Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,196,196	T→C	intergenic (‑97/+136)	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	4,196,196	0	T	C	100.0%	68.7 / NA	24	intergenic (‑97/+136)	thiC/rsd	phosphomethylpyrimidine synthase/regulator of sigma D
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (9/15);  total (9/15)

CCCGGGCGCGTTGTTCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCA  >  NC_000913/4196057‑4196327                                                                                                                                            |                                                                                                                                    cccGGGCGCGTTGTTCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAGAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTcc                                                                                                                                  >  1:343267/1‑143 (MQ=255)      gcgtGTTGTTCGCGGCGGGTCAGTTTTGGTGCCGACATAGCTCAGTCCAAAAAGTTAACGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCg                                                                                                                             <  2:25694/143‑1 (MQ=255)                          cAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAgg                                                                                                         >  1:105996/1‑143 (MQ=255)                          cAGTTTGGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTGGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAgg                                                                                                         <  1:219243/143‑1 (MQ=255)                           aGTTTTGTGGCCGACATAGCTCACTCCAAAACGTTAAGCACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGt                                                                                                        <  2:546559/143‑1 (MQ=255)                                tgttgCAGACATAGTTCATGCGAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCcgc                                                                                                   <  2:578997/143‑1 (MQ=255)                                      aGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGAGCTCCGCTGGGGCGATGCGATAGCCGACTAACTCTTGCTCCCTTCGCAGGAATTAGCCTGATCAGGTACCGCGGATcc                                                                                             >  2:498918/1‑143 (MQ=255)                                         cATGGCTCATTCCAAAAAGTTAAGGGCGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGa                                                                                          <  2:615920/143‑1 (MQ=255)                                                  ttgcAAAAGGTTGAGGTGGTCGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGt                                                                                 <  2:17064/140‑1 (MQ=255)                                                  gtgcAAAAAGGTACGGACGGGGGGTGGCAGACGGCGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGt                                                                                 <  1:148486/140‑1 (MQ=255)                                                       aaaaGTTAGGGTCGTGGCTTGTCAGATGATGGATGAAGCAAGAGTCGATTGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAg                                                                            <  1:354052/143‑1 (MQ=255)                                                           gTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGGCTCAGCAAg                                                                        >  2:582798/1‑143 (MQ=255)                                                           gTTAAGGACGGGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAg                                                                        <  2:392883/143‑1 (MQ=255)                                                                 gACGTGGCTTGTCAGACGACGGAGGAAGCAAGAGACGTTCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAgg                                                                  <  2:615754/143‑1 (MQ=255)                                                                         ttGTCATGCGACGTATGAAGCAAGGCACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGa                                                          <  2:522786/143‑1 (MQ=255)                                                                         ttGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGa                                                          <  1:454481/143‑1 (MQ=255)                                                                           gTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGACGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTACGACa                                                        >  1:482716/1‑143 (MQ=255)                                                                                acgacgGCTGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGaaa                                                   <  1:252667/143‑1 (MQ=255)                                                                                           aGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCa                                        >  2:561246/1‑143 (MQ=255)                                                                                                                     ggtggatGGCAGGTTGACTCTTGCTCCCGTCGCAGGTAGTAGCCTGATCAGGTGCCGCGGATCCCGAATAAACGGTCTCAGCCATTTAAGGCACGCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTAcgc              <  2:280450/139‑1 (MQ=255)                                                                                                                         gatAGCAGATTAACTCTTGCTCACTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAACTGGGGCCTAGAATGTGAAGAAcgcgaca          >  2:496605/1‑140 (MQ=255)                                                                                                                               aGATTACCGCTTGCTCCCTTCGCAGGTATTGGCCTGATCAGGTTCCGCCGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAgcg    <  2:569932/143‑1 (MQ=255)                                                                                                                                 aTTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGTTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAACTTACGCGTTAACAGCGCa  >  2:457480/1‑143 (MQ=255)                                                                                                                                 aTTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCa  >  1:550099/1‑143 (MQ=255)                                                                                                                                            |                                                                                                                                    CCCGGGCGCGTTGTTCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCA  >  NC_000913/4196057‑4196327

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑