Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,880,635	T→C	L138L (TTA→TTG)	casD ←	type I‑E CRISPR system Cascade subunit CasD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,880,635	0	T	C	96.2%	66.2 / ‑4.3	26	L138L (TTA→TTG)	casD	type I‑E CRISPR system Cascade subunit CasD
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (15/10);  total (15/11)
Fisher's exact test for biased strand distribution p-value = 4.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.89e-01

CCTCCTTTAATCACATACCATTCTCGGGAAGCAAATTGTCGAGGCAAGGTGATCATCGGTTCGTCGCGCGCCGTAAATTTTAAATGATGCCCTGTAACTGATTCCTCACTATATATATCGCCGCCAACGGGCTCATAATTTAATAGCGCCTTCTGAGGATCCGATGCCTGACATGTCCCCAAAAAAAGCGGGTGTGTTAGTGGGCAACTTCTCCGCCCCAGGTAAGGTGTATACCGAGGCTTTAATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGGTGTTAACCAGAGAGCGACGGTAAAGGAGGCATCACATAAATATTCGCGCCATGTTTGAATCGTTTCATGACTTTTCAAACCACGGTAATCTTCTCGCGCTCCAAGGACTGTATGGTAATCACGCAACCCCGTTACAGACACACGACGATCGTCAAGAATGAGTTCATCGCAGCGCACTGCAAATTGCACACT  >  NC_000913/2880393‑2880871                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                             cctcctTTAATCACATACCATTCTCGGGAAGCAAATTGTCGAGGCAAGGTGATCATCGGTTCGTCGCGCGCCGTAAATTTTAAATGATGCCCTGTAACTGATTCCTCACTATATATATCGCCGCCAACGGGCTCATAATTTAATAGCGCCT‑CTGAAGATCCGATGCCTTGCCTGTCCCCAAAAAAAACCGGGGGGTTAGTGGGCAACTTCTCCGCCCCAGGTAAGGTGTATACCGAGGCTTCAATACTGCt                                                                                                                                                                                                                                     >  1:195954/1‑251 (MQ=255)         aaTCACATACCATTCTCGGGAAGCAAATTGTCGAGGCAAGGTGATCATCGGTTCGTCGCGCGCCGTAAATTTTAAATGATGCCCTGTAACTGATTCCTCACTATATATATCGCCGCCAACGGGCTCATAATTTAATAGCGCCTTCTGAGGATCCGATGCCTGACATGTCCCCAAAAAAAGCGGGTGTGTTAGTGGGCAACTTCTCCGCCCCAGGTAAGGTGTATACCGAGGCTTCAATACTGCTTTTTCa                                                                                                                                                                                                                               <  1:209933/250‑1 (MQ=255)              caTACCATTCTCGGGAAGCAAATTGTCGAGGCAAGGTGATCATCGGTTCGTCGCGCGCCGTAAATTTTAAATGATGCCCTGTAACTGATTCCTCACTATATATATCGCCGCCAACGGGCTCATAATTTAATAGCGCCTTCTGAGGATCCGATGCCTGACATGTCCCCAAAAAAAGCGGGTGTGTTAGTGGGCAACTTCTCCGCCCCAGGTAAGGTGTATACCGAGGCTTCAATACTGCTTTTTCAAGTTCt                                                                                                                                                                                                                         >  1:71977/1‑251 (MQ=255)                          gggAAGCAAATTGTCGAGGCAAGGTGATCATCGGTTCGTCGCGCGCCGTAAATTTTAAATGATGCCCTGTAACTGATTCCTCACTATATATATCGCCGCCAACGGGCTCATAATTTAATAGCGCCTTCTGAGGATCCGATGCCTGACATGTCCCCAAAAAAAGCGGGTGTGTTAGTGGGCAACTTCTCCGCCCCAGGTAAGGTGTATACCGAGGCTTCAATACTGCTTTTTCAAGTTCTGAGATAACCATc                                                                                                                                                                                                             <  1:63107/251‑1 (MQ=255)                                          aGGCAAGGGTATCATCGGTTCGTCGCGCGCCGTAAATTTTAAATTATGCCCTGTAACTGATTCCTCACTATATATATCGCCGCCAACGGGCTCATAATTTAATAGCGCCTTCTGAGGATCCGATGCCTGACATTTCCCCAAAAAAAGCGGGTGTGTTAGTGGGCAACTTCTCCGCCCCAGGTAAGGTGTATACCGAGGCTTCAATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGGTGTTa                                                                                                                                                                                             <  1:74131/251‑1 (MQ=255)                                                   gATCATAGGTTCGTCGCGCGACGTCAATTTTCAATGATGCCCTGTAACTGATTCCTCACGATATATATCGCCGCCAACGGGCACATAATTTAATAGCGCCTTCTGAGGATCAGATGCCTGACATGTCCCCAAAAAAAGCGGATGTGTTAGAGGGAAACTTCTCCGCCCATGGTAAGGAGAATAACGAGGCTTCAATACTGCTTTTTCACGTTCTGAAGTAAACTACGTTGCATGGGGTGTTAACCagaga                                                                                                                                                                                     >  2:332766/1‑250 (MQ=255)                                                     tcatcGGTTCGTCGCGCGCCGTAAATTTTAAATGATGCCCTGTAACTGATTCCTCACTATATAGATCGCCGCCAACGGGCTCATAATTTAATAGCGCCTTCTGAGGATCCGATGCCTGACATGTCCCCAAAAAAAGCGGGTGTGTTAGTGGGCAACTTCTCCTCCCCATGTAAGGTGTATATCGAGGCTTCAATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGGTGTTAACCAGAGAGc                                                                                                                                                                                   <  1:253627/250‑1 (MQ=255)                                                                     ggcCGTAAATTTTAAATGATGCTCTGTAACTGATTCCTCTCGATATATATCGCCGCCAACGGGCTCATAATTTAATAGCGCCTTCTGAGGATCCGATGCCTGACATGTCCCCAAAAAAAGCGGGTGTGTTAGTGGTCAACTTCTCCGCCCCAGGTAAGGTGTATACCGAGGCTTCAATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGGTGTTAACCAGAGAGCGACGGTAAAGGAGGCAt                                                                                                                                                                  <  1:94019/250‑1 (MQ=255)                                                                                  aaaagtttccttttaacgttgtCCTCACTATATATATCGCCGTCTACGGGCTCATAATTTTATGGCTCCTTCTGAGGATCCGCTGCCGGACATGTCACCAAAAAAAGCGGGTGTGTTAGTGGGCAACTTCACCGCCCCAGGTAAGGTGTATACCGAGGCTGCAATACTGCTTTTTTAAGTTCTGAGATAACCTTCGTTGAATGGGGTGTTAACAAGAGAGCGGCTGTAAAGGAGGCATCTCATGAATAtt                                                                                                                                                      <  2:156951/229‑1 (MQ=255)                                                                                              gTAACTGATTCCTCACTATATATATCGCCGCCAACGGGCTCATAATTTAATAGCGCCTTCTGAGGATCCGATGCCTGACATGTCCCCAAAAAAAGCGGGTGTGTTAGTGGGCAACTTCTCCGCCCCAGGTAAGGTGTATACCGAGGCTTCAATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGGTGTTAACCAGAGAGCGACGGTAAAGGAGGCATCACATAAATATTCGCGCCATGttt                                                                                                                                          <  1:4028/250‑1 (MQ=255)                                                                                                          tCACTATATATATCGCCGCCAACGGGCTCATAATTTAATAGCGCCTTCTGAGGATCCGATGCCTGACATGTCCCCAAAAAAAGCGGGTGTGTTAGTGGGCAACTTCTCCGCCCCAGGTAAGGTGTATACCGAGGCTTCAATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGGTGTTAAACAGAGAGCGACGGTAAAGGAGGCATCACATAAATATTCGCGCCATGTTTGAATCGTTTCATg                                                                                                                             >  2:235855/1‑251 (MQ=255)                                                                                                            aCTATATATATCGCCGCCAACGGGCTCATAATTTAATAGCGCCTTCTGAGGATCCGATGCCTGACATGTCCCCAAAAAAAGCGGGTGTGTTAGTGGGCAACTTCTCCGCCCCAGGTAAGGTGTATACCGAGGCTTCAATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGGTGTTAACCAGAGAGCGACGGTAAAGGAGGCATCACATAAATATTCGCGCCATGTTTGAATCGTTTCATGAc                                                                                                                           <  1:235855/251‑1 (MQ=255)                                                                                                                           gccAACGGGCTCATAATTTAATAGCGCCTTCTGAGGATCCGATGCCTGACATGTCCCCAAAAAAAGCGGGTGTGCTAGTGGGCAACTTCTCCGCCCCAGGTAAGGTGTATACCGAGGCTTCAATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGTTGTTAACCAGAGAGCGACGGTAAAGGAGGCCTCACATCAATATTCGCGCCATGGTTGAATCGTTTCATGACTTTTCAAACCACGGt                                                                                                            >  2:67852/1‑251 (MQ=255)                                                                                                                                      cATAATTTAATAGCGCCTTCTGAGGATCCGATGCCTGACATGTCCCCAAAAAAAGCTGGTGTGTTAGTGGGCAACTTCTCCGCCCCAGGTAAGGTGTATTCCGAGGCTTTAATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGGTGTTAACCAGAGAGCGACGGTAAAGGAGGCATCACATAAATATTCGCGCCATGTTTGAATCGTTTCATGACTTTTCAAACCACGGTAATCTtctc                                                                                                   <  2:162545/249‑1 (MQ=255)                                                                                                                                         aaTTTAATAGCGCCTTCTGAGGATCCGATGCCTGACATGTCCCCAAAAAAAGCGGGTGTGTTAGTGGGCAACTTCTCCGCCCCAGGTAAGGTGTATACCGAGGCTTCAATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGGTGTTAACCAGAGAGCGACGGTAAAGGAGGCATCACATAAATATTCGCGCCATGTTTGAATCGTTTCATGACTTTTCAAACCACGGTAATCTTCTCGCGCt                                                                                              >  1:333123/1‑251 (MQ=255)                                                                                                                                                 aGCGCCTTCTGAGGATCCGATGCCTGACATGTCCCCAAAAAAAGCGGGTGTGTTAGTGGGCAACTTCTCCGCCCCAGGTAAGGTGTATACCGAGGCTTCAATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGGTGTTAACCAGAGAGCGACGGTAAAGGAGGCATCACATAAATATTCGCGCCATGTTTGAATCGTTTCATGACTTTTCAAACCACGGTAATCTTCTCGCGCTCCAAGGAc                                                                                      >  1:103935/1‑251 (MQ=255)                                                                                                                                                            aGGATCCGATGCCTGACATGTCCCCAAAAAAAGCGGGTGTGTTAGAGGGCAACTTCTCCGCCACAGGTAAGGTGTATACCGAGGCTTCAATACTGCTTTTTCAAGTTCTGAGATAAACATCGTTGCATGGGGTGTTATCCAGAGAGCGACGGTAAAGGAGGCATCACATAAATATTCTCGCCATGTTTGAATAGTTTCATGACATTTCAAAACACGGTAATCTTCTCGCGCTCCAATGACTGTATGTTAAt                                                                           >  2:128757/1‑251 (MQ=255)                                                                                                                                                                 ccGAAGCCTGAAATGTCCCCAAAAAAAGCGGGTGTGTTAGTGGTCAACTTCTCCGCCCCAGGAAAGGTGTATACCGAGGCTTCAATACTGCTTTTTCAAGTTCTGAGATAACCCTCGTTGCATGGGGGGTTAACCAGCGAGCGACGGTAAAGGAGGCATCACATAAATATTCGCGCCATGTTTGAATAGTTTCATGACTTTTCAAACCACGGTAATCTTCTATCGATCCAAGGCCTGTaatgcaataaagc                                                                      >  2:382246/1‑239 (MQ=255)                                                                                                                                                                    aTGCCTGACATGGCCCCAAAAAAAGCGGGTGTGTTAGTGGGCAACTTCTCCGCCCCAGGTAAGGTGTATACCGAGGCTTCAATACTGCTTTTTCAAGTGCTGAGATAACCATCGTTGCATGGGGTGTTAACCAGAGAGCGACGGTAAAGGAGGCATCACATAAATATTCGCGCCATGTTTGAATCGTTTCATGACTTTTCAAACCACGGTAATCTTCTCGCGCTCCAAGGACTGTATGGTAATCACGCAAc                                                                   <  2:103935/251‑1 (MQ=255)                                                                                                                                                                                   ccAAAAAAAGCGGGTGTGTTAGTGGGCAACTTCTCCGCCCCAGGTAAGGTGTATACCGAGGCTTCAATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGGTGTTAACCAGAGAGCGACGGTAAAGGAGGCATCACATAAATATTCGCGCCATGTTTGAATCGTTTCATGACTTTTCAAACCACGGTAATCTTCTCGCGCTCCAAGGACTGTATGGTAATCACGCAACCCCGTTACAGacac                                                     >  1:33439/1‑250 (MQ=255)                                                                                                                                                                                            gggggggtgtTAGTGGGCAACTTCTTCGCCCCAGGTAAGGTGTATACCGAGGCATCAATACTGCGTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGGTGTTAACCAGAGAGCGACGGTAAAGGAGGCATCACATAAATATTCGCGCCATGTTTGAAACGTTTCATGACTTTTCAAACCACGGTAATCTTCTCGCGCTCCAAGGACTGTATGGTAATCACGCAACCCCGTTACAGACACACGACGATCg                                           <  2:95820/245‑1 (MQ=255)                                                                                                                                                                                                 tgtgtTAGTGGGCAACTTCTCCGCCCCAGGTAAGGTGTATACCGAGGCTTCAATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGGTGTTAACCAGAGAGCGACGGTAAAGGAGGCATCACATAAATATTCGCGCCATGTTTGAATCGTTTCATGACTTTTCAAACCACGGTAATCTTCTCGCGCTCCAAGGACTGTATGGTAATCACGCAACCCCGTTACAGACACACGACGATCGTCa                                        >  1:204736/1‑249 (MQ=255)                                                                                                                                                                                                   tgtTAGTGGGCAACTTCTCCGCCCCAGGTAAGGTGTATACCGAGGCTTCAATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGGTGTTAACCAGAGAGCGACGGTAAAGGAGGCATCACATAAATATTCGCGCCATGTTTGAATCGTTTCATGACTTTTCAAACCACGGTAATCTTCTCGCGCTCCAAGGACTGTATGGTAATCACGCAACCCCGTTACAGACACACGACGATCGTCAAGa                                     >  1:345677/1‑250 (MQ=255)                                                                                                                                                                                                    gtTAGTGGGCAACTTCTCCGCCCCAGGAAAGGGGTATACAGAGGATTCAATAATGCATTTACAAGTTCTGAGATAAACATCGTGGCATGGGGTGTTAACCAGAGAGCGACGGTAAAGGAGGCATCAAATAAATATTCGCGCCATGTTTGAATCGTTTCATGACTTTTCAAACCGAGGTAATCTGCTCGCGCTCCAAGGAATGTATGGTAATCACGCAACCCCGTTACAGACACAAGACGATCGTCAAGAAt                                   >  1:339390/1‑251 (MQ=255)                                                                                                                                                                                                                 ttCTCCGCCCCAGGTAAGGTGTATACCGAGGCTTCAATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGGTGTTAACCAGAGAGCGACGGTAAAGGAGGCATCACATAAATATTCGCGCCATGTTTGAATCGTTTCATGACTTTTCAAACCACGGTAATCTTCTCGCGCTCCAAGGACTGTATGGTAATCACGCAACCCCGTTACAGACACACGACGATCGTCAAGAATGAGTTCAttgc                        >  1:336247/1‑246 (MQ=255)                                                                                                                                                                                                                                     gtATACCGAGGCTTCAATACTGCTTTTTCAAGTTCTGAGATACCCATCGTTGCATGGGGTGTTAACCAGAGAGCGACGGTAAAGGAGGCATCACATAAATATTCGCGCCATGTTTGAATCGTTTCATGACTTTTCAAACCACGGTAATCTTCTCGCGCTCCACGGACTGTATGGTAATAACGCAACCCCGTTACAGACACACGACGATCGTCAAGAATGCGTTCATCGCCGCGCCCTGCAAATTGCACAct  >  2:161104/1‑251 (MQ=255)                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                             CCTCCTTTAATCACATACCATTCTCGGGAAGCAAATTGTCGAGGCAAGGTGATCATCGGTTCGTCGCGCGCCGTAAATTTTAAATGATGCCCTGTAACTGATTCCTCACTATATATATCGCCGCCAACGGGCTCATAATTTAATAGCGCCTTCTGAGGATCCGATGCCTGACATGTCCCCAAAAAAAGCGGGTGTGTTAGTGGGCAACTTCTCCGCCCCAGGTAAGGTGTATACCGAGGCTTTAATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGGTGTTAACCAGAGAGCGACGGTAAAGGAGGCATCACATAAATATTCGCGCCATGTTTGAATCGTTTCATGACTTTTCAAACCACGGTAATCTTCTCGCGCTCCAAGGACTGTATGGTAATCACGCAACCCCGTTACAGACACACGACGATCGTCAAGAATGAGTTCATCGCAGCGCACTGCAAATTGCACACT  >  NC_000913/2880393‑2880871

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑