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	93.5%	64.4 / ‑1.6	31	noncoding (67/1542 nt)	rrsC	16S ribosomal RNA
Reads supporting (aligned to +/- strand):  ref base C (2/0);  new base T (22/7);  total (24/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.52e-01

GCACACCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAGACGAAAAATGAATACCAAGTCTCAAGAGTGAACACGTAATTCATTACGAAGTTTAATTCTTTGAGCATCAAAC‑TTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGG  >  NC_000913/3941627‑3942109                                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                            gCACACCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAGACGAAAAATGAATACCAAGTCTCAAGAGTGAACACGTAATTCATTACGAAGTTTAATTCTTTGAGCATCAAAC‑TTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGt                                                                                                                                                                                                                                          <  1:420292/251‑1 (MQ=14)                      aacagcaaagcGGCACTGCTCTTTAACAATTTATCAGACAATCAGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAGACGACAAATGAATCCCAAGTCTCAAGAGTGAACACGTAATTCATTACGAAGTTTAATTCTTTGAGCATCAAAC‑TTTTAAATTGCAGCGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGCACCAGCTTGCTGtt                                                                                                                                                                                                                     >  2:48509/4‑251 (MQ=11)                       aaagcaaagcGGCACTGCTCTTTAACAATTTATCAGACAATCTGAGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAGACGAAAAATGAATACCAAGTCTCAAGAGTGAACACGTAATTCATTAAGAAGTTTAATTCTTTGAACAGCAAAC‑TTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGACAGGGCTAACACATGCAAGTCGAATGGTAACAGGAACAAGCTTGCAGttt                                                                                                                                                                                                                    >  1:325313/1‑251 (MQ=11)                                 gccACTGATCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGCAGATACGGATTCATAACGTCGCAAGACGAAAAATGAATACCAAGTCTCAAGAGTGAACACGTAATTCATTACGAAGTTTAATTCTTTGAGCATCAAAC‑TTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGACACAGCTGGCTGTTTCGCTGACggg                                                                                                                                                                                                          >  2:49294/3‑249 (MQ=2)                                                                                                                                           cGTAATTCATTACGCAGATTAATTCTTCGAG‑AACAAACCTTTTAAATTGAAGAGTTTGCTCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACCCATGCAAGTCGCATGGTAACAGGAAACAGATTGCTGTTTCGCTGACGAGCGGCGGACGGGTGAGTAATGCCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGAACAAAGCGGGGGACCt                                                                                                >  2:423109/1‑251 (MQ=11)                                                                                                                                                  cATTACGAAGTTTAATTCTTTGAGCATCAAAC‑TTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGTTGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCCTAACGTCGCACGACCAAAGAAGGGGACCTTCg                                                                                             >  2:9988/1‑247 (MQ=9)                                                                                                                                                  cATTACGAAGTTTAATTCTTTGAGCATCAAAC‑TTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGGCCAAAGAGGGGGACCTTCg                                                                                             <  1:9988/247‑1 (MQ=14)                                                                                                                                                   aTTACGAAGTATAATTCTTTGAGCATCAAAC‑TTTTAAATTGCAGAATTTGAACATGGCTCAGCTTGAACCCTGGCGGCAGGCCTAACACATGCAAGTCGAATAATAACAGGAAACCGCTTGAAGTTTCGATGACGAGTGGCGGACGGGTGAGTACAGTCCGGGAAACTGCCTGCTGGGGGGGGCTAAATAATGGAAACGGTCGCTAATACCGCATAACGACGCAAGACCCACGGGGGGGACATCCGGGCct                                                                                        >  2:307695/1‑251 (MQ=2)                                                                                                                                                         aaGTTTAATTCTTTGAGCATCAAAC‑TTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGCGAGTAATGTCTGGGAAACTGCCTGCTGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGCCCAAAACGGGGGACCTTCGGGCCTCtttcc                                                                                  >  2:364546/1‑248 (MQ=11)                                                                                                                                                                          cATCAAAC‑TTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCACGTCGAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGAGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGGTAAATACTGGAAACGGTAGCTAATACCGCATAACGTCGCCAGACCAAAGAGGGGGAACTTCGGGCATCTTGcccgcggatgagcccag                                                                   >  2:252969/1‑234 (MQ=11)                                                                                                                                                                                 c‑TTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGGGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAAGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATggggtt                                                           >  2:3796/1‑247 (MQ=16)                                                                                                                                                                                      tAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATAACGCCTAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCCGAGGTGCCCAGATGGGATTGGCt                                                       >  2:247725/1‑250 (MQ=255)                                                                                                                                                                                       aaaTTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCta                                                      <  1:231509/250‑1 (MQ=18)                                                                                                                                                                                         aTTGAAGCGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCtagt                                                    >  1:335009/1‑250 (MQ=21)                                                                                                                                                                                            gAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAgg                                                 <  1:269571/250‑1 (MQ=25)                                                                                                                                                                                              agagTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTgg                                              >  2:366064/1‑251 (MQ=37)                                                                                                                                                                                              agagTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTgg                                              >  1:127031/1‑251 (MQ=37)                                                                                                                                                                                                agTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCCGATGGAGGGGGCCAACTACTGGAAACGGTAGCTAATAACGCAAAACGTCGGAAGACCAAAGAGGGGGACACTCGGGCACCTAGCCAGCAGAAGAGCCCAGAGGGGAATAGCTAGGAGgggggg                                            >  1:395396/1‑251 (MQ=11)                                                                                                                                                                                                       tCATGGCTCAGCTCGAACGCTGGCGGCAGGCCCAACACAAGCAAGCCGCATGGCAACAGGAAACCGCTTGCTGTTTCGCTGACGAGTGGCGGAAGGGTGAGTAATGTCCGGGAAACTGCCTGATGGAGGGGGCAAACTACCGGAAACCGCAGCTAATACCGCATCACGTCGCAAGACCAAAGTGGGGGACCCTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGGTTAGCTAGAAGGTGGGGTAACGGc                                     >  2:24546/1‑251 (MQ=255)                                                                                                                                                                                                        cATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACCTGCCAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGAAGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATAACGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGGGGGGTAACGGCt                                    >  2:275252/1‑251 (MQ=255)                                                                                                                                                                                                        cATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGAGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAAATACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGAACTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTTGCTAGTAGGGGGGGTAACGGCt                                    >  1:404541/1‑251 (MQ=255)                                                                                                                                                                                                            gCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGAAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGAAGGGAGAGTGATGGCTGGGAAACTGCCTGCTGGAGGGGGATAAATACTGGAAAAGGTAGCTAATAACCCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGAGCCCAGATAGGATTAGCTAGTAGGAGGGGTAACGGccaccc                                >  2:454310/1‑246 (MQ=11)                                                                                                                                                                                                               cAGATTGAACGATGGCGGCAGGCCTCACACATGCCAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAAAGTCGCAAGACCAAAAAGGGGGACCTTAGGGCCTCTTGCCATCAGATGTGCCCCGATGGGATTATCTAGTAGGCGGGGTAACGGCTCACCt                               >  2:199520/1‑249 (MQ=11)                                                                                                                                                                                                                    tGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGAAACCGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCCTAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGAAGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGcgac                        >  1:312452/1‑251 (MQ=255)                                                                                                                                                                                                                     gAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGcgacg                       <  1:75389/251‑1 (MQ=38)                                                                                                                                                                                                                     gAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGcgacg                       <  1:48509/251‑1 (MQ=38)                                                                                                                                                                                                                            ggcggcAGGCCTAACACATGCAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCt                 >  1:253982/1‑250 (MQ=39)                                                                                                                                                                                                                                  aGGCCTAACACATGCAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGTGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCCACTAGGCGAAGATCCCTAGCTggg          >  1:290960/1‑250 (MQ=255)                                                                                                                                                                                                                                    gCCTAACACATGCAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCCGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCt        >  1:208088/1‑251 (MQ=255)                                                                                                                                                                                                                                     ccTAACACATGCAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCGGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTATCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTGCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGTCGACGATCCTTATCTGGTCTg       <  2:279564/251‑1 (MQ=14)                                                                                                                                                                                                                                          cacaTGCAAGTCGAATGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAgg  >  2:176656/1‑251 (MQ=38)                                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                            GCACACCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAGACGAAAAATGAATACCAAGTCTCAAGAGTGAACACGTAATTCATTACGAAGTTTAATTCTTTGAGCATCAAAC‑TTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGG  >  NC_000913/3941627‑3942109

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: ‑