Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,241,314	T→C	10.5%	intergenic (+61/‑220)	gltX → / → PP_t25	glutamate‑‑tRNA ligase/tRNA‑Ala

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,241,314	0	T	C	10.5%	94.9 / 3.1	39	intergenic (+61/‑220)	gltX/PP_t25	glutamate‑‑tRNA ligase/tRNA‑Ala
Reads supporting (aligned to +/- strand):  ref base T (14/20);  new base C (2/2);  total (17/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.41e-01

CCGCCTGCGCCAGGCTCTGGACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATCCGAACTTAATATGCG  >  NC_002947/2241166‑2241461                                                                                                                                                      |                                                                                                                                                    ccGCCTGCGCCAGGCTCTGGACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAat                                                                                                                                                     <  7:234743/149‑1 (MQ=255)  cGCCTGCGCCAGGCTCTGGACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAata                                                                                                                                                    >  5:208003/1‑149 (MQ=255)   gCCTGCGCCAGGCTCTGGACCTGCTGGGTGGGGTGTCGAAGGAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATACAATGGTAAATTCAata                                                                                                                                                    >  2:73433/1‑148 (MQ=255)     cTGCGCCAGGCTCTGGACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCg                                                                                                                                                 <  6:208003/149‑1 (MQ=255)        cgcCAGGCTCTGGACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCa                                                                                                                                               <  5:104561/148‑1 (MQ=255)        cgcCAGGCTCTGGACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCa                                                                                                                                               <  7:109135/148‑1 (MQ=255)         gcCAGGCTCTGGACCTGCTGTGTGGGTTGTAGAAGAAAGAAAACAAAGAGTTGGAAATTCTGTTGGCTTCCATAGCATGATTCAGCTTTGCACCTAAACAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCAtt                                                                                                                                             <  5:188790/149‑1 (MQ=255)                tctGGACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCATTCGCCGGc                                                                                                                                      >  3:295712/1‑149 (MQ=255)                  tGGACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATTTc                                                                                                                                                  <  2:306092/135‑1 (MQ=255)                    gACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCGGCGAATGCGATATTGAATTTACCATTGCATTCGCGGGCAc                                                                                                                                    <  4:339464/147‑1 (MQ=25)                    gACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCGGCGAATGCGATATTGAATTTACCATTGCATTCGCGGGCACGc                                                                                                                                  <  5:111261/149‑1 (MQ=25)                                                        ctggggtaaacGCTGTTGGCTTCCATCGCCTGATTCCGCTTTCCACCAACCCTGTGGCCGC‑GGGCGGGCCCGCTAAGGAAATGGTAAATTCAATATCCCATGCCCCGCCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCgg                                                                                              <  2:190359/142‑1 (MQ=255)                                                               aaaaGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAggg                                                                                       <  7:117956/149‑1 (MQ=255)                                                                     tGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGGGTGGCCCCGCATTGAATGGGTAATTTAATATAGGATTAGCCGGGCCGCCCCCGCCCCCAGGGCCACAAAGCCCCAAAAAAACGGGGGAgggggggga                                                                                 >  6:2478/1‑146 (MQ=255)                                                                       ttGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCATTCGCCGGCAc                                                                                                                                    <  7:337167/96‑1 (MQ=255)                                                                       ttGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCATTCGCCGGCAc                                                                                                                                    >  8:337167/1‑96 (MQ=255)                                                                       ttGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTAAATATCGCATTCGCCGGCACGCCCGCGCCCCCAGGCGCACTAAGCCCCAAAAAACCGGGGTAGGGCGGGAAGt                                                                               >  8:90693/1‑149 (MQ=255)                                                                         ggCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGGCCCCGAATTGAAATGTTAATTGAATATAGCATTGGCCCGCCCGCCCCCACCCCCAGGCCCACGAAGCCCCAAAAAACCCGGGGTGGGCGGTTAGTgg                                                                             >  4:97725/1‑148 (MQ=255)                                                                         ggCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGt                                                                               <  3:97725/147‑1 (MQ=255)                                                                          gCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATTGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGa                                                                             <  4:295712/148‑1 (MQ=255)                                                                           cTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGAtt                                                                           <  8:76677/149‑1 (MQ=255)                                                                            ttCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTTCCCGCGCATGCAATGGTAAATTAAATATAGCATTCGCCGGCACGCCCCCTCCCACAGGCCCACTAAGCCCCAAAAAACCGGGGGAGGGCGGTAAGTGATTg                                                                          >  5:121937/1‑149 (MQ=255)                                                                               cATCGCCTCATACAGTTTTGCACCTAACCTGGGGGAGC‑GGGGGTGCCCGCCAATGAAATTGAAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGtt                                                                        <  2:340985/148‑1 (MQ=255)                                                                                 tCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATACAATGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATc                                                                     <  1:73433/149‑1 (MQ=255)                                                                                                     ccTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTAAATATAGCATTAGCCGGCACGCCCGCTGCCCCAGGCCAACTAAGCCCCAAAAAACCCGGGTAGGGCGGTAAGTGATTGTTTTCTGTGTAAAAATTTTTGAatt                                                 >  6:185734/1‑148 (MQ=255)                                                                                                        aaCCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAAATGTAAATTCAATTAAGCATTCGCCGGCCCGCCCGCTGCCACAGGGCAACTAAGCCCCAAAAAAACGGGGTAGGGGGGTAAGTGATTGTTATATGTGAAAAAATTTTTGAATtttt                                              >  6:359389/1‑149 (MQ=255)                                                                                                           cAGTGGGAGCGGGGCGTGCCCCCGAATGCAATGGTAAATTAAAAATAGCAATACCCGGCCCCCCCCCACCCCCAGGCCAACTAAGCCCCAAAAAACCGGGGGAGGGCGGTTATTGATTGTTTTAAGTGTAAAAAttttt                                                      >  4:289364/1‑139 (MQ=255)                                                                                                           cAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAAttttt                                                      <  3:289364/138‑1 (MQ=255)                                                                                                              tGGGCGC‑GGGCGTGCCCGCTAATGCAATTGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGaaa                                        <  3:201640/149‑1 (MQ=255)                                                                                                                              cggcgAATGCGATATTGAATTTACCATTGCATTCGCGGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGcc                         >  1:85190/3‑149 (MQ=25)                                                                                                                              cggcgAATGCGATATTGAATTTACCATTGCATTCGCGGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGcc                         >  4:42326/3‑149 (MQ=25)                                                                                                                               cgcgAATGCAATGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGt                                                                                   <  4:186059/90‑1 (MQ=255)                                                                                                                               cgcgAATGCAATGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGt                                                                                   >  3:186059/1‑90 (MQ=255)                                                                                                                                        aaTGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATcc                >  4:182389/1‑148 (MQ=255)                                                                                                                                          tGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATCCGaa             >  2:98530/1‑149 (MQ=255)                                                                                                                                            gTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATCCGAAc            <  6:121937/148‑1 (MQ=255)                                                                                                                                            gTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATCCGAACt           >  7:112370/1‑149 (MQ=255)                                                                                                                                             tAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGATTTTTTTTGAAAATTAGTTTGACAGACCTGCAATCCGAACt           >  8:244006/1‑148 (MQ=255)                                                                                                                                               aaTTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATCCGAACTTaa        <  5:2478/149‑1 (MQ=255)                                                                                                                                                  tCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATCCGAACTTAatat     >  2:294719/1‑149 (MQ=255)                                                                                                                                                    aaTATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGa                                                    <  4:313587/100‑1 (MQ=255)                                                                                                                                                    aaTATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATCCGAACTTAATATgc   <  1:98530/149‑1 (MQ=255)                                                                                                                                                     atatCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATCCGAACTTAata      <  3:118804/145‑1 (MQ=255)                                                                                                                                                     atatCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATCCGAACTTAata      >  4:118804/1‑145 (MQ=255)                                                                                                                                                     atatCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATCCGAACTTAATATgcg  >  3:136306/1‑149 (MQ=255)                                                                                                                                                      |                                                                                                                                                    CCGCCTGCGCCAGGCTCTGGACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATCCGAACTTAATATGCG  >  NC_002947/2241166‑2241461

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑