Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,445,831	G→A	100%	P152L (CCG→CTG)	rplC ←	50S ribosomal subunit protein L3

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,445,831	0	G	A	100.0%	76.4 / NA	32	P152L (CCG→CTG)	rplC	50S ribosomal subunit protein L3
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (16/16);  total (16/16)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATTCCATTGCTATCTCCTTACGCCTTCACAGCTGGTTTAACGATCAGGTCGCTACCGGTTGCACCCGGGACAGCACCTTTAACCAGCAGCAGGTTGCGCTCAGCGTCAACGCGTACTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCGGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTAGCGTCCTGGGTACGGAAGTTCCAGCGCTTAACGGTACCTGCGAAACCTTTACCTTTAGAGGTGCCAGTTACGTCAACTTTTTTAACGTCAGCAAACAGTTCAACGCTAATGCTCTGACCTACAGTGAACTCTTCGCCTTCAGCCAGGCGGAATTCCCACAGACCACGGCCAGCTTCTACGCCAGCTTTAGCGAAGTGGCCAGCTTCAGGCT  >  CP009273/3445639‑3446101                                                                                                                                                                                                 |                                                                                                                                                                                                                                                                               aTTCCATTGCTATCTCCTTACGCCTTCACAGCTGGTTTAACGATCAGGTCGCTACCGGTTGCACCCGGGACAGCACCTTTAACCAGCAGCAGGTTGCGCTCAGCGTCAACGCGTACTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTc                                                                                                                                                                                                                                                                     >  1:574580/1‑204 (MQ=255)     cATTGCTCTCTNTTTACGCCTGCACCGCTGGTTTGTGCCTCCTGTCGCTACCGGTTGCTCTCGTGACATCGCCGTTAACCAGCAGCAGGTTATGCTCAGCGTCAACGCGTACTACGTAACGGCTCTGTACTGTTACACGTTCGTTACCGATCTTACCTGCCATTTTCTTTCCTTTTCACACTTTGTCTAGAGTCTGGTTCTGACCGCTAGAACCCGGAGTGCGGTGAGACAAGAAGTTACCGTGAGTGGCGTGCTGGGTACGGAAGTTCCAgcgc                                                                                                                                                                                          <  2:51735/275‑1 (MQ=255)     cATTGCTCTCTCCTTACGCCTTCACAGCTGGTTTAACGATCAGGTCGCTACCGGTTGCACCCGGGACAGCACCTTTAACCAGCAGCAGGTTGCGCTCAGCGTCAACGCGTACTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGAc                                                                                                                                                                                                                                                                 <  2:574569/204‑1 (MQ=255)             tctcCTTACGCCTTCACAGCTGGTTTAACGATCAGGTCGCTACCGGTTGCACCCGGGACAGCACCTTTAACCAGCAGCAGGTTGCGCTCAGCGTCAACGCGTACTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTAGCGTCCTGGTTACGGAAGATCCAGCGCTTAACGGt                                                                                                                                                                                  >  1:186283/1‑275 (MQ=255)                          tCACAGCTGGTTTAACGATCAGGTCGCTACCGGTTGCACCCGGGACAGCACCTTTAACCAGCAGCAGGTTGCGCTCAGCGTCAACGCGTACTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTAGCGTCCTGGGTACGGAAGt                                                                                                                                                                                                  >  1:568295/1‑246 (MQ=255)                              aGCTGGTTTAACGATCAGGTCGCTACCGGTTGCACCCGGGACAGCACCTTTAACCAGCAGCAGGTTGCGCTCAGCGTCAACGCGTACTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTAGCGTCCTGGGTACGGAAGTTCCa                                                                                                                                                                                              <  2:568284/246‑1 (MQ=255)                                   gTTTAACGATCAGGTCGCTACCGGTTGCACACGGGACAGCACCTTTAACCAGCAGCAGGTTGCGCTCAGCGTCAACGCGTACTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTAGCGTCCTGGGTAAGGAAGTTCCAGCGCTTAACGGGACCTGCGAAAccattacattta                                                                                                                                                            >  1:165294/1‑275 (MQ=255)                                                gTCGCTACCGGTTGCACCCGGGACAGCACCTTTAACCAGCAGCAGGTTGCGCTCAGCGTCAACGCGTACTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTAGCGTCCTGGGTa                                                                                                                                                                                                         >  2:640684/1‑217 (MQ=255)                                                    cTACCGGTTGCACCCGGGACAGCACCTTTAACCAGCAGCAGGTTGCGCTCAGCGTCAACGCGTACTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTAGCGTCATGGGTACGGa                                                                                                                                                                                                     <  1:640695/217‑1 (MQ=255)                                                          gTTGCACCCGGGACAGCACCTTTAACCAGCAGCAGGTTGCGCTCAGCGTCAACGCGTACTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGCCCGATAGAACCCGGAACGCGGTgaga                                                                                                                                                                                                                                        >  2:191393/1‑176 (MQ=255)                                                              cACCCGGGACAGCACCTTTAACCAGCAGCAGGTTGCGCTCAGCGTCAACGCGTACTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAg                                                                                                                                                                                                                                    <  1:191397/176‑1 (MQ=255)                                                                         gCACCTTTAATCAGCAGCAGGTTGCGCTCAGCGTCAACGCGTACTACGTCAAGTCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTAGCGTCCTGGGTACGGaa                                                                                                                                                                                                    >  1:636948/1‑197 (MQ=255)                                                                          cACCTTTAACCAGCAGCAGGTTGCGCTCAGCGTCAACGCGTACTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTg                                                                                                                                                                                                                         >  2:14984/1‑175 (MQ=255)                                                                          cACCTTTAACCAGCAGCAGGTGGCGCTCAGCGTCAACGCGTACTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGaa                                                                                                                                                                                                                                                  >  1:473178/1‑150 (MQ=255)                                                                              tttAACCAGCAGCAGGTTGCGCTCAGCGTCAACGCGTACTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAAcgcg                                                                                                                                                                                                                                              <  2:473170/150‑1 (MQ=255)                                                                              tttAACCAGCAGCAGGTTGCGCTCAGCGTCAACGCGTACTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTa                                                                                                                                                                                                                     <  1:14984/175‑1 (MQ=255)                                                                               ttAACCAGCAGCAGGTTGCGCTCAGCGTCAACGCGTACTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAAcca                                                                                                                                                                                                                                                      >  1:650241/1‑140 (MQ=255)                                                                                   ccAGCAGCAGGTTGCGCTCAGCGTCAACGCGTACTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGaa                                                                                                                                                                                                                                                  <  2:650230/141‑1 (MQ=255)                                                                                          aagGTTGCGCTCAGCGTCAACCGGTACTTCGTCAATGCTCTGACCGGTTTCACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTAGCGTCCTGGGTACGGAAGTTCCAGCGCTTAACGGTACCTGCGAAACCTTTACCTTTAGAGGTGCCAGTTACGTCAACTTTTTTAACGTCAGCAAACAGTTCAAAGCTa                                                                                                         <  2:186279/270‑1 (MQ=255)                                                                                            ggTTGCGCTCAGCGTCAACGCGTCCTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTga                                                                                                                                                                                                                                          >  1:481467/1‑140 (MQ=255)                                                                                                gcgcTCAGCGTCAACGCGTACTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACa                                                                                                                                                                                                                                      <  2:481459/140‑1 (MQ=255)                                                                                                            aaCGCGTACTACGTCAAGGCTCTGAACTGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTc                                                                                                                                                                                                                                                                           <  2:3350/91‑1 (MQ=255)                                                                                                                            aGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTAg                                                                                                                                                                                                                    >  2:618897/1‑130 (MQ=255)                                                                                                                                tctGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTAGCGTc                                                                                                                                                                                                                <  1:618908/130‑1 (MQ=255)                                                                                                                                                 tcgttACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTAGCGTCCTGGGTACGGAAGt                                                                                                                                                                                                  >  1:94554/1‑127 (MQ=255)                                                                                                                                                   gttACCCATCTGACCTGCCCTTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTAGCGTCCTGGGTACGGAAGTTCCAGCGCTTAACGTTACCTGCGAAACCTTTACCTTTAGAGGTGCCAGTTACGTCAACTTTTTTAACGTCAGCAAACAGTTCAACGCTAATGCTCTGACCTACATTGAACTCTTCGCCTTCAGCCAGGCGGAATTcccgtcccttctac                                             >  1:533410/1‑263 (MQ=255)                                                                                                                                                     tACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTAGCGTCCTGGGTACGGAAGTTCCa                                                                                                                                                                                              <  2:94554/127‑1 (MQ=255)                                                                                                                                                                 cTGCCATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTAGCGTCCTGGGTACGGAAGt                                                                                                                                                                                                  >  2:119092/1‑111 (MQ=255)                                                                                                                                                                     cATTTTCTTGCCTTTGAACACTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTAGCGTCCTGGGTACGGAAGTTCCa                                                                                                                                                                                              <  1:119093/111‑1 (MQ=255)                                                                                                                                                                                      acacTTTGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTg                                                                                                                                                                                                                         >  2:386123/1‑67 (MQ=255)                                                                                                                                                                                          tttGCCCAGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTa                                                                                                                                                                                                                     <  1:386128/67‑1 (MQ=255)                                                                                                                                                                                             gCCCAGAGTCTTGTTCTTACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTAGCGTCCTGGGTACGGAAGTTCCAGCGCTTAACGATACCTGCGAAACCTTTACCTTTAGAGGTGCCAGTTACGTAAACTTTTTTAACGTCAGCAAACAGTTCAACGCTAATGCTCTGACCTACAGTGAACTCTTCGCCTTCAGCCAGGCGGAATTCCCACAGACCACGGCCAGCTTCTACGCCAGCTTTAGCGAAGTGGCCAGCTTCAGGCt  <  1:371080/275‑1 (MQ=255)                                                                                                                                                                                                 |                                                                                                                                                                                                                                                                               ATTCCATTGCTATCTCCTTACGCCTTCACAGCTGGTTTAACGATCAGGTCGCTACCGGTTGCACCCGGGACAGCACCTTTAACCAGCAGCAGGTTGCGCTCAGCGTCAACGCGTACTACGTCAAGGCTCTGAACGGTTACACGTTCGTTACCCATCTGACCTGCCATTTTCTTGCCTTTGAACACTTTGCCCGGAGTCTGGTTCTGACCGATAGAACCCGGAACGCGGTGAGACAAGGAGTTACCGTGAGTAGCGTCCTGGGTACGGAAGTTCCAGCGCTTAACGGTACCTGCGAAACCTTTACCTTTAGAGGTGCCAGTTACGTCAACTTTTTTAACGTCAGCAAACAGTTCAACGCTAATGCTCTGACCTACAGTGAACTCTTCGCCTTCAGCCAGGCGGAATTCCCACAGACCACGGCCAGCTTCTACGCCAGCTTTAGCGAAGTGGCCAGCTTCAGGCT  >  CP009273/3445639‑3446101

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑