Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	161,068	A→C	38.0%	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	38.0%	22.0 / 11.4	41	intergenic (+47/‑149)	hrpB/mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
Reads supporting (aligned to +/- strand):  ref base A (13/12);  new base C (5/11);  total (18/23)
Fisher's exact test for biased strand distribution p-value = 2.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGC  >  CP009273/160922‑161205                                                                                                                                                   |                                                                                                                                          tGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCAt                                                                                                                                          >  1:2857770/1‑148 (MQ=255)   aGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCa                                                                                                                                        >  2:1907360/1‑148 (MQ=255)    ggTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCCTccg                                                                                                                                       >  2:325252/1‑146 (MQ=255)          aaaaGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCCGCGCGCa                                                                                                                                 >  1:1850728/1‑148 (MQ=255)           aaaGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCCTCAGCGCGCAc                                                                                                                                >  1:2015765/1‑148 (MQ=255)            aaGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCCTCAGCGCGCACg                                                                                                                               >  2:3275959/1‑148 (MQ=255)            aaGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACg                                                                                                                               >  2:149567/1‑148 (MQ=255)            aaGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACg                                                                                                                               >  2:2801639/1‑148 (MQ=255)            aaGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACg                                                                                                                               >  2:719010/1‑148 (MQ=255)             agagATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGt                                                                                                                              >  2:590245/1‑148 (MQ=255)               agaTGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCCTCAGCGCGCACgggg                                                                                                                            >  2:1405105/1‑145 (MQ=255)               agaTGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGtgg                                                                                                                            >  2:214515/1‑146 (MQ=255)                    aaaGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCCTCAGCGCGCACGTgcgcccg                                                                                                                       >  1:2336427/1‑147 (MQ=255)                       ggggtttAACCAAAAAATGTGGGGCGGTACGACCCGCAAAATCCGCCACCGACGCGAGGTACAAAAATTTATTCTTATGTTTGGTTTACACCCTCTCGGTGTGGGTGTGGGCGGGGTTGTGGGCCTCAGCGCGCACGTtcaccctcac                                                                                                                    <  2:3515316/143‑1 (MQ=255)                                    aaCATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTGGGCCCGCGCCCCAAcccccgcc                                                                                                       >  2:880366/1‑143 (MQ=37)                                    aaCATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTGGCCCCCCACCCAAAaccaaaac                                                                                                       >  2:880235/1‑143 (MQ=37)                                       aTGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCCGCGCGCACGTGGCCCCTCCCCCCCACCCACTccccc                                                                                                    >  2:2229048/1‑146 (MQ=37)                                        tGTCTGGCCGGACGCCCGGGAAAATCCTGCCCCCCCGCCACGCACTAAAAATAATGCTTAAGGTTGTTTTTCCCCCTCTCCCTGTGGGAGTGGGCGGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCa                                                                                                   <  2:296453/148‑1 (MQ=21)                                                     gacCCGTCAAATAGGCCCCCGACGCGACTGACCAAAATTTATACGTATGTTGGGTTTCCTCCCACCCCGGGGGGGACCGGCCGGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTACCCCTCTCCCTCAAGGGAGAGGGGAc                                                                                      <  2:91913/148‑1 (MQ=255)                                                                  cgccACCGACGCGCCGGACGAAAAAGTATGCCTACGGTGGGTTTTCTCCCTCCCCGTGGGGGCTAGGGCGGGGGTGAGGCCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACaa                                                                         <  2:3365775/145‑1 (MQ=255)                                                                   ggCACCGCCGCGCGGGACTAAAAAGTATTCTTAAGGTTGTTTTTCTCCCTCTCCGTGTGGGAGAGGGCGGGGGTGTGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACaaa                                                                        <  2:3163081/147‑1 (MQ=255)                                                                     cACCGCCGGGAGGGACTAAAATGTTTTGGTATGTTTGTTTTTAGCCCTCTCCGGGTGGGAGCGGGCGGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAAtt                                                                      <  2:2336427/148‑1 (MQ=255)                                                                          ccgccacgCACCAAAATGTTTTCTAAAGTTTGTTTTACACCCTCACCCTGTGGGAGTGGGCGGGGGTGAGGGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTgag                                                                 <  2:162130/147‑1 (MQ=255)                                                                             cgcgggccgAAAAAGTTTTCGTAGGGTTGGTTTTCTCCCTCTCCGTGTGGGAGTGGGCCGGGGTGCGGGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTgagaga                                                              <  2:2015765/141‑1 (MQ=255)                                                                               acggacgAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACTCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGata                                                            >  2:2360570/1‑148 (MQ=255)                                                                                cggactAAAATGTATGCCAACGGTTGTTTTCCCCCCACTCCCTGTGGTAGCGGCCGGGGGTGAGGCCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGatat                                                           <  2:458830/148‑1 (MQ=255)                                                                                         aattataCGTCAGGTTGGTTGGCGCCCGCGCCCGGGGGGAGTGGGCCGGGGTGAGGGCCTCAGCGCGCACGGTCACCCTCACCCTAACCCTCGCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGAGATCTTCTTCTg                                                  <  2:3043336/145‑1 (MQ=255)                                                                                               gcgtttggttggttTGCTCCCTCTCCGTGGGGTAGTGGGCGGGGGTGTGGGCATCAGCGCGCACGCTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGt                                            <  2:859429/142‑1 (MQ=255)                                                                                                  aaaGGTTTGTTTGCTCCCACCCCCGGGGGGGGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAAc                                         <  2:488965/147‑1 (MQ=255)                                                                                                   atgtttgtttTTCGCCCTCCCCCTGTGGGTGTGGGCGGGGGTGCGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACa                                        <  2:222579/144‑1 (MQ=255)                                                                                                    aGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACag                                       <  2:3346417/148‑1 (MQ=255)                                                                                                     ggttggttTTCGCCCTCGCCCGGGGGGTGTGGGCGGGGGTGAGGCCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACaga                                      <  2:1754320/148‑1 (MQ=255)                                                                                                        tggttTTCTCCCAGCCCCGGTGGGACCGGGCGGGGGTGCGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACagaaga                                   <  2:1880161/148‑1 (MQ=255)                                                                                                                          tgtgGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTGCCCCCCCCCCCCAAACCCCAACCCCCAGCGGGGGGGGGCCGGGCGCGCACACAAATTGAGAGATATGTTATTATGTTGTGGAACAGAAGGACACCCAATCgggggttt                 >  2:3382786/1‑143 (MQ=255)                                                                                                                             gggggggggCGGGGGTGCGCCCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTgcg              <  1:2054024/142‑1 (MQ=255)                                                                                                                             gggTGAGGGCGGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTgcg              <  2:243195/148‑1 (MQ=255)                                                                                                                                ggcggcccGGGGTGCGGCCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCt           <  1:1848739/142‑1 (MQ=255)                                                                                                                                      ccGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAatat     <  2:2082566/148‑1 (MQ=255)                                                                                                                                        ggggTGAGGCCCTCAGCGCGCACGTTCACCCTCACCCGAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTg   <  2:1747363/148‑1 (MQ=255)                                                                                                                                         gggTGCGGGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGc  <  2:1383025/148‑1 (MQ=255)                                                                                                                                         gggTGCGGCCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGc  <  2:1383053/148‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                          TGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGC  >  CP009273/160922‑161205

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: ‑