Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	164,581	A→C	36.4%	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
*	NC_000913	164,581	0	A	C	36.4%	35.8 / 7.7	45	intergenic (+47/‑149)	hrpB/mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
Reads supporting (aligned to +/- strand):  ref base A (9/19);  new base C (2/15);  total (11/34)
Fisher's exact test for biased strand distribution p-value = 1.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGGAGAAAAAGCA  >  NC_000913/164432‑164730                                                                                                                                                      |                                                                                                                                                      ccGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCa                                                                                                                                                       >  1:1018180/1‑150 (MQ=255)       ggTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCACATACTGCACCGACGCGACGGACGAAAAAGTCTTCGGCAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCCTCcgcg                                                                                                                                                 >  2:459425/1‑150 (MQ=39)         tgaaaaatGATATTAATGGGGTTTATCCCAAACTTGTCTGGCGGTACGACCCGGCAAATACTGAACCGAGGCGACGTACGAAAATGTTTTCGTATGTTTGGTTTTCTCCCTCTCCCTGTGGTATTGGGCCGGGGTGTGGGCATCAgcgcg                                                                                                                                               <  2:964706/147‑1 (MQ=255)           caaactgagtTGAATGGGGTTTACCCCAACAATGGCGGGCGGGACGCCCGGGAAAATACGCCACCCACGCCAGGTCCCAAAATGTTTGCTTAGGTTTGGTTTTCTCCCTCTCCCTGGGGTAGTGGGCGGGGGTGAGGGCCTCAGCGCGCa                                                                                                                                             <  2:345776/144‑1 (MQ=255)           aaaaaaTAGTTTAAAGGGCGTTATCCCAAACATGTCTGGCGGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAATTTATTCTTATGGTTGGTTTTCTCCCTCTCCGTGTGGGTGTGGGCGGGGGTGAGGGCATCAGCGCGCa                                                                                                                                             <  2:1130106/149‑1 (MQ=37)            aaaaaGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCAGCAGCGCGCAc                                                                                                                                            >  1:1608523/1‑150 (MQ=255)                 gagaTGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACggggc                                                                                                                                       >  2:1486463/1‑146 (MQ=255)                  atttGACAGGGCGTTATCCCAAACATGTCGGGCCGGACGACCCGGCAAATACGGCACCGTCGCGACGGACGATAAAGTTTTCGTAAGGTTGGTTTTCTCCGTCTCCCTGTGGGTGAGGGCCGGGTTGAGGGCATCAGCGCGCACGTtcac                                                                                                                                      <  2:1289256/147‑1 (MQ=255)                  agaTGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTtcac                                                                                                                                      <  2:1289245/150‑1 (MQ=255)                   gaTGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAGGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTtcacc                                                                                                                                     >  1:1130132/1‑150 (MQ=255)                       aaaGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGAAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGTGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTtcaccctca                                                                                                                                 <  2:1575343/150‑1 (MQ=255)                                    ccAAACTTGTCTGGCGGGACGACCCGGAAAATACTGCACCGACGCGAGGGACTAAAAATTTTTGTTATGTTTGTTTTTCTCCCTCGCCCTGTGGGTGTGGGCCGGGGTGTGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCtctc                                                                                                                    <  2:1639241/150‑1 (MQ=255)                                    ccAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAACAAGAATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGAGAGGGCATCAGCGCGCACGGTCCCACACACCCCAAccccccc                                                                                                                    >  1:834103/1‑146 (MQ=37)                                     cAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGACAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCCTCAGCGCGCACGGGCCCCCCCCCCCCAAcccccgcc                                                                                                                   >  1:527455/1‑145 (MQ=37)                                          ttgtggggCGGGCCGACCCGGCAAATAGTGCACCGAGGCTACGGACTAAAATGTTTTCTTTTGTTTGTTTTTCTCCCTCTCCCTGGGGGTGTGGGCGGGGGTGCGGGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCaa                                                                                                              <  2:60118/144‑1 (MQ=255)                                            ggcgggCCGGAGGCCCCGGCACCGCCGGCACCGACGCGCGGGCCGCCATAGTCTTGGTCCGGGTGGGTTGCGCCCGCTCCCTGTGGTTGTGGGCCGGGGTGCGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAgg                                                                                                            <  2:969233/146‑1 (MQ=255)                                            ggcTGGCCGGCCGACCCGGCAAATACGGCCCCGCCGCGACGGACTAAAATTTTTTCTTATGGTTGTTTTTCTCCCCCGCCGTGTGGGAGCGGGCGGGGGTGCGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCttgagg                                                                                                            <  2:83536/148‑6 (MQ=255)                                            gccgggCGGGACGACCCGGCAAATACGGCCCCGCCGCGACGGACGACACAGGATGCGGAAGGTTGGTTGTCGCCCTCGCCCGGGGGGCGAGGGCGGGGGTGAGGGCCTCAGCGCGCACGTTCACCCTCACCCGAACCCTCTCCCTCAAgg                                                                                                            <  2:969146/146‑1 (MQ=255)                                            gTCGGGCGGGACGACCCGCCAAAGCCTGCACCGCCGCGCCGGCCGAAACTGTTTTGTTACGGTTGGTTTTCGCCCCCGCCCGGGGGGAGTGGGCGGGGGTGCGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCttgagg                                                                                                            <  2:94076/150‑6 (MQ=255)                                                 gCCGGACGACCCGGCAAAGCCTGCCCCGACGCGCCGGACGAAAAAGTATGCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGagag                                                                                                       <  2:1052374/150‑1 (MQ=38)                                                 cccGGACGCCCGGGCAAATACTGCCCCGCCGCGACGCACGAAAATGCCTTCGAACGGTTGGTTTCCACCCCCGCCCTGGGGTTGCGGGCGGGGGTGCGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGagag                                                                                                       <  2:1464087/149‑1 (MQ=255)                                                  ccGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTGCACCCACCCCCCAAACCACGCCCGCAAGGGGGAgg                                                                                                      >  1:1710890/1‑150 (MQ=37)                                                    ggACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTAACCCACACCCAAAACCACAACCACAACGGCGAgggg                                                                                                    >  2:979317/1‑150 (MQ=25)                                                           ccGGCAAATCCGGCACCGACGCGAGGCACTAAAATGTATGGGTAGGGTTGGTTTTCCCCCTCCCCCTGTGGGCGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATc                                                                                             <  2:1048282/150‑1 (MQ=37)                                                             ggCAAACCCTCCACCGACGCGCCGGACGAAAAAGTATGCGAATGGTGGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGa                                                                                           <  2:1420471/150‑1 (MQ=37)                                                                      tGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCCCACCCCAACCCACACCCACAAGGGGGTGGGGGCCCAGCGAGCCCaaaat                                                                                  >  1:581777/1‑148 (MQ=25)                                                                          ccgccgCGACGTCCTAAAAATTATTCTTATGTTTGTTTTTCTCCCCCTCCGTGGGGTTGTGGGCGGGGGTGTGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTga                                                                              <  2:46950/150‑1 (MQ=255)                                                                          ccgccgCGACGGAATAAAATGTTTTCTTACGGTTGTTTTTCTCCCTCGCCGTGTGGTATTGGGCGGGGGTGCGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTga                                                                              <  2:46948/150‑1 (MQ=255)                                                                            gacgcgacgGACGAAAAAGTATGCGTACGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTgaga                                                                            <  1:1559603/150‑1 (MQ=255)                                                                              cgcgccgGACTAAAATGTTTTCGTATGGTTGGTTTTCTCCCTCGCCCTGGGGGTGTGGGCGGGGGTGCGGGCATCAGCGCGCACGTTCACCCTCACGCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTgagaga                                                                          <  2:816781/150‑1 (MQ=255)                                                                              cgcgaggGACTAAAATTTATTCTTATGGTTGGTTTTCTCCATCTCCCTGTGGTTGTGGGCGGGGGTGAGGCCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTgagaga                                                                          <  1:1718469/150‑1 (MQ=255)                                                                                    ggacgAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCACACCCTAAACCACTCCCTCCAGGGCGAGGGGGCCCATAGAGCCCAAAATTTGAGAGATAtcat                                                                    >  2:1568325/1‑148 (MQ=25)                                                                                                agtCGTAAGGTTGGCTTGCGCCCCCCCCCTGTGGGAGCGGGCCGGGGTGAGGGCCTCAGCGCGCCCGTTCACCCTCACCCTAACCCTCTCCCACAAGGGAGAGGGGACCGAACGAGCACAAATTTTGAGAGATAACTTCTTCTGTCTTGt                                                        <  2:720645/148‑1 (MQ=255)                                                                                                   gttatggttggttTTCTCCCTCTCCCTGTGGGAGTGGGCGGGGGTGTGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAAc                                                     <  1:968349/145‑1 (MQ=255)                                                                                                    gtttgtttgtttTTCTCCCAATCCCTGTGGGTGTGGGCGGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCATAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACa                                                    <  2:388459/144‑1 (MQ=255)                                                                                                           tggttTTCTCCCTCTCCGTGGGGGTGGGGGCGGGGGTGCGGGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAAc                                             <  1:1616793/150‑1 (MQ=255)                                                                                                                 tctccctctccgTGTGGGTGCGGGCGGGGGTGTGGGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGaaaa                                       <  1:724891/150‑1 (MQ=255)                                                                                                                   tccctctccctGTGGGAGAGGGCCGGGGTGAGGGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGGGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATc                                     <  1:258562/150‑1 (MQ=255)                                                                                                                   tccctctccctGGGGGAGAGGGCCGGGGTGAGGGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATc                                     <  1:258590/150‑1 (MQ=255)                                                                                                                              gtgGGAGCGGGCCGGGGTGCGGGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAACTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTgcg                          <  2:923874/150‑1 (MQ=255)                                                                                                                                gggAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGGTGACCCCCACCCAAACCCACACCCCCAAGGGGGGGGGGGCCCCGCGGGCCCAAAATTTGTGGGATATATTCTTCTGTCTTGTGAGAGAAGAACAGAAAAAAGGGCGTTTggggc                        >  2:203135/1‑146 (MQ=255)                                                                                                                                 gttgtgggCGGGGGTGCGCGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCt                       <  1:789473/145‑1 (MQ=255)                                                                                                                                 ggtgtgggCCGGGGTGAGGGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCt                       <  1:828386/145‑1 (MQ=255)                                                                                                                                 ggcgcgggCCGGGGGGGGGGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCt                       <  2:1316290/145‑1 (MQ=255)                                                                                                                                        gcgggggTGCGGGCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATAtt                <  1:1486463/147‑1 (MQ=255)                                                                                                                                                   ggCCTCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGGAGaaaaa     <  2:1255088/150‑1 (MQ=255)                                                                                                                                                      aTCAGCGCGCACGTTCACCCACAACCAAAACCAAAACCAAAACGGAGAGTGGACCCAACCAGCACAAAAATTGAGAGATAAATTATTATTTATTTTAAAAAAAGAAAAAAAAAAAGGGCTTTTGAGCCAGAAAATTTCGGAGaaaaaaaa  >  2:418708/1‑147 (MQ=255)                                                                                                                                                      |                                                                                                                                                      CCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGGAGAAAAAGCA  >  NC_000913/164432‑164730

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑