Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,817,583	+C	intergenic (+44/‑177)	yicC → / → dinD	putative RNase adaptor protein YicC/DNA damage‑inducible protein D

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,817,583	1	.	C	96.7%	103.9 / ‑2.8	30	intergenic (+44/‑177)	yicC/dinD	putative RNase adaptor protein YicC/DNA damage‑inducible protein D
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base C (14/15);  total (15/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCCTCGAAGCGCATGTCAAAGAGACCTACAACATTCTGAAGAAAAAAGAAGCGGTTGGTCGTCGTCTGGATTTTATGATGCAGGAGTTCAACCGCGAGTCGAACACTCTTGCGTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCCATCGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAACATCGAATAACTCGTAACGCCAATTCTTACTTTTCCGCCTTCACAAATGCCGC‑C‑ACTCAAACAGAGCGGCATTTTTCTTCCCCGCAACATTCAATTCTGTTTTGCGTGCCTGCTCCAGATTTTGCGATGTTTTTTTGCCCAGCACACTGAGAACGTGAGATACTCACAACTGTATATAAATACAGTTACAGATTTACTTTCTTTGCAATTGATATCACATGGAGTGGGCAATGAACGAACATCATCAACCTTTTGAAGAGATAAAACTGATTAATGCAAACGGAGC  >  NC_000913/3817333‑3817815                                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                         cGCCTCGAAGCGCATGTTAAAGAGACGTACAACATTCTGAAGAAAAAAGAAGCCGTTGGTCGTCGTCTGGACTTTATGATGCAGGAGTTCAACCGCGAGTCGAACACTCTTGCGTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATgccgc‑c                                                                                                                                                                                                                                           >  1:247803/1‑251 (MQ=255)        aaGCGCATGTTAAAGAGACGTACAACATTCTGAAGAAAAAAGAAGCCGTTGGTCGTCGTCTGGACTTTATGATGCAGGAGTTCAACCGCGAGTCGAACACTCTTGCGTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCa                                                                                                                                                                                                                                     >  1:89850/1‑250 (MQ=255)                   aaaGAGACGTACAACATTCTGAAGAAAAAAGAAGCCGTTGGTCGTCGTCTGGACTTTATGATGCAGGAGTTCAACCGCGAGTCGAACACTCTTGCGTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGc                                                                                                                                                                                                                          >  1:263765/1‑250 (MQ=255)                   aaaGAGACGTACAACATTCTGAAGAAAAAAGAAGCCGTTGGTCGTCGTCTGGACTTTATGATGCAGGAGTTCAACCGCGAGTCGAACACTCTTGCGTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCa                                                                                                                                                                                                                         <  1:418963/251‑1 (MQ=255)                   aaaGAGACGTACAACATTATGAAGAAAAAAGAAGCCGTTGGTCGTCGTCTGGCCTTTATGATGCAGGAGTTCAAACGCGAGTCGAACACTCTTGCGTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAACGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGCAC‑ACTCAACCAGAGCgtc                                                                                                                                                                                                                          >  2:38857/1‑248 (MQ=255)                    aaGAGACGTACAACATTCTGAAGAAAAAAGAAGCCGTTGGTCGTCGTCTGGACTTTATGATGCAGGAGTTCAACCGCGAGTCGAACACTCTTGCGTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATgccgc‑ccact                                                                                                                                                                                                                                       >  2:51998/1‑232 (MQ=255)                    aaGAGACGTACAACATTCTGAAGAAAAAAGAAGCCGTTGGTCGTCGTCTGGACTTTATGATGCAGGAGTTCAACCGCGAGTCGAACACTCTTGCGTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATgccgc‑ccact                                                                                                                                                                                                                                       <  1:51998/236‑5 (MQ=255)                        gacgtACAACATTCTGAAGAAAAAAGAAGCCGTTGGTCGTCGTCTGGACTTTATGATGCAGGAGTTCAACCGCGAGTCGAACACTCTTGCGTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCAttttt                                                                                                                                                                                                                    <  2:247803/247‑1 (MQ=255)                         acgtACAACATTATGAAGAAAAAAGAAGCCGTTGGTCGTCGTCTGGACTTTATGATGCAGGAGTTCAACCGCGAGTCGAACACTCTTGCGTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTttc                                                                                                                                                                                                                   >  1:108936/4‑251 (MQ=255)                           gtACAACCTTCTGAAGAAAAAAGAAGCCGTTGGTCGTCGTCTGGACTTTATGATGCAGGAGTTCAACCGCGAGTCGAACACTCTTGCGTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAACCAGAGCGGCATTTttctt                                                                                                                                                                                                                 >  2:378119/2‑251 (MQ=255)                              caacaTTCTGAAGAAAAAAGAAGCCGTTGGTCGTCGTCTGGACTTTATGATGCAGGAGTTCAACCGCGAGTCGAACACTCTTGCGTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTTTCTTccc                                                                                                                                                                                                              >  2:17657/1‑251 (MQ=255)                                           aaaaaaGCAGCCGTTGGTCGTCGTCTGGACTTTATGATGCAGGAGTTCAACCGCGAGTCGAACACTCTTGCGTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTTTCTTCCCCGCAAC‑TTCAAtt                                                                                                                                                                                                >  2:213254/1‑251 (MQ=255)                                                  aagCCGTTGGTCGTCGTCTGGACTTTATGATGCAGGAGTTCAACCGCGAGTCGAACACTCTTGCGTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTTTCTTCCCCGCAAC‑TTCAATTCTGtttt                                                                                                                                                                                         >  2:288378/1‑251 (MQ=255)                                                                           tATGATGCAGGAGTTCAACCGCGAGTCGAACACTCTTGCGTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTTTCTTCCCCGCAAC‑TTCaa                                                                                                                                                                                                  >  1:427766/1‑217 (MQ=255)                                                                                  cAGGAGTTCAACCGCGAGTCGAACACTCTTGCGTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTTTCTTCCCCGCAAC‑TTCAATTCTGTTTTGCGTGCCTGCTCCAGATTTGGCGATGtttttt                                                                                                                                                         <  1:368457/251‑1 (MQ=255)                                                                                            aCCGCGAGTCGAACACTCTTGCGTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTTTCTTCCCCGCAAC‑TTCAATTCTGTTTTGCGTGCCTGCTCCAGATTTTGCGATGTTTTTTTGCCCAGcac                                                                                                                                               <  2:89850/251‑1 (MQ=255)                                                                                                               tGCGTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTTTCTTCCCCGCAAC‑TTCAATTCTGTTTTGCGTGCCTGCTCCAGATTTTGCGATGTTTTTTTGCCCAGCACACTGAGAACGTGAGATACt                                                                                                                            >  1:374473/1‑251 (MQ=255)                                                                                                                  gTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGGAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTTTCTGCCCCGCAAC‑TTCAATTCTGTTTTGCGTGCCTGCTCCAGATTTTGCGATGTTTTTTTGCCCAGCACACTGAGAACGTGAGATACTcac                                                                                                                         <  1:159501/251‑1 (MQ=255)                                                                                                                       aGTCTATCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTTTCTTCCCCGCAAC‑TTCAATTCTGTTTTGCGTGCCTGCTCCAGATTTTGCGATGTTTTTTTGCCCAGCACACTGAGAACGTGAGATACTCACAACTg                                                                                                                    <  2:263765/251‑1 (MQ=255)                                                                                                                            aTCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCTGCATTTTGCTTCCCCGCAAct                                                                                                                                                                                                       <  2:404734/164‑2 (MQ=255)                                                                                                                            aTCAATGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTTTCTTCCCCGCAAct                                                                                                                                                                                                       >  1:404734/1‑163 (MQ=255)                                                                                                                               aaTGCCGAAGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATTCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTTTCTTCCCCGCAAC‑TTCAATTCTGTTTTGCGTGCCTGCTCCAGATGTTGCGATGTTTTTTTGCCCAGCACACTGAGAACGTGAGATACTCACAACTGTATATaaa                                                                                                            <  1:56867/251‑1 (MQ=255)                                                                                                                                       aGTGACAACCTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCg                                                                                                                                                                                                                            >  2:420683/1‑132 (MQ=255)                                                                                                                                       aGTGACAAACTCCGCGATTGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCg                                                                                                                                                                                                                            <  1:420683/132‑1 (MQ=255)                                                                                                                                                     cgattgAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAATATTGAGTAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTTTCTTCCCCGCAAC‑TTCAATTCTGTTTTGCGTGCCTGCTCCAGATTTTGCGATGTTTTTTTGCCCAGCACACTGAGAACGTGAGATACTCACAACTGTATATAAATACAGTTACAGATTTActttct                                                                                      <  1:58230/246‑1 (MQ=255)                                                                                                                                                                         attgaGCAGATGCGCGAGCAGATTCAGAATATTGAATAACGCGTAACACTAAGTCTTACTTGTCAGCCTTCACAAGTGCCGC‑CCACTCAAACAGAGCGGCATTTTGCTTCCCCGCAAC‑TTCAATGCTGTTTTGCGTGCCTGCTCCAGATTTTGCGATGTTTTTTTGCCCAGCACACTGAGAACGTTAGATACTCACAACTGTATATAAATACAGGTACAGAATTACTTCCTGTGCAATCAATATCCCATgg                                                                  <  2:389470/251‑1 (MQ=255)                                                                                                                                                                              gCAGATGCTCGAGCAGATTCAGAATATTGAGGAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTTTCTTCCCCGCAAC‑TTCAATTCTGTTTTGCGTGCCTGCTCCAGATTTTGCGATGTGTTTTTGCCCAGCCCACTGAGAACGTGAGATACTCACAACTGTATATAAATACAGTTACAGATGTACTTTCTTTGCAATCGATATCACATGGAGTgg                                                             <  1:141969/251‑1 (MQ=255)                                                                                                                                                                                                    aatattgagtAACTCGTAACACTAATTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTTTCTTCCCCGCAAC‑TTCAATTCTGTTTTGCGTGCCTGCTCCAGATTTTGCGATGTTTTTTTGCCCAGCACACTGAGAACGTGAGATACTCACAACTGTATATAAATACAGTTACAGATTTACTTTCTTTGCAATCGATATCACATGGAGTGGGCAATGAACGAACATCATCAAc                                       >  2:193880/10‑251 (MQ=255)                                                                                                                                                                                                                     aacactaaTTCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTTTCTTCCCCGCAAC‑TTCAATTCTGTTTTGCGTGCCTGCTCCAGATTTTGCGATGTTTTTTTGCCCAGCACACTGAGAACGTGAGATACTCACAACTGTATATAAATACAGTTACAGATTTACTTTCTTTGCAATCGATATCACATGGAGTGGGCAATGAACGAACATCATCAACCTTTTGAAGAAATacgg                      <  1:107278/245‑4 (MQ=255)                                                                                                                                                                                                                              tCTTACTTTTCAGCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTTTCTTCCCCGCAAC‑TTCAATTCTGTTTTGCGTGCCTGCTCCAGATTTTGCGATGTTTTTTTGCCCAGCACACTGAGAACGTGAGATACTCACAACTGTATATAAATACAGTTACAGATTTACTTTCTTTGCAATCGATATCACATGGAGTGGGCAATGAACGAACATCATCAACCTTTTGAAGAAATacggcattatgg              <  1:193880/250‑12 (MQ=255)                                                                                                                                                                                                                                       tcagCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTTTCTTCCCCGCAAC‑TTCAATTCTGTTTTGCGTGCCTGCTCCAGATTTTGCGATGTTTTTTTGCCCAGCACACTGAGAACGTGAGATACTCACAACTGTATATAAATACAGTTACAGATTTACTTTCTTTGCAATCGATATCACATGGAGTGGGCAATGAACGAACATCATCAACCTTCTGAAGAAATacggcattatggcactgaagg     <  1:165763/247‑21 (MQ=255)                                                                                                                                                                                                                                          gCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTTTCTTCCCCGCAAC‑TTCAATTCTGTTTTGCGTGCCTGCTCCAGATTTTGCGATGTTTTTTTGCCCAGCACACTGAGAACGTGAGATACTCACAACTGTATATAAATACAGTTACAGATTTACTTTCTTTGCAATCGATATCACATGGAGTGGGCAATGAACGAACATCATCAACCTTTTGAAGAAATacggcattatggcactgaagggca  >  2:354197/1‑227 (MQ=255)                                                                                                                                                                                                                                          gCCTTCACAAATGCCGC‑CCACTCAAACAGAGCGGCATTTTTCTTCCCCGCAAC‑TTCAATTCTGTTTTGCGTGCCTGCTCCAGATTTTGCGATGTTTTTTTGCCCAGCACACTGAGAACGTGAGATACTCACAACTGTATATAAATACAGTTACAGATTTACTTTCTTTGCAATCGATATCACATGGAGTGGGCAATGAACGAACATCATCAACCTTTTGAAGAAATacggcattatggcactgaagggca  >  2:328706/1‑227 (MQ=255)                                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                         CGCCTCGAAGCGCATGTCAAAGAGACCTACAACATTCTGAAGAAAAAAGAAGCGGTTGGTCGTCGTCTGGATTTTATGATGCAGGAGTTCAACCGCGAGTCGAACACTCTTGCGTCGAAGTCTATCAATGCCGAAGTGACAAACTCCGCCATCGAGCTGAAAGTGTTGATTGAGCAGATGCGCGAGCAGATTCAGAACATCGAATAACTCGTAACGCCAATTCTTACTTTTCCGCCTTCACAAATGCCGC‑C‑ACTCAAACAGAGCGGCATTTTTCTTCCCCGCAACATTCAATTCTGTTTTGCGTGCCTGCTCCAGATTTTGCGATGTTTTTTTGCCCAGCACACTGAGAACGTGAGATACTCACAACTGTATATAAATACAGTTACAGATTTACTTTCTTTGCAATTGATATCACATGGAGTGGGCAATGAACGAACATCATCAACCTTTTGAAGAGATAAAACTGATTAATGCAAACGGAGC  >  NC_000913/3817333‑3817815

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑