Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,593,877	T→C	A89A (GCA→GCG)	rpoH ←	RNA polymerase sigma factor RpoH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,593,877	0	T	C	100.0%	82.6 / NA	24	A89A (GCA→GCG)	rpoH	RNA polymerase sigma factor RpoH
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (13/11);  total (13/11)

TTTGCGCTGCGCTTTGGTGGTCGCAACTTTGACGATACGCCAGTTACGCAGAACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACTGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAACAACAAACCGCAGGTGAGACAGGATCAGCGTTTTAGC  >  NZ_CP009273/3593742‑3593996                                                                                                                                        |                                                                                                                        tttGCGCTGCGCTTTGGTGGTCGCAACTTTGACGATACGCCAGTTACGCAGAACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCt                                                                                                                      <  2:232954/139‑1 (MQ=255) tttGCGCTGCGCTTTGGTGGTCGCAACTTTGACGATACGCCAGTTACGCAGAACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCt                                                                                                                      >  2:148811/1‑139 (MQ=255)           gctTTGGTGGTCGCAACTTTGACGATACGCCAGTTACGCAGAACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGc                                                                                                            >  1:306096/1‑139 (MQ=255)               tggtggTCGCAACTTTGACGATACGCCAGTTACGCAGAACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGa                                                                                                         <  1:186338/138‑1 (MQ=255)                       gCAACTTTGACGATACGCCAGTTACGCAGAACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCtt                                                                                                >  1:420286/1‑139 (MQ=255)                                                      cGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAg                                                                                                              <  1:132676/94‑1 (MQ=255)                                                      cGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAg                                                                                                              >  2:132676/1‑94 (MQ=255)                                                        tATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGc                                                               <  1:148811/139‑1 (MQ=255)                                                        tATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGc                                                               <  1:321958/139‑1 (MQ=255)                                                                  tctcTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAAt                                                      >  1:345483/1‑138 (MQ=255)                                                                     ctGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGc                                                                         >  1:268929/1‑116 (MQ=255)                                                                     ctGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGc                                                                         <  2:268929/116‑1 (MQ=255)                                                                     ctGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTAc                                                   >  1:284061/1‑138 (MQ=255)                                                                             aTCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATTAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAatat                                          >  1:306258/1‑139 (MQ=255)                                                                             aTCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGc                                                                         <  1:411113/108‑1 (MQ=255)                                                                             aTCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGc                                                                         >  2:411113/1‑108 (MQ=255)                                                                                cAGTGAACGGCGAAGGAGACCAGGCGCACCCCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGaa                                       <  2:76126/139‑1 (MQ=255)                                                                                               gagaCCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAACAACAAACCGCAGGt                        <  2:420286/139‑1 (MQ=255)                                                                                                  aCCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAACAACAAACCGCAGGt                        >  1:296475/1‑136 (MQ=255)                                                                                                  aCCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTCCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAACAACAAACCGCAGGt                        >  2:40596/1‑136 (MQ=255)                                                                                                     aGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAACAACAAACCGCAGGTGAGACa                  <  2:29160/139‑1 (MQ=255)                                                                                                         gcACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAACAACAAACCGCAGGTGAGACAGGAt              >  2:38162/1‑139 (MQ=255)                                                                                                                     ccGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAACAACAAACCGCAGGTGAGACAGGATCAGCGTTTTAgc  >  2:123784/1‑139 (MQ=255)                                                                                                                      cGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAACAACAAACCGCAGGTGAGACAGGATCAGCGTTTTAgc  <  1:356431/138‑1 (MQ=255)                                                                                                                                        |                                                                                                                        TTTGCGCTGCGCTTTGGTGGTCGCAACTTTGACGATACGCCAGTTACGCAGAACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACTGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAACAACAAACCGCAGGTGAGACAGGATCAGCGTTTTAGC  >  NZ_CP009273/3593742‑3593996

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑