Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,938,895	Δ1 bp	10.0%	coding (307/807 nt)	tcdA ←	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,938,895	0	T	.	10.0%	130.6 / 7.1	40	coding (307/807 nt)	tcdA	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA
Reads supporting (aligned to +/- strand):  ref base T (17/19);  new base . (2/2);  total (19/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.51e-01

CTCGCGCAACTTCGCCGCCAGCGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGATCAATCTGCCCACCCGCGCCACCGGTTGTGACCAGTGGGATTTTATTGCGCCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGCCCAACGTTATCGCGCAGGGCATGAATTTGCCGATTGGTATTGGTGACGCACACATCATCCATATCGATAAGCGTGATTGCGCCAATCCCCGTGCGCGCCAGCGCTTCCGCCGCCCAGGAACCGACACCACCGATACCAACCACACAAATATGCGCGTCAGCAAACAGTTGCAACGCTTTTTCACCATACAG  >  CP009273/2938653‑2939147                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                             cTCGCGCAACTTCGCCGCCAGCGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGATCAATCTGCCCACCCGCGCCACCGGTTGTGACCAGTGGGATTTTATTGCGCCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATccctgctctt                                                                                                                                                                                                                               >  1:343302/1‑265 (MQ=255)                         gtacTGAATCGTTTTCGCCAGATCGTTAACCTGAATCTGCGTCGGATCAATCTGCCCACCCGCGCCACCGGTTGTGACCAGTGGGATTTTATTGCGCCGAAAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCAGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTg                                                                                                                                                                                                      <  1:1478/272‑1 (MQ=255)                               aaTCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGATCAATCTGCCCACCCGCGCCACCGGTTGTGACCAGTGGGATTTTATTGCGCCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGcc                                                                                                                                                                                                <  1:374303/275‑1 (MQ=255)                                                        tGAATCTGCGTCGGATCAATCTGCCCACCCGCGCCACCGGTTGTGACCAGTGGGATTTTATTGCGCCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGa                                                                                                                                                                                                                                  >  1:712913/1‑216 (MQ=255)                                                            tCTGCGTCGGATCAATCTGCCCACCCGCGCCACCGGTTGTGACCAGTGGGATTTTATTGCGCCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAAAAc                                                                                                                                                                                                                              <  2:712903/216‑1 (MQ=255)                                                                                    ccGCGCCACCGGTTGTGACCAGTGGGATTTTATTGCGCCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATa                                                                                                                                                                                                                               >  1:162554/1‑191 (MQ=255)                                                                                        gcCACCGGTTGTGACCAGTGGGATTTTATTGCGCCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGCt                                                                                                                                                                                                                           <  2:162551/191‑1 (MQ=255)                                                                                         ccACCGGTTGTGACCAGTGGGATTTTATTGCGCCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACgg                                                                                                                                                                                                                                                       >  2:257018/1‑162 (MQ=255)                                                                                             cGGTTGTGACCAGTGGGATTTTATTGCGCCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACt                                                                                                                                                                                                                                                   <  1:257023/162‑1 (MQ=255)                                                                                                ttGGGACCAGTGGGATTTTATTGCGCCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCCGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGCCCAACGTTATCGCGCAGGGCATGAATTTGCCGATTGGTATTGGTGACGCACACATCATCCATATCg                                                                                                                               <  1:629951/275‑1 (MQ=255)                                                                                                                                           cgccgcTTTGGGCCGTACACTATAAATGTCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATc                                                                                                                                                                                                                                        >  1:499197/1‑127 (MQ=255)                                                                                                                                               gcTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGc                                                                                                                                                                                                                                    <  2:499190/127‑1 (MQ=255)                                                                                                                                                  tggggCCGTCANATATAAATGGCATCAATCACGTACGAACACCCCCCGCTCTTTTACTGAGCTACATTATCCGGCGTCACGAAATCATCAACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGATCCGCCATAACTTCCGATTTTGCCAGCCCAACGTTATCGCGCAGGGCATGAATTTGCCGATTGGTATTGGTGACGCACACATCATCCATATCGATAAGCGTGATTGCGCCAATCCCCGTGCGCGCCAGCGCTTCCGCCGCCCa                                                                             <  2:64508/273‑1 (MQ=255)                                                                                                                                                          tACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGCCCAACGTNATCGCGCAGGGCATGAATTTGCCGATTGGTATTGGTGACGCACACATCATCCATATCGATAAGCGTTATTGCGCCAATCCCCGTGCGCGCCAGCGCTTCCGCCGCCCAGGAACCGa                                                                     >  1:652915/1‑275 (MQ=255)                                                                                                                                                              cTATCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTa                                                                                                                                                                                                                                                            <  2:388302/88‑1 (MQ=255)                                                                                                                                                                         atcaatcaCGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGCCCAACGTTATCGCGCAGGGCATGAATTTGCCGATTGGTATTGGTGa                                                                                                                                                   >  2:5160/1‑182 (MQ=255)                                                                                                                                                                           caatccCTTACGAATAACCCACGCTCATATCCTGCGCTACGTTATCCGGCGTCACGAAATCATCCCCACCCGTTACACGGCACTCCGNGTTAATTTGTCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGCCCAACGTTATCGCGCAGGGCATGAATTTGCCGATTGGTATTGGTGACGCACACATCATCCATATCGATAAGCGTGATTGCGCCAATCCCCGTGCGCGCCAGCGCTTCCGCCGCCCAGGAACCGACACCACCGATacc                                                        <  1:552974/271‑1 (MQ=255)                                                                                                                                                                             atcaCGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGCCCAACGTTATCGCGCAGGGCATGAATTTGCCGATTGGTATTGGTGACGca                                                                                                                                               <  1:5160/182‑1 (MQ=255)                                                                                                                                                                                        aTAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGCCCAACGTTATCGCGCAGGGCATGAATTTGCCGattggtat                                                                                                                                                         >  2:388635/1‑161 (MQ=255)                                                                                                                                                                                            cccACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGCCCAACGTTATCGCGCAGGGCATGAATTTGCCGattggtattggt                                                                                                                                                     <  1:388641/161‑1 (MQ=255)                                                                                                                                                                                            cccACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCG‑TACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGCCCAACGTTATc                                                                                                                                                                                      >  2:478620/1‑127 (MQ=255)                                                                                                                                                                                            cccACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCG‑TACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGCCCAACGTTATc                                                                                                                                                                                      >  2:93166/1‑127 (MQ=255)                                                                                                                                                                                                cGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCG‑TACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCTCTTTTGCCAGCCCAACGTTATCgcgc                                                                                                                                                                                  <  1:478627/127‑1 (MQ=255)                                                                                                                                                                                                cGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCG‑TACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGCCCAACGTTATCgcgc                                                                                                                                                                                  <  1:93167/127‑1 (MQ=255)                                                                                                                                                                                                           tGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGCCCAACGTTATCGCGCAGGGCATGAATTTGCCGattggta                                                                                                                                                          >  2:392047/1‑141 (MQ=255)                                                                                                                                                                                                           tGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTACGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTGTTGCCAGCCCAACGTTATc                                                                                                                                                                                      >  1:116829/1‑113 (MQ=255)                                                                                                                                                                                                             cgcTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTg                                                                                                                                                                                                                                      >  1:584269/1‑63 (MQ=255)                                                                                                                                                                                                             cgcTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATAc                                                                                                                                                                                                                              >  2:561854/1‑71 (MQ=255)                                                                                                                                                                                                             cgcTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGc                                                                                                                                                                                                 >  2:313870/1‑100 (MQ=255)                                                                                                                                                                                                             cgcTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGCCCAACGTTATCGCGCAGGGCATGAATTTGCCGATTGGTATTGGTGACGCACACATCATCCATATCGATAAGCGTGATTGCGCCAATCCCCGTGCCCCCCAGCGCTTCCGCCGCCCAAGACACGACACCACCAAAACCAACCCACCAAAGATACCCGCCAACAAAccatttccact                  >  2:578322/1‑265 (MQ=255)                                                                                                                                                                                                               cTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACgg                                                                                                                                                                                                                                                       >  2:402965/1‑44 (MQ=255)                                                                                                                                                                                                               cTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGCCCAACGTTATCGCGCAGGGCATGAATTTGCCGattggtattgg                                                                                                                                                      <  1:392053/141‑1 (MQ=255)                                                                                                                                                                                                               cTACGTTAGCCGGCGTCACGAAATCAGCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAAGACGCTCCGCTATAACTGCCGCTTTTGCCAGCCCAACGTTATCgcgc                                                                                                                                                                                  <  2:116828/113‑1 (MQ=255)                                                                                                                                                                                                                 aCGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGa                                                                                                                                                                                                                                  <  2:584260/63‑1 (MQ=255)                                                                                                                                                                                                                 aCGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGCTc                                                                                                                                                                                                                          <  1:561863/71‑1 (MQ=255)                                                                                                                                                                                                                 aCGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGCCCaa                                                                                                                                                                                             <  1:313876/100‑1 (MQ=255)                                                                                                                                                                                                                   gTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACt                                                                                                                                                                                                                                                   <  1:402972/44‑1 (MQ=255)                                                                                                                                                                                                                              tCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGCCCAACGTTCTCGCCCAGGGCATGAATTTGCCGATTGGTATTGGTGACGCACACATCATCCATATCGATAAGCGTGATTGCCCCAATCCCCGTTCGCGCCAGCGCTTCCGCCCCCCCGCAACCGACACCACCGATACCCACCACACAAACATTCACGTCACCAAACCGCTCCAACGCttttcacccatccac  >  2:250650/1‑263 (MQ=255)                                                                                                                                                                                                                              tCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGCCCAACGTTATCGCGCAGGGCATGAATTTGCCGATTGGTATTGGTGACGCACACATCATCCATATCGATAAGCGt                                                                                                                       >  2:62355/1‑157 (MQ=255)                                                                                                                                                                                                                                  gAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGCCCAACGTTATCGCGCAGGGCATGAATTTGCCGATTGGTATTGGTGACGCACACATCATCCATATCGATAAGCGTGAtt                                                                                                                   <  1:62356/157‑1 (MQ=255)                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                             CTCGCGCAACTTCGCCGCCAGCGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGATCAATCTGCCCACCCGCGCCACCGGTTGTGACCAGTGGGATTTTATTGCGCCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAATCATCCACCACCGTTACACGGCACTCCGGGTTAATCTGGCGAATACGCTCCGCCATAACTTCCGCTTTTGCCAGCCCAACGTTATCGCGCAGGGCATGAATTTGCCGATTGGTATTGGTGACGCACACATCATCCATATCGATAAGCGTGATTGCGCCAATCCCCGTGCGCGCCAGCGCTTCCGCCGCCCAGGAACCGACACCACCGATACCAACCACACAAATATGCGCGTCAGCAAACAGTTGCAACGCTTTTTCACCATACAG  >  CP009273/2938653‑2939147

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: ‑