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%	147.7 / 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 (26/21);  total (26/21)

GCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATG  >  NC_000913/4196073‑4196343                                                                                                                                    |                                                                                                                                            gcggcgGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGc                                                                                                                                  <  1:219401/143‑1 (MQ=255) gcggcgGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGc                                                                                                                                  >  2:704525/1‑143 (MQ=255)        gTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCa                                                                                                                           <  1:320033/143‑1 (MQ=255)               ttgttgCAGACATAGCTCATTCCAAAAAGTTAAGTACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCcg                                                                                                                    <  2:620015/143‑1 (MQ=255)                              cTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGCGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGCATaaa                                                                                                     >  2:591860/1‑143 (MQ=255)                               tCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGCCGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAAc                                                                                                    >  1:506088/1‑143 (MQ=255)                                cATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACg                                                                                                   <  1:175511/143‑1 (MQ=255)                                cATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACg                                                                                                   <  1:556161/143‑1 (MQ=255)                                    ccAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGtct                                                                                               <  1:193955/143‑1 (MQ=255)                                     cAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGtctc                                                                                              >  1:350290/1‑143 (MQ=255)                                     cAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGtctc                                                                                              >  1:425893/1‑143 (MQ=255)                                      aaaaaGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCCGGGGCGATGCGATAGCAGATTAACGCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAAAAAACGGCCTCa                                                                                             >  2:102326/1‑143 (MQ=255)                                      aaaaaGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGAACCCGAATAAACGGACTCa                                                                                             >  2:72503/1‑143 (MQ=255)                                       aaaaGTTAAGGACGTGTCTTGTCAGTCGACGGATGAAGCAAGATACGATCGCCGCAGGGGCGATGCTATAGCAGATTAACTCTTGTTCCCTTCACATGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAg                                                                                            <  2:379101/143‑1 (MQ=255)                                          aGTTAGGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCGGGGGCGATGCGATAGCAGATGAACTCTTGTTCCCTTCACAGGCATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCa                                                                                         <  2:231650/143‑1 (MQ=255)                                                  aCGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTGTTGTTCCCTTCACAGGTATAAGCCTGATCAGGTTCCGCGGATCCAGAAGAAACGGTCACAGCCAggcaacgc                                                                                 >  2:330784/1‑136 (MQ=255)                                                      ggCTTGTCAGACGACGGACGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTc                                                                             <  1:199765/143‑1 (MQ=255)                                                       gCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTcc                                                                            >  1:747658/1‑143 (MQ=255)                                                          tGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGAc                                                                         <  2:643253/143‑1 (MQ=255)                                                           gTCAGACCACGGATCAAGCAAGCGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACGCTTGTTCCCTTCACAGGCATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACa                                                                        <  1:190801/143‑1 (MQ=255)                                                              aGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAGGGCACTCCGACAAGa                                                                     >  1:489212/1‑143 (MQ=255)                                                                  gacgGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAAtt                                                                 >  1:200127/1‑143 (MQ=255)                                                                          aaGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGc                                                         >  1:344236/1‑143 (MQ=255)                                                                            gCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCaa                                                       >  1:607640/1‑143 (MQ=255)                                                                             cAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCCGATCAGGTTCCGCAGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCaaa                                                      <  2:389466/143‑1 (MQ=255)                                                                                gagaCGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATaaa                                                                                                     >  2:52860/1‑93 (MQ=255)                                                                                gagaCGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATaaa                                                                                                     <  1:52860/93‑1 (MQ=255)                                                                                  gaCGATCGCCGCAGGGGCGATGCGATAGCAGATGAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATgggg                                                 <  2:619185/143‑1 (MQ=255)                                                                                          ccgcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCCAATGGGGCATTGAAt                                         >  1:342953/1‑143 (MQ=255)                                                                                          ccgcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAAt                                         <  1:554150/143‑1 (MQ=255)                                                                                               ggggggATGCGTTGGCTGATTAACTGTTGTTCCCTTCATAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTaaa                                    <  2:136494/143‑1 (MQ=255)                                                                                                gggCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAAt                                   <  2:779932/143‑1 (MQ=255)                                                                                                      tgcgatAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTAcgcg                             >  1:308080/1‑143 (MQ=255)                                                                                                        cgatAGTCGATTAAGTCTTGTCCCATTCACACGTATTAGCCTGATCAGGTTCAGAGGCTCCCGAATAAACGGTCTCAGCCAGTTAAGCCACCCCGACAACACACTCGCCCCGCAAATGCGGCATTGAATGTAAATTACGCGtt                           <  2:132212/143‑1 (MQ=255)                                                                                                         gatAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCAGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAAGTAGCCCCGCAAATGGGGCATGGAATGTAAATAACGCGATa                          >  2:618704/1‑143 (MQ=255)                                                                                                             gCAGACTACCTCTTGTTCCCTTCACAGGTCTTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAg                      <  1:83297/143‑1 (MQ=255)                                                                                                                 aTTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCa                  >  2:740544/1‑143 (MQ=255)                                                                                                                  ttAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAg                 >  2:485479/1‑143 (MQ=255)                                                                                                                     aCTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAAc              >  1:484540/1‑143 (MQ=255)                                                                                                                            ttCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCa       >  2:266273/1‑143 (MQ=255)                                                                                                                            ttCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAAGTAGCCGCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCa       >  2:725725/1‑143 (MQ=255)                                                                                                                                cTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGaa                                          >  1:651434/1‑104 (MQ=255)                                                                                                                                cTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGaa                                          <  2:650086/104‑1 (MQ=255)                                                                                                                                cTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGaa                                          <  2:651434/104‑1 (MQ=255)                                                                                                                                cTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGaa                                          >  1:650086/1‑104 (MQ=255)                                                                                                                                cTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACCGAAGCAggct   >  2:572396/1‑141 (MQ=255)                                                                                                                                 ttCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTCACAGCGGAGAACTCAAGCAGGATg  >  1:697782/1‑143 (MQ=255)                                                                                                                                    |                                                                                                                                            GCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATG  >  NC_000913/4196073‑4196343

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: ‑