Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	161,068	A→C	24.0%	intergenic (+47/‑149)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	161,068	0	A	C	24.0%	57.8 / 4.0	38	intergenic (+47/‑149)	hrpB/mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
Reads supporting (aligned to +/- strand):  ref base A (17/11);  new base C (3/7);  total (20/18)
Fisher's exact test for biased strand distribution p-value = 1.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGGAGAAAA  >  CP009273/160920‑161213                                                                                                                                                     |                                                                                                                                                  cGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCa                                                                                                                                                   >  1:4238473/1‑149 (MQ=255)   ttaGGTGAAAAAATATATTAAAGGGCGTTATCCCAAACATGTCTGGCCGTACGACCCGGAAAAAACTGCACCGACGCGACGGACTAAAAATTTTTCGTAAGGTTGGTTTTCCCCCCCTCCCTGTGGGTGAGGGCCGGGGTGAGGGCATc                                                                                                                                                 <  2:3806682/147‑1 (MQ=255)     aGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACTGACGAAAAAGAATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATccg                                                                                                                                               >  1:261047/1‑147 (MQ=255)         gCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCCTCcgcgcg                                                                                                                                           >  1:1094430/1‑149 (MQ=255)            aaaaGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCAc                                                                                                                                        >  1:3077915/1‑149 (MQ=255)            aaaaGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCAc                                                                                                                                        >  1:3077965/1‑149 (MQ=255)            aaaaGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCAc                                                                                                                                        >  1:3077966/1‑149 (MQ=255)            aaaaGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCAc                                                                                                                                        >  2:2445698/1‑149 (MQ=255)               agagATGAAAGGGCGTTATCCCAAACATGACTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGCGGGCCTCCGCGCGCACggg                                                                                                                                     >  1:2108663/1‑147 (MQ=255)                  gaTGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCCGCGCGCACGtggcg                                                                                                                                  >  1:2929721/1‑145 (MQ=255)                   aTGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGtggacc                                                                                                                                 >  2:3618329/1‑144 (MQ=255)                    tGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCCTCAGCGCGCACGtgggccc                                                                                                                                >  2:782426/1‑143 (MQ=255)                    tGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACggggggcc                                                                                                                                >  2:782448/1‑142 (MQ=255)                        aGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTtgacccaacc                                                                                                                            >  2:2770181/1‑145 (MQ=255)                           gCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTgcacccaccccca                                                                                                                         >  2:1722049/1‑148 (MQ=255)                                   ccAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGGTGACCCacacccacacccaca                                                                                                                 >  2:2770549/1‑146 (MQ=38)                                                                      cccccgccgCGCCGGACCAAAATTTTTTGGTTTGGTTGTTTTTCCCCCTCGCCGTGTGGTTGTGGGCGGGGGTGTGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAAtt                                                                              <  2:42576/146‑1 (MQ=255)                                                                                gacggcctAAATATTATTCGTATGGTTGTTGTTCTCCCACCCCCTGTGGGTGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGata                                                                    <  2:538738/149‑1 (MQ=38)                                                                                gacggactAAAACGTTTTCGTAGGGTGGGTTTACGCCCTGACCCTGGGGGAGTGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGata                                                                    <  2:4417468/149‑1 (MQ=255)                                                                                   ggacgAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTGAACCCCACCCAAAAACAAACCCACAACGGAGGGGGGGCCCCACGAGCCCCAAATATGTGAGataatt                                                                 >  2:4271924/1‑146 (MQ=12)                                                                                    gacgAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCACACCCGAACCCACTCCCACAAGGGAGAGGGGACCGATCGAGAACAACTTTTGATTGATAtcta                                                                >  2:618401/1‑148 (MQ=37)                                                                                      ctaaaaaGTATTCGTAAGGTTGGTTTACCCCCTCTCCCTGGGGGAGTGGGCCGGGGTGTGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATAtcttct                                                              <  2:2862501/147‑1 (MQ=255)                                                                                                     aaGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTGGACCCACACCCAAACCCTCAACCCCAAAGGGGAGGGGACCGATCGAGCCCAAAAATTTAGAGAAATAATATTATGTCTTGTTACac                                               >  2:2737704/1‑148 (MQ=16)                                                                                                     aaGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTGCACCCGCACCCAAAACCCCACCCACAAGCGAGAGGGGACCGATCCAGCACAAAAATTTTGAGATATATTATTTTGTGATGTAACag                                               >  2:2737991/1‑149 (MQ=18)                                                                                                        gttggttTTCCCCCTCCCCGTGTGGGAGAGGGCGGGGGTGTGGGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACagaag                                            <  2:3896084/149‑1 (MQ=255)                                                                                                           ggttTTCTCCCTCTCCGTGTGGGTGTGGGCCGGGGTGTGGGAATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGTGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAAc                                         <  2:2108663/149‑1 (MQ=255)                                                                                                                tctccgtctccgTGGGGGAGAGGGCCGGGGTGTGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGaaa                                    <  2:2753680/149‑1 (MQ=255)                                                                                                                   ccctctcggtGGGGGCGGGGGCGGGGGTGAGGGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATc                                 <  2:3073663/149‑1 (MQ=255)                                                                                                                          cgggtgggtggGGGCGGGGGTGAGGGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCttt                          <  1:4335352/146‑1 (MQ=255)                                                                                                                                   gtgggggggggTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGa                 <  2:2870139/142‑1 (MQ=255)                                                                                                                                   ggggggcggggggcggGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGa                 <  1:3975614/147‑1 (MQ=255)                                                                                                                                   gagGGCGGGGGTGGGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGa                 <  2:2869870/149‑1 (MQ=255)                                                                                                                                    cgggCCGGGGGGCGCGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGaa                <  2:894609/148‑1 (MQ=255)                                                                                                                                        ccGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATAtt            <  2:728356/149‑1 (MQ=255)                                                                                                                                           gggTGTGGGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCg         <  2:2710462/149‑1 (MQ=255)                                                                                                                                           gggTGCGGCCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCg         <  1:3976991/149‑1 (MQ=255)                                                                                                                                           gggTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGGGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCg         >  2:495614/1‑149 (MQ=255)                                                                                                                                           gggTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGGGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCg         >  2:495257/1‑149 (MQ=255)                                                                                                                                                  gccATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGGAGaaaa  <  2:2318657/147‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                  CGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGGAGAAAA  >  CP009273/160920‑161213

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑