Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,331,059	2 bp→AT	coding (12‑13/2598 nt)	topA →	DNA topoisomerase 1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,331,059	0	T	A	96.3%	95.4 / ‑6.1	27	A4A (GCT→GCA)	topA	DNA topoisomerase 1
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base A (18/8);  minor base C (0/1);  total (18/9)
Fisher's exact test for biased strand distribution p-value = 3.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
*	NC_000913	1,331,060	0	C	T	100.0%	94.3 / NA	27	L5F (CTT→TTT)	topA	DNA topoisomerase 1
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (18/9);  total (18/9)

CTTTCGTCAATCTGGCAATAGATTTGCTTGACATTCGACCAAAATTCCGTCGTGCTATAGCGCCTGTAGGCCAAGACCTGTTAACTCAGTCACCTGAATTTTCGTGAACAGAGTCACGACAAGGGGTTGATATCCGCAGAGAGCGAGTCCATATCGGTAACTCGTTGCCAGTGGAAGGTTTATCAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCTCTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGTGGCTCAGCTGCCAAAAAGAGTGCCGACTCTACCTCCACCAAGACGGCTAAAAAGCCTAAAAAGGATGAACGTGGCGCTCTCGTCAACCGTATGGGGGTTGACCCGTGGCACAATTGGGAGGCGCACTATGAAGTG  >  NC_000913/1330819‑1331302                                                                                                                                                                                                                                                 ||                                                                                                                                                                                                                                                   cTTTCGTCAATCTGGCAATAGATTTGCTTGACATTCGACCAAAATTCCGTCGTGCTATAGCGCCTGTAGGCCAAGACCTGTTAACTCAGTCACCTGAATTTTCGTGAACAGAGTCACGACAAGGGGTTGATATCCGCAGAGAGCGAGTCCATATCGGTAACTCGTTGCCAGTGGAAGGTTTATCAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCg                                                                                                                                                                                                                                           >  1:88298/1‑251 (MQ=255)      gTCAATCGGGCAATAGACTTGCTTGACATTCGATCAAAATTCCGTCATGCTATAGCGCCTGTGGGTAAAGCCCTTGTAACTCATTCAGCATAATGTTCGTGAACAGAGTTACGACTAGGGGTTGATATCCGCAGAGAGCGAGTCCATATCGGTAACTCTTTGCGAGTGGAAGGTTTATCAACATGTGACGCATTCTTGGAATAATCAAATGAGGTAAGGTGAATATGGGGAAAGCCTTTGTCATCGttca                                                                                                                                                                                                                                       <  2:477475/250‑3 (MQ=255)       tCAATCTGGCAATAGATTTGCTTGACATTCGACCAAAATTCCGTCGTGCTATAGCGCCTGTAGGCCAAGACCTGTTAACTCAGTCACCTGAATTTTCGTGAACAGAGTCACGACAAGGGGTTGATATCCGCAGAGAGCGAGTCCATATCGGTAACTCGTTGCCAGTGGAAGGTTTATCAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGt                                                                                                                                                                                                                                     >  1:494561/1‑251 (MQ=255)                                                cgtcgtGCTATAGCGCCTGTAGGCCAAGACCTGTTAACTCAGTCACCTGAATTTTCGTGAACAGAGTCACGACAAGGGGTTGATATCCGCAGAGAGCGAGTCCATATCGGTAACTCGTTGCCAGTGGAAGGTTTATCAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGt                                                                                                                                                                                            >  2:440113/1‑251 (MQ=255)                                                       cTATAGCGCCTGTAGGCCAAGACCTGTTAACTCAGTCACCTGAATTTTCGTGAACAGAGTCACGACAAGGGGTTGATATCCGCAGAGAGCGAGTCCATATCGGTAACTCGTTGCCAGTGGAAGGTTTATCAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGGAGTGACTACg                                                                                                                                                                                     >  2:160742/1‑251 (MQ=255)                                                         ataGCGCCTGTAGGCCAAGACCTGTTAACTCAGTCACCTGAATTTTCGTGAACAGAGTCACGACAAGGGGTTGATATCCGCAGAGAGCGAGTCCATATCGGTAACTCGTTGCCAGTGGAAGGTTTATCAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACgtg                                                                                                                                                                                   >  2:178483/1‑251 (MQ=255)                                                                 tGTAGGCCAAGACCTGTTAACTCAGTCACCTGAATTTTCGTGAACAGAGTCACGACAAGGGGTTGATATCCGCAGAGAGCGAGTCCATATCGGTAACTCGTTGCCAGTGGAAGGTTTATCAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATc                                                                                                                                                                           >  1:381944/1‑251 (MQ=255)                                                                           gACCTGTTAACTCAGTCACCTGAATTTTCGTGAACAGAGTCACGACAAGGGGTTGATATCCGCAGAGAGCGAGTCCATATCGGTAACTCGTTGCCAGTGGAAGGTTTATCAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGt                                                                                                                                                                 <  2:481957/251‑1 (MQ=255)                                                                             ccTGTTAACTCAGTCACCTGAATTTTCGTGAACAGAGTCACGACAAGGGGTTGATATCCGCAGAGAGCGAGTCCATATCGGTAACTCGTTGCCAGTGGAAGGTTTATAAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTc                                                                                                                                                                >  1:552790/1‑250 (MQ=255)                                                                                                    tttCGTGAACAGAGTCACGACAAGGGGTTGATATCCGCAGAGAGCGAGTCCATATCGGTAACTCGTTGCCAGTGGCAGGTTTATCAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGCATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGTg                                                                                                                                        >  1:478481/1‑251 (MQ=255)                                                                                                    tttCGTGAACAGAGTCACGACAAGGGGTTGATATCCGCAGAGAGCGAGTCCATATCGGTAACTCGTTGCCAGTGGAAGGTTTATCAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGt                                                                                                                                         <  2:19882/250‑1 (MQ=255)                                                                                                              agagTCACGAAAAGGGGTTGATATCCGCAGAGAGCGAGTCCATATCGGTCACTCGTTGCCAGTGGAAGGTTTATCAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGTGGCTCAGCTGc                                                                                                                              >  1:363865/1‑251 (MQ=255)                                                                                                                           ggggTTGATATCCGCAGAGAGCGAGTCCATATCGGTAACTCGTTGCCAGTGGAAGGTTTATCAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGTGGCTCAGCTGCCAAAAAGAGTGcc                                                                                                                 >  1:378966/1‑251 (MQ=255)                                                                                                                                      ccGCAGAGAGCGAGTCCATATCGGTAACTCGTTGCCAGTGGAAGGTTTATCAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGTGGCTCAGCTGCCAAAAAGAGTGCCGACTCTACCTc                                                                                                      >  2:533351/1‑251 (MQ=255)                                                                                                                                              agCGAGTCCATATCGGTAACTCGTTGCCAGTGGAAGGTTTATCAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGTGGCTCAGCTGCCAAAAAGAGTGCCGACTCTACCTCCACCAAGa                                                                                              <  1:42443/251‑1 (MQ=255)                                                                                                                                                                 cTCGTTGCCAGTGGAAGGTTTATCAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGCTCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGTGGCTCAGCTGCCAAAAAGAGTGCCGACTCTACCTCCACCAAGACGGCTAAAAAGCCTaaac                                                                            >  1:327382/1‑249 (MQ=255)                                                                                                                                                                 cTCGTAGCCAGAGGAAGGTTTATCAACGTGCGACGCATTCCTGGAAGAATCAACTTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGAAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGTGGCTCAGCTGCCAAAAAGAGTGCCGACTCTACCTCAACCAAGACGGCTAAAAAGCCTaaaa                                                                            >  2:371026/1‑250 (MQ=255)                                                                                                                                                                       gCCATTGGAAGGTTTATCAACGGGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTAGCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACATCCGCGATGTGCCGACCAGTGGCTCAGCTGCCAAAAAGAGTGCCGACTCTACCTCCGCCAAGACTGCTAAAAAGCCTAAAAAGGATg                                                                      <  2:494561/250‑1 (MQ=255)                                                                                                                                                                        ccAGTGGAAGGTTTATCAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACTTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGTTGCTCAGCTGCCAAAAAGAGTGCCGACTCTACCTCCTCCAATACGGCTAAAAAGCCTAAAAAGGATGac                                                                    <  2:183889/251‑2 (MQ=255)                                                                                                                                                                             ggAAGGTTTATCAACGTGCGACGCATTCCTGGAAGACTCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGTGGCTCAGCTGCCAAAAAGAGTGCCGACTCTACCTCCACCAAGACGGCTAAAAAGCCTAAAAAGGATGAACGTgg                                                               >  2:292345/1‑251 (MQ=255)                                                                                                                                                                                      aTCAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGTGGCTCAGCTGCCAAAAAGAGTGCCGACTCTACCTCCACCAAGACGGCTAAAAAGCCTAAAAAGGATGAACGTGGCGCTCTCGt                                                      <  1:160742/251‑1 (MQ=255)                                                                                                                                                                                        cAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGTGGCTCAGCTGCCAAAAAGAGTGCCGACTCTACCTCCACCAAGACGGCTAAAAAGCCTAAAAAGGATGAACGTGGCGCTCTCGTCa                                                    <  1:496309/251‑1 (MQ=255)                                                                                                                                                                                                   gCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAACACGATCAACAAGTATCTGGGTAGTGACTCCGTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGTGGCTCAGCTGCCAAAAAGAGTGCCGACTCTACCTCCACCAAGACGGCTAAAAAGCCTAAAAAGGATGAACGTGGCGCTCTCGTCAACCGTATgggg                                         >  2:271374/1‑251 (MQ=255)                                                                                                                                                                                                            gaagaaTCAAATTAGGTAAGGTGAATATGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGTGGCTCAGCTGCCAAAAAGAGTGCCGACTCTACCTCCACCAAGACGGCTAAAAAGCCTAAAAAGGATGAACGTGGCGCTCTCGTCAACCGTATGGGGGTTGACCCg                                <  1:428077/251‑1 (MQ=255)                                                                                                                                                                                                                                     tatGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGTGGCTCAGCTGCCAAAAAGAGTGCCGACTCTACCTCCACCAAGACGGCTAAAAAGCCTAAAAAGGATGAACGTGGCGCTCTCGTCAACCGTATGGGGGTTGACCCGTGGCACAATTGGGAGGCGCACTATg       >  2:34012/1‑251 (MQ=255)                                                                                                                                                                                                                                     tatGGGTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGTGGCTCAGCTGCCAAAAAGAGTGCCGACTCTACCTCCACCAAGACGGCTAAAAAGCCTAAAAAGGATGAACGTGGCGCTCTCGTCAACCGTATGGGGGTTGACCCGTGGCACAATTGGGAGGCGCACTATg       >  1:182185/1‑251 (MQ=255)                                                                                                                                                                                                                                          gTAAAGCATTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGTGGCTCAGCTGCCAAAAAGAGTGCCGACTCTACCTCCACCAAGACGGCTAAAAAGCCTAAAAAGGATGAACGTGGCGCTCTCGTCAACCGTATGGGGGTTGACCCGTGGCACAATTGGGAGGCGCACTATGAAgtg  >  1:502549/1‑251 (MQ=255)                                                                                                                                                                                                                                                 ||                                                                                                                                                                                                                                                   CTTTCGTCAATCTGGCAATAGATTTGCTTGACATTCGACCAAAATTCCGTCGTGCTATAGCGCCTGTAGGCCAAGACCTGTTAACTCAGTCACCTGAATTTTCGTGAACAGAGTCACGACAAGGGGTTGATATCCGCAGAGAGCGAGTCCATATCGGTAACTCGTTGCCAGTGGAAGGTTTATCAACGTGCGACGCATTCCTGGAAGAATCAAATTAGGTAAGGTGAATATGGGTAAAGCTCTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGTGGCTCAGCTGCCAAAAAGAGTGCCGACTCTACCTCCACCAAGACGGCTAAAAAGCCTAAAAAGGATGAACGTGGCGCTCTCGTCAACCGTATGGGGGTTGACCCGTGGCACAATTGGGAGGCGCACTATGAAGTG  >  NC_000913/1330819‑1331302

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑