Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,310,402	T→A	I162F (ATC→TTC)	nusA ←	transcription termination factor NusA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,310,402	0	T	A	100.0%	126.0 / NA	33	I162F (ATC→TTC)	nusA	transcription termination factor NusA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (17/16);  total (17/16)

TCAGCATTTCCGGCTTGGAACGAGTGACGAACAGTTGCGCGCCACGCGCTTCCGGGCGAACGGAATAGAGCACGCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGATCACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGCCGGTGATGATTTCACCTTCGTGTTCACGGAACTGATCAACCACCATCGCACGTTCGGCTT  >  NZ_CP009273/3310270‑3310527                                                                                                                                     |                                                                                                                              tCAGCATTTCCGGCTTGGAACGAGTGACGAACAGTTGCGCGCCACGCGCTTCCGGGCGAACGGAATAGAGCACGCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGc                                                                                                                         >  1:9825/1‑139 (MQ=255)      aTTTCCGGCTTGGAACGAGTGACGAACAGTTGCGCGCCACGCGCTTCCGGGCGAACGGAATAGAGCACGCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAg                                                                                                                    <  2:498950/139‑1 (MQ=255)           cGGCTTGGAACGAGTGACGAACAGTTGCGCGCCACGCGCTTCCGGGCGAACGGAATAGAGCACGCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCgttg                                                                                                               <  1:840657/139‑1 (MQ=255)                 ggAACGAGTGACGAACAGTTGCGCGCCACGCGCTTCCGGGCGAACGGAATAGAGCACGCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGcc                                                                                                          <  2:428212/138‑1 (MQ=255)                 ggAACGAGTGACGAACAGTTGCGCGCCACGCGCTTCCGGGCGAACGGAATAGAGCACGCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGcc                                                                                                          <  1:70315/138‑1 (MQ=255)                                 aGTTGCGCGCCACGCGCTTCCGGGCGAACGGAATAGAGCACGCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGcc                                                                                                          <  1:34146/122‑1 (MQ=255)                                 aGTTGCGCGCCACGCGCTTCCGGGCGAACGGAATAGAGCACGCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGcc                                                                                                          >  2:34146/1‑122 (MQ=255)                                   ttGCGCGCCACGCGCTTCCGGGCGAACGGAATAGAGCACGCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGcc                                                                                                          <  2:50723/120‑1 (MQ=255)                                   ttGCGCGCCACGCGCTTCCGGGCGAACGGAATAGAGCACGCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGcc                                                                                                          >  1:50723/1‑120 (MQ=255)                                   ttGCGCGCCACGCGCTTCCGGGCGAACGGAATAGAGCACGCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGAtgttg                                                                                       >  2:757110/1‑139 (MQ=255)                                           cACGCGCTTCCGGGCGAACGGAATAGAGCACGGCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGtt                                                                               >  1:744143/1‑139 (MQ=255)                                                       ggCGAACGGAATAGAGCACGCCACGAACGCGGTCGCCAGGGCGGCAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTcac                                                                   >  2:777875/1‑139 (MQ=255)                                                              ggAATAGAGCACGCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGCCg                                                            <  1:604760/139‑1 (MQ=255)                                                                  tAGAGCACGCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGCCGGtga                                                        <  2:142509/139‑1 (MQ=255)                                                                          gCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGc                                                              <  2:47616/125‑1 (MQ=255)                                                                          gCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGc                                                              >  1:47616/1‑125 (MQ=255)                                                                          gCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGCCGGTGATGATTTCa                                                >  1:847906/1‑139 (MQ=255)                                                                          gCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGCCGGTGATGATTTCa                                                >  2:229269/1‑139 (MQ=255)                                                                          gCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGCCGGTGATGATTTCa                                                >  1:53946/1‑139 (MQ=255)                                                                          gCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGCCGGTGATGATTTCa                                                >  2:555319/1‑139 (MQ=255)                                                                            cACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGCCGGTGATGATTTCAcc                                              >  1:633387/1‑139 (MQ=255)                                                                                      gTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCgttgt                                                                                                              <  1:729405/65‑1 (MQ=255)                                                                                      gTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCgttgt                                                                                                              >  2:729405/1‑65 (MQ=255)                                                                                      gTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGCCGGTGATGATTTCACCTTCGTGTTCa                                    >  1:227122/1‑139 (MQ=255)                                                                                          ccAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTGCTTTTTTCACCACGCCGGTGATGATTTCACCTTCGTGTTCACGGa                                <  2:152581/139‑1 (MQ=255)                                                                                            aGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGCCGGTGATGATTTCACCTTCGTGTTCACGGAAc                              <  1:624423/139‑1 (MQ=255)                                                                                            aGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGCCGGTGATGATTTCACCTTCGTGTTCACGGAAc                              <  2:744143/139‑1 (MQ=255)                                                                                             gggCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGCCGGTGATGATTTCACCTTCGTGTTCACGGAACt                             >  2:218815/1‑139 (MQ=255)                                                                                             gggCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGCCGGTGATGATTTCACCTTCGTGTTCACGGAACt                             <  2:633387/139‑1 (MQ=255)                                                                                                    aGTTTTCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGCCGGTGATGATTTCACCTTCGTGTTCACGGAACTGATCAac                      <  2:9825/139‑1 (MQ=255)                                                                                                         tCACGCGGCAGCATATCTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGCCGGTGATGATTTCACCTTCGTGTTCACGGAACTGATCAaccacc                  <  2:227122/138‑1 (MQ=255)                                                                                                                         cTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGCCGGTGATGATTTCACCTTCGTGTTCACGGAACTGATCAACCACCATCGCACGTTCGGCtt  >  2:77421/1‑138 (MQ=255)                                                                                                                         cTTCGCGCAGGAACACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGCCGGTGATGATTTCACCTTCGTGTTCACGGAACTGATCAACCACCATCGCACGTTCGGCtt  >  1:327087/1‑138 (MQ=255)                                                                                                                                     |                                                                                                                              TCAGCATTTCCGGCTTGGAACGAGTGACGAACAGTTGCGCGCCACGCGCTTCCGGGCGAACGGAATAGAGCACGCCACGAACGCGGTCGCCAGGGCGGAAGTTTTCACGCGGCAGCATATCTTCGCGCAGGATCACGGCTTCAGCGTTGTTGCCCAGATCCAGAGAGATGTTGTCGCGGTTTACTTTTTTCACCACGCCGGTGATGATTTCACCTTCGTGTTCACGGAACTGATCAACCACCATCGCACGTTCGGCTT  >  NZ_CP009273/3310270‑3310527

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑