Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,196,204	G→A	intergenic (‑105/+128)	thiC ← / ← rsd	phosphomethylpyrimidine synthase/regulator of sigma D

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,196,204	0	G	A	100.0%	150.1 / NA	47	intergenic (‑105/+128)	thiC/rsd	phosphomethylpyrimidine synthase/regulator of sigma D
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (24/23);  total (24/23)

TCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGAT  >  NC_000913/4196071‑4196342                                                                                                                                      |                                                                                                                                           tCGCGGCGGGTCAGTTTTGTTGCAGACCTAAATCGTATAAGGAGGTTGTGTGTGTGGCTTGTCCGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTa                                                                                                                                   >  1:547720/1‑143 (MQ=255) tCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTa                                                                                                                                   >  1:541969/1‑143 (MQ=255)  cgcgGCGGGTCAGTTTTGTTGCAGACATCGCTCATTCCAACAAGTTAAGGACGTGGCTTGTCAGACGACGGATGGAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTGTTAg                                                                                                                                  >  2:416536/1‑143 (MQ=255)   ggggcggGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGc                                                                                                                                 <  1:476153/141‑1 (MQ=255)         ggTCAGTTTTGTTGCAGACATCGCTCATTCCAAAATGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATc                                                                                                                           <  1:158209/143‑1 (MQ=255)            cAGTTTTGTTGCAGACATAGCTCATTCCAAACAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAgg                                                                                                                        <  1:654562/143‑1 (MQ=255)            cAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAgg                                                                                                                        <  1:686456/143‑1 (MQ=255)                     tgCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGa                                                                                                               <  1:395280/143‑1 (MQ=255)                       cAGACATAGCGCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATc                                                                                                             <  2:25755/143‑1 (MQ=255)                        aGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTGCCCTTCACAGGTATTAGCCTGATCAGGCTCCGCGGATcc                                                                                                            >  2:537988/1‑143 (MQ=255)                         gACATAGCAGAGTCCGAAAAGCTAAGGACGGGGCGGGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACGCTTGTTCCCTTCACAGGGATTAGCCTGATCAGGTTCCGCGGATccc                                                                                                           <  1:631111/143‑1 (MQ=255)                                 tCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGAACGCTTCAGGTGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGACTAAAc                                                                                                   >  1:217986/1‑143 (MQ=255)                                  cATTCCAAAAAGTTAAGGACGTGGCTGGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACg                                                                                                  <  2:85204/143‑1 (MQ=255)                                       cAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGtctc                                                                                             >  1:626276/1‑143 (MQ=255)                                        aaaaaGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCa                                                                                            <  1:133256/143‑1 (MQ=255)                                            aGTCAAGGACGTGGCTTGCCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCCTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCa                                                                                        <  1:39079/143‑1 (MQ=255)                                                 aGGACGTGGCTTGTCAGACGACGGATGAAGCGAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTaa                                                                                   <  2:530058/143‑1 (MQ=255)                                                            tGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGCGGCGATGCGAGAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGATAAGGCACTCCGAc                                                                        >  1:185308/1‑143 (MQ=255)                                                                  acgacgGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGATGAGTGGCTGTTGTTGGATAGATATACGATTTCGTGGTCAGGTTCCGCGGATCACGACTAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGaca                                                                  >  1:796714/1‑141 (MQ=255)                                                                   cgacgGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAAt                                                                 <  1:485291/143‑1 (MQ=255)                                                                           gAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCCGACCGTGAAGACACTCCGACAAGAAATTAGCCCCg                                                         >  1:539195/1‑143 (MQ=255)                                                                           gAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCCCTCCGACAAGAAATTAGCCCCg                                                         >  1:244462/1‑143 (MQ=255)                                                                               cAAGAGACGATCGCCGCAGGGGCGATGCGATCGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTGTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCaac                                                     >  1:605076/1‑142 (MQ=255)                                                                                aaGAGACGATCGCCGCAGGGGCGATGCGATAACAGATTAACTCTTGTTCCCTGCACAGGTATTAGACTGATCAGGTTCCGCGGATCCCGAATAAACGTTCTCAGCCAGTCAAGGCACTCCGACAAGAAATTAGACCCGCaaag                                                    >  2:652485/1‑142 (MQ=255)                                                                                       gATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCCGTTCAGGCACTCCGCCAAGAAATTAGCCCCGCAAAAGGAGCAt                                             >  1:487880/1‑143 (MQ=255)                                                                                        agcgccgcCGGGGCGACGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCAtt                                            <  1:118142/141‑1 (MQ=255)                                                                                          cgccgcACGGGCGATTCAATAGCATATTAACTCTTGTTCCCTTCACACGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGa                                          <  1:4540/143‑1 (MQ=255)                                                                                           gccgcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGaa                                         <  1:437997/143‑1 (MQ=255)                                                                                            ccgcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCGCCGCAACTGGGGCATTGAAt                                        >  1:163057/1‑143 (MQ=255)                                                                                            ccgcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAAt                                        <  1:70049/143‑1 (MQ=255)                                                                                             cgcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATg                                       <  1:41454/143‑1 (MQ=255)                                                                                                  gggCGATGCGATAGCAGACTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGTGTTTAGCCCCGCAAATGGGGCATTGAATGTAAAt                                  <  2:654132/143‑1 (MQ=255)                                                                                                    gcgatgcgatAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGCATGTAAATTa                                >  1:782666/1‑143 (MQ=255)                                                                                                             tAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAAGTTCCGCGGATCCCGAATAAACGGTCTCCGCCAGTTAAGGCACTCCGGCAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAAc                       >  2:471377/1‑143 (MQ=255)                                                                                                              aGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTACGGCACTCCGACAAGAAATTAGCCCCGCAAATGGTGCTTTTCCTGTAACTTAGGCGGCAACa                      >  1:230433/1‑143 (MQ=255)                                                                                                                  gATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCCCTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAgcgc                  >  1:553172/1‑143 (MQ=255)                                                                                                                   aTTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCGAATGGGGCATTGAATGTAAATTACGCTGTAACAgcgaa                 >  2:374861/1‑141 (MQ=255)                                                                                                                   aTTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAGATGGGGCATTGAATATAAATTACGCGTTAACAGCGCa                 >  1:292519/1‑143 (MQ=255)                                                                                                                   aTTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCa                 <  2:541969/143‑1 (MQ=255)                                                                                                                   aTTAACTCGTGTTCCCGTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGTCAGTTACGGCACTCCTACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCa                 <  1:247922/143‑1 (MQ=255)                                                                                                                   aTTAACTCCTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCa                 <  2:547720/143‑1 (MQ=255)                                                                                                                    ttAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGGAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAg                >  1:657068/1‑143 (MQ=255)                                                                                                                      aaCTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGaa              <  1:571622/143‑1 (MQ=255)                                                                                                                        ctctTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGACCt            >  1:176313/1‑143 (MQ=255)                                                                                                                           tcgtccccTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAACAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCaa         <  1:416536/138‑1 (MQ=255)                                                                                                                                  cTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAATTTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGGAGAACGCGAGCAGGac  >  1:737295/1‑142 (MQ=255)                                                                                                                                  cTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGGCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGAt  >  1:358007/1‑143 (MQ=255)                                                                                                                                      |                                                                                                                                           TCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGAT  >  NC_000913/4196071‑4196342

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑