                                                                                                                                      >  2:323384/1‑245 (MQ=2)          aagcaaagcGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAGACGAAAAATGAATACCAAGTCTCAAGAGTGAACACGTAATTCATTACGAAGTTTAATTCTTTGAGCATCAAACTTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGA‑AACAGCTTGCTGTTTc                                                                                                                                                                                                                             >  1:265378/1‑251 (MQ=21)               aagcGGCACTGCTCTGTAACAATTTATCAGACAATCTGTGTGGGCACGTGAAGATACTGATTCTTAACGTCGCAAGACGAAAAATGAATACCAAGTCTCAAGAGTGAACACGTAATTCATTACGAAGTTTAATTCTTTGAGCATCAAACTTTTAAATTGAAGAGTTTGATCATGGCTCATATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGA‑AACAGCTTGCTGTTTCGCTGa                                                                                                                                                                                                                        <  2:430090/251‑1 (MQ=255)                                                                                                                                 aTTCATTACGAAGTTTAATTCTTTGAGCATCAAACTTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGA‑AACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCC‑TGATGGAGGGGGATAACTACTGGAAACG‑GTAGCTAATACCGCATAACGTCGCAAGACCAAA‑GAGGGGGACCTTCgg                                                                                                   <  1:46108/251‑1 (MQ=14)                                                                                                                                      ttACGAAGATTAATTCTTTGAGCATCAAACTTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGATGGCGGCAGGCCTAACACATGCACGACGAATGGAAATAGGA‑ACTAGCTTGCTGTTTCGCTGACGAGTGGCGGCCGGACGAGTAATGGCAGGGACACTGCC‑TGCTGGAGGGGGATAAGTACTGGACAAG‑AGAGATAATACCGAATAACGCTGCAA‑ACAAAAAGAGGGGGACCTACGGGctcc                                                                                              >  2:373611/1‑248 (MQ=2)                                                                                                                                            aGTTTAATTCTTTGAGCATCAAACTTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGA‑AACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCC‑TGATGGAGGGGGATAACTACTGGAAACG‑GTAGCTAATACCGCATAACGTCGCAAGACCAAA‑GAGGGGGACCTTCGGGCCTCTTGCCa                                                                                        <  1:137464/251‑1 (MQ=14)                                                                                                                                                     cTTTGAGCATCAAACTTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGA‑AACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCC‑TGATGGAGGGGGATAACTACTGGAAACG‑GTAGCTAATACCGCATAACGTCGCAAGACCAAA‑GAGGGGGACCTTCGGGCCTCTTGCCATCAG‑Atgtg                                                                              >  1:175237/1‑251 (MQ=18)                                                                                                                                                               cAAACTTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGA‑AACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCC‑TGATGGAGGGGGATAACTACTGGAAACG‑GTAGCTAATACCGCATAACGTCGCAAGACCAAA‑GAGGGGGAACTTCGGGCCTCTTGCCATCAG‑ATGTGCCCAGATggg                                                                    >  1:531082/1‑251 (MQ=18)                                                                                                                                                                       tAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGA‑AACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCC‑TGATGGAGGGGGATAACTACTGGAAACG‑GTAGCTAATACCGCATAACGTCGCAAGACCAAA‑GAGGGGGACCTTCGGGCCTCTTGCCATCAG‑ATGTGCCCAGATGGGATTAGCt                                                             <  1:201682/250‑1 (MQ=18)                                                                                                                                                                        aaaagtaaGAGTGTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATTCAAGTCGAATGGTAACAGGA‑AACAGCTTGCTGTGTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCC‑TGATGGAGGGGGATAACTACTGGAAACG‑GTAGCTAATACCGCATAACGTCGCAAGACCAAA‑GATGGGGACCTTTGGGTTTCGTGCCATCAG‑ATGTGCCCAGATGGGATTAGCta                                                            <  1:560295/244‑1 (MQ=11)                                                                                                                                                                         aaTTGAAGAGTTTGATCATGGCTCAGAGTGAACGCTTGCGGCAGGCCTAACACATGTAAGTCGGATGGTAACAGGA‑AACAGCTTGCGGTTTCGCTGACGAGGTGCGGACGGGTTAGTAATGTCTGGGAAACTGCC‑TGATGGAGGGGGATAACTACTGGAAACG‑GTAGCTAATATCGCATAACGGCGCAAGACCAAA‑GAGGGGGACCTTCGGGCCTCTTGCCATCAG‑ATGTGCCCAGATGTGATTAGCtagg                                                          <  2:315829/251‑2 (MQ=11)                                                                                                                                                                          aTTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGA‑AACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCC‑TGATGGAGGGGGATAACTACTGGAAACG‑GTAGCTAATACCGCATAACGTCGCAAGACCAAA‑GAGGGGGACCTTCGGGCCTCTTGCCATCAG‑ATGTGCCCAGATGGGATTAGCtagta                                                         <  1:250222/251‑1 (MQ=21)                                                                                                                                                                                    ttGATCATGGCTCAGAGTGAACGCTGGGGGCAGGGCTTACACATGCAAGTCGAATGGTAACAGGA‑AACAGCTTGCTGGTTCGCTGACGAGTGGCGGACGGGTGAGTAATGGCTGGGAAACTGCC‑TGATGGAGGGGGATAACTACTGGAAACG‑GTAGCTAATACCGCATAACGTCGCAAGACCAAA‑GAGGGGGACCTTCGGGCCTCTTGCCATCAG‑ATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTa                                                <  1:185786/250‑1 (MQ=11)                                                                                                                                                                                      gATCATGGCTCAGATTGAACGCTGGCGGAAGGCCTAACACATGCCAGTCGAATGGTAACAGGA‑AACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCC‑TGCTGGAGGGGGATAACTACTGGAAACG‑GTAGCTAATACCGCATAACGTCGCAAGACCAAA‑GAGGGGGACCTTCGGGCCTCTTGCCATCAG‑ATGAGCCCAGATGGGATTAGCTAGTAGGTggggacacg                                             >  1:494622/1‑246 (MQ=255)                                                                                                                                                                                         cATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGA‑AACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCC‑TGATGGAGGGGGATAACTACTGGAAACG‑GTAGCTAATACCGCATAACGTCGCAAGACCAAA‑GAGGGGGACCTTCGGGCCTCTTGCCATCAG‑ATGTGCCCAGATGGGATTAGCTAGTAGGGGGGGTAACGGcc                                          >  1:236005/1‑250 (MQ=37)                                                                                                                                                                                                      gAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGA‑AACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCC‑TGATGGAGGGGGATAACTACTGGAAACG‑GTAGCTAATACCGCATAACGTCGCAAGACCAAA‑GAGGGGGACCTTCGGGCCTCTTGCCATCAG‑ATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACg                                             <  1:399764/235‑1 (MQ=37)                                                                                                                                                                                                      gAACGCTGGCGGCAGGACTAACACATGCCAGTCGTATGGTAACAGGA‑AACAGCTTGCTGTTTCGCTGACGAGAGGCGGGAGGGGGTGAAATTAATCAGCAACTGCC‑TGGTAGGGGGGGGTAACTTCTGGAAACGCGAAAGTA‑TACCCCATAACGTCGCAAAACCAAA‑ACGGGGGCCCTTTGGGACTCTTGCCAACCG‑ATGTGCCCAGATGGGGTTAGCAAGTAGGTGGGGTAACgcgatcacaaggacgcc                             >  2:399764/1‑235 (MQ=2)                                                                                                                                                                                                           cTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGA‑AACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCC‑TGATGGAGGGGGATAACTACTGGAAACG‑GTAGCTAATACCGCATAACGTCGCAAGACCAAA‑GAGGGGGACCTTCGGGCCTCTTGCCATCAG‑ATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGGAACGGCTCACCTAGGCGACGATccc                        >  1:412373/1‑251 (MQ=255)                                                                                                                                                                                                                ggcAGGCCTAACACATGCAAGTCGAATGGTAACAGGA‑AACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCC‑TGATGGAGGGGGATAACTACTGGAAACG‑GTAGCTAATACCGCATAACGTCGCAAGACCAAA‑GAGGGGGACCTTCGGGCCTCTTGCCATCAG‑ATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCt                   >  1:520810/1‑251 (MQ=38)                                                                                                                                                                                                                ggcAGGCCTAACACATGCAAGTCGAACGGTAACAGGA‑AACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCC‑TGATGGAGGGGGATAACTACTGGAAACG‑GTAGCTAATACCGCATAACGTCGCAAGACCAAA‑GAGGGGGACCTTCGGGCCTCTTGCCATCGG‑ATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCt                   >  1:484371/1‑251 (MQ=21)                                                                                                                                                                                                                 gcAGGCCTAACACATGCAAGACGAATGG‑AAAACGAGAACAGCTCGCTGTTTCGCTAACGAGGGGCGGACGGGTGAACAAAGACTGGGAAGC‑GCCGTGGTGGAGGGGGATAACTACTGGAAACG‑GTAGCTAGGACCGCAGAACGACGCCAGACCAAA‑GAGGGGAACCTTCGGACCCTTTGCCATAAGTAGGT‑CCCAGAGGATATTGGGTAGTAGGGGGGGTAACGGCTCACCGAGGcctccaacccatatct                  >  2:570719/1‑236 (MQ=2)                                                                                                                                                                                                                       cTAACACATGCAAGTCGAATGGTAACAGGA‑AACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCC‑TGATGGAGGGGGATAACTACTGGAAACG‑GTAGCTAATACCGCATAACGTCGCAAGACCAAA‑GAGGGGGACCTTCGGGCCTCTTGCCATCAG‑ATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTgg            >  1:330295/1‑250 (MQ=38)                                                                                                                                                                                                                         aaCACATGTAAGGGGAATGGTAACAGGA‑AACAGCATGCTGGTTCGCTGACGAGTGGCGGACGTGTGAGTAATGTCTGGGAAACTGCC‑GGATGGAGTGGGATAACTACTGGAAACG‑GTAGCTAATACCGCATAACGTCGCAAGACCAAA‑GAGGGGGACCTTCGGGCCTCGGTCCATCAT‑ATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTATGGGCTCACCTAGTCGACGATCCCTAGCTGGTCTgag           <  2:557151/250‑1 (MQ=14)                                                                                                                                                                                                                             caTGCAAGTCGAATGGTAACAGGA‑AACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCC‑TGATGGAGGGGGATAACTACTGGAAACG‑GTAGATAATACCGCATAACGTCGCAAGACCAAA‑GAGGGGGACCTTCGGGCCTCTTGCCATCAG‑ATGTGCCCAGATGGGATTAGCTAGTACGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGAt      >  1:337005/1‑251 (MQ=255)                                                                                                                                                                                                                                  aaGTCGAATGGTAACAGGA‑AACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGGAATGTCTGGGAAACTGCC‑TGATGGAGGGGGATACCTACTGGAAACG‑GTAGCTAATACCGCATAACGTCGCAAGACCAAA‑GAGGGGGACCTTCGGGCCTCTTGCCATCAG‑ATTTGCCACGATGGGGTTAGCTAGGAGGCGGGGTGACGGCTCACCTCGGCGACGATCCCTACCTGGTCTGAGGGGAAGAcc  >  2:268741/1‑250 (MQ=14)                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                                       GCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAGACGAAAAATGAATACCAAGTCTCAAGAGTGAACACGTAATTCATTACGAAGTTTAATTCTTTGAGCATCAAACTTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGA‑AACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCC‑TGATGGAGGGGGATAACTACTGGAAACG‑GTAGCTAATACCGCATAACGTCGCAAGACCAAA‑GAGGGGGACCTTCGGGCCTCTTGCCATCAG‑ATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACC  >  NC_000913/3941641‑3942115

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑