Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	254,371	T→A	11.9%	L19Q (CTA→CAA)	crl →	RNA polymerase holoenzyme assembly factor crl

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	254,371	0	T	A	11.9%	99.3 / 3.7	43	L19Q (CTA→CAA)	crl	RNA polymerase holoenzyme assembly factor crl
Reads supporting (aligned to +/- strand):  ref base T (19/18);  new base A (2/3);  total (22/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

AATCACCGACTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTT  >  CP009273/254225‑254516                                                                                                                                                   |                                                                                                                                                  aaTCACCGACTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATGTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAg                                                                                                                                                 >  2:468512/1‑149 (MQ=255)   tCACCGACTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGCTTGATCAAAAAATTTACCGCACAAGGc                                                                                                                                               >  2:259916/1‑149 (MQ=255)        gaagggATCGGAAAACGATTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACAAGGCCCGta                                                                                                                                          <  1:569193/145‑1 (MQ=255)        gACTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACAAGGCCCGta                                                                                                                                          <  1:545025/149‑1 (MQ=255)                   aaaaCGTTTGTGTTAAAAATTTGCTAAATTTGGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAg                                                                                                                               <  1:112015/149‑1 (MQ=255)                   aaaaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCCATTTGGTCACAAGGTGGCACATCAACAGGAGATAGCAATGACGTTACCGATTGGACACCTGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAg                                                                                                                               <  1:831216/149‑1 (MQ=255)                       cGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTaa                                                                                                                           <  1:123263/149‑1 (MQ=255)                                  aaaaTTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCACGTATATTCGTGAAGGTAAGTGCAAAGATa                                                                                                                >  1:368566/1‑149 (MQ=255)                                          cTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAGGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTc                                                                                                        >  1:48820/1‑149 (MQ=255)                                           tAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACCAGGCCCGTAAATTCGTGAAGGTACGTGCAAAGATAAACGaaccc                                                                                                       >  1:43489/1‑145 (MQ=255)                                                      aaTTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACGCGAAGAGCAGATTGATCAAAGAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCGTTGTCGATTGt                                                                                            >  1:286810/1‑149 (MQ=255)                                                         ttGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTg                                                                                         >  2:138492/1‑149 (MQ=255)                                                             ttaaaCAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTg                                                                                     <  1:734212/147‑1 (MQ=255)                                                                        cATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAAc                                                                          <  2:776519/149‑1 (MQ=255)                                                                             caacaGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGaa                                                                     >  1:639175/1‑149 (MQ=255)                                                                              aacaGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGaaa                                                                    <  2:623860/149‑1 (MQ=255)                                                                              aacaGGAGATAGCAATGACGTTACCGAGTGGAAACCCGAAGAGCAGATTGATCAAAAAATTTACCGCAAAAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGCACACGTGaaa                                                                    >  1:193553/1‑149 (MQ=255)                                                                                  ggAGATAGCAATGTCTTTACCGAGTGGACACCCGAAGTGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCgg                                                                <  1:30090/149‑1 (MQ=255)                                                                                  ggAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAGAGTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCgg                                                                <  1:30026/149‑1 (MQ=255)                                                                                  ggAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCgg                                                                <  1:146942/149‑1 (MQ=255)                                                                                   gagaTAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGc                                                               >  1:583151/1‑149 (MQ=255)                                                                                              gACGTTACCGAGTGGAAACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGc                                                    >  1:750339/1‑149 (MQ=255)                                                                                                cGTTACCGGGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGCTAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGt                                                  <  1:697934/149‑1 (MQ=255)                                                                                                     ccGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAAACGGCACCGGCAGTGCGGGAAtt                                             >  2:64907/1‑149 (MQ=255)                                                                                                      cGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAAGGTGAAACCGGCGCCGTAAGTGCCTTAATTc                                            >  2:197962/1‑149 (MQ=255)                                                                                                        ggtcgACACCCGAAGACCATATTGATCAAAAAACTTACCGCACTAGCGCCGTACATTCCTGAAGGCAAGTGCAAAGACAATCGATTCTTTTTCGATTGTCTGGCTGTATCCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTg                                          <  1:496162/145‑1 (MQ=255)                                                                                                        aGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATCCTTTTTCGATCGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTg                                          <  2:247622/149‑1 (MQ=255)                                                                                                         gTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTgg                                         <  1:138492/149‑1 (MQ=255)                                                                                                          tGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTggg                                        >  2:304473/1‑149 (MQ=255)                                                                                                            gACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGc                                      >  2:672504/1‑149 (MQ=255)                                                                                                             caacCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCt                                     <  1:235265/147‑1 (MQ=255)                                                                                                             acacCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCt                                     >  2:15509/1‑149 (MQ=255)                                                                                                               acCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCtgg                                   <  1:274497/149‑1 (MQ=255)                                                                                                                        gaaGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAg                          <  2:19566/147‑1 (MQ=255)                                                                                                                        gCAGATTGATCAAAAAATTTGCCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAg                          <  1:712042/149‑1 (MQ=255)                                                                                                                         cAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGGGc                         >  1:744974/1‑149 (MQ=255)                                                                                                                            aTTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATACACGATTCTTTTTCGATCACCTCACCGGATGCGTCAACGAAAAAGCGGCACCGGAAGGGCGGGAGTTCTGGGGCTGGTGGAGGGGGCggg                      >  2:636552/1‑149 (MQ=255)                                                                                                                              tGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTCTACGTCAACGTGAAACCTGCACCCGCAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGaa                    >  1:267713/1‑149 (MQ=255)                                                                                                                              tGATCAAAAAATTTACCGCACAAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGaa                    <  1:259916/149‑1 (MQ=255)                                                                                                                                   aaaaaaTTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCa               >  2:14293/1‑149 (MQ=255)                                                                                                                                             ccGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTTGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGt     <  2:639175/149‑1 (MQ=255)                                                                                                                                                cACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGGTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGtgtt  >  1:250660/1‑149 (MQ=255)                                                                                                                                                cACTAGGCCCGTATATTAGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTATGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAATGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGtttt  >  1:641965/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                  AATCACCGACTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTT  >  CP009273/254225‑254516

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑